New upstream version 0.16.0.1+ds
authorAndreas Tille <tille@debian.org>
Fri, 2 Oct 2020 06:11:01 +0000 (08:11 +0200)
committerAndreas Tille <tille@debian.org>
Fri, 2 Oct 2020 06:11:01 +0000 (08:11 +0200)
commit324a081b63e717816423520cecc55c72a79dbc69
treea7cdaa9c28d6225dfcb2d2ab5f45fea5c0ae201a
parentf4cfe1fb151bb1d64dda10ff78b974e968826c5e
New upstream version 0.16.0.1+ds
300 files changed:
.travis.yml
README.rst
bcftools/LICENSE
bcftools/bam2bcf.c
bcftools/bam2bcf.c.pysam.c
bcftools/bam2bcf.h
bcftools/bcftools.h
bcftools/call.h
bcftools/cols.c [new file with mode: 0644]
bcftools/cols.c.pysam.c [new file with mode: 0644]
bcftools/cols.h [new file with mode: 0644]
bcftools/consensus.c
bcftools/consensus.c.pysam.c
bcftools/convert.c
bcftools/convert.c.pysam.c
bcftools/csq.c
bcftools/csq.c.pysam.c
bcftools/filter.c
bcftools/filter.c.pysam.c
bcftools/gvcf.c
bcftools/gvcf.c.pysam.c
bcftools/hex.h [new file with mode: 0644]
bcftools/htslib-1.10.2/LICENSE [new file with mode: 0644]
bcftools/htslib-1.10.2/README [new file with mode: 0644]
bcftools/htslib-1.9/LICENSE [deleted file]
bcftools/htslib-1.9/README [deleted file]
bcftools/main.c
bcftools/main.c.pysam.c
bcftools/mcall.c
bcftools/mcall.c.pysam.c
bcftools/mpileup.c
bcftools/mpileup.c.pysam.c
bcftools/plugins/GTisec.c [deleted file]
bcftools/plugins/GTisec.c.pysam.c [deleted file]
bcftools/plugins/GTsubset.c [deleted file]
bcftools/plugins/GTsubset.c.pysam.c [deleted file]
bcftools/plugins/ad-bias.c [deleted file]
bcftools/plugins/ad-bias.c.pysam.c [deleted file]
bcftools/plugins/af-dist.c [deleted file]
bcftools/plugins/af-dist.c.pysam.c [deleted file]
bcftools/plugins/check-ploidy.c [deleted file]
bcftools/plugins/check-ploidy.c.pysam.c [deleted file]
bcftools/plugins/check-sparsity.c [deleted file]
bcftools/plugins/check-sparsity.c.pysam.c [deleted file]
bcftools/plugins/color-chrs.c [deleted file]
bcftools/plugins/color-chrs.c.pysam.c [deleted file]
bcftools/plugins/contrast.c [deleted file]
bcftools/plugins/contrast.c.pysam.c [deleted file]
bcftools/plugins/counts.c [deleted file]
bcftools/plugins/counts.c.pysam.c [deleted file]
bcftools/plugins/dosage.c [deleted file]
bcftools/plugins/dosage.c.pysam.c [deleted file]
bcftools/plugins/fill-AN-AC.c [deleted file]
bcftools/plugins/fill-AN-AC.c.pysam.c [deleted file]
bcftools/plugins/fill-from-fasta.c [deleted file]
bcftools/plugins/fill-from-fasta.c.pysam.c [deleted file]
bcftools/plugins/fill-tags.c [deleted file]
bcftools/plugins/fill-tags.c.pysam.c [deleted file]
bcftools/plugins/fixploidy.c [deleted file]
bcftools/plugins/fixploidy.c.pysam.c [deleted file]
bcftools/plugins/fixref.c [deleted file]
bcftools/plugins/fixref.c.pysam.c [deleted file]
bcftools/plugins/frameshifts.c [deleted file]
bcftools/plugins/frameshifts.c.pysam.c [deleted file]
bcftools/plugins/guess-ploidy.c [deleted file]
bcftools/plugins/guess-ploidy.c.pysam.c [deleted file]
bcftools/plugins/impute-info.c [deleted file]
bcftools/plugins/impute-info.c.pysam.c [deleted file]
bcftools/plugins/isecGT.c [deleted file]
bcftools/plugins/isecGT.c.pysam.c [deleted file]
bcftools/plugins/mendelian.c [deleted file]
bcftools/plugins/mendelian.c.pysam.c [deleted file]
bcftools/plugins/missing2ref.c [deleted file]
bcftools/plugins/missing2ref.c.pysam.c [deleted file]
bcftools/plugins/prune.c [deleted file]
bcftools/plugins/prune.c.pysam.c [deleted file]
bcftools/plugins/setGT.c [deleted file]
bcftools/plugins/setGT.c.pysam.c [deleted file]
bcftools/plugins/smpl-stats.c [deleted file]
bcftools/plugins/smpl-stats.c.pysam.c [deleted file]
bcftools/plugins/split.c [deleted file]
bcftools/plugins/split.c.pysam.c [deleted file]
bcftools/plugins/tag2tag.c [deleted file]
bcftools/plugins/tag2tag.c.pysam.c [deleted file]
bcftools/plugins/trio-stats.c [deleted file]
bcftools/plugins/trio-stats.c.pysam.c [deleted file]
bcftools/plugins/trio-switch-rate.c [deleted file]
bcftools/plugins/trio-switch-rate.c.pysam.c [deleted file]
bcftools/regidx.c
bcftools/regidx.c.pysam.c
bcftools/regidx.h
bcftools/reheader.c
bcftools/reheader.c.pysam.c
bcftools/smpl_ilist.c
bcftools/smpl_ilist.c.pysam.c
bcftools/smpl_ilist.h
bcftools/tabix.c
bcftools/tabix.c.pysam.c
bcftools/test/test-rbuf.c [deleted file]
bcftools/test/test-rbuf.c.pysam.c [deleted file]
bcftools/test/test-regidx.c [deleted file]
bcftools/test/test-regidx.c.pysam.c [deleted file]
bcftools/variantkey.h [new file with mode: 0644]
bcftools/vcfannotate.c
bcftools/vcfannotate.c.pysam.c
bcftools/vcfbuf.c
bcftools/vcfbuf.c.pysam.c
bcftools/vcfbuf.h
bcftools/vcfcall.c
bcftools/vcfcall.c.pysam.c
bcftools/vcfcnv.c
bcftools/vcfcnv.c.pysam.c
bcftools/vcfconcat.c
bcftools/vcfconcat.c.pysam.c
bcftools/vcfconvert.c
bcftools/vcfconvert.c.pysam.c
bcftools/vcffilter.c
bcftools/vcffilter.c.pysam.c
bcftools/vcfgtcheck.c
bcftools/vcfgtcheck.c.pysam.c
bcftools/vcfindex.c
bcftools/vcfindex.c.pysam.c
bcftools/vcfisec.c
bcftools/vcfisec.c.pysam.c
bcftools/vcfmerge.c
bcftools/vcfmerge.c.pysam.c
bcftools/vcfnorm.c
bcftools/vcfnorm.c.pysam.c
bcftools/vcfplugin.c
bcftools/vcfplugin.c.pysam.c
bcftools/vcfquery.c
bcftools/vcfquery.c.pysam.c
bcftools/vcfroh.c
bcftools/vcfroh.c.pysam.c
bcftools/vcfsom.c
bcftools/vcfsom.c.pysam.c
bcftools/vcfsort.c
bcftools/vcfsort.c.pysam.c
bcftools/vcfstats.c
bcftools/vcfstats.c.pysam.c
bcftools/vcfview.c
bcftools/vcfview.c.pysam.c
bcftools/version.c
bcftools/version.c.pysam.c
bcftools/version.h [deleted file]
bcftools/version.sh [new file with mode: 0755]
devtools/buildwheels.sh
devtools/import.py
devtools/run_tests_travis.sh
doc/faq.rst
doc/index.rst
doc/release.rst
pysam/bcftools.py
pysam/htslib_util.h
pysam/libcalignedsegment.pyx
pysam/libcalignmentfile.pxd
pysam/libcalignmentfile.pyx
pysam/libcbcf.pyx
pysam/libcfaidx.pyx
pysam/libchtslib.pxd
pysam/libchtslib.pyx
pysam/samtools.py
pysam/utils.py
pysam/version.h [new file with mode: 0644]
pysam/version.py
samtools/LICENSE
samtools/README
samtools/bam.c
samtools/bam.c.pysam.c
samtools/bam.h
samtools/bam2bcf.c
samtools/bam2bcf.c.pysam.c
samtools/bam2bcf.h
samtools/bam2bcf_indel.c
samtools/bam2bcf_indel.c.pysam.c
samtools/bam2depth.c
samtools/bam2depth.c.pysam.c
samtools/bam_addrprg.c
samtools/bam_addrprg.c.pysam.c
samtools/bam_aux.c
samtools/bam_aux.c.pysam.c
samtools/bam_cat.c
samtools/bam_cat.c.pysam.c
samtools/bam_fastq.c [new file with mode: 0644]
samtools/bam_fastq.c.pysam.c [new file with mode: 0644]
samtools/bam_import.c [deleted file]
samtools/bam_import.c.pysam.c [deleted file]
samtools/bam_index.c
samtools/bam_index.c.pysam.c
samtools/bam_lpileup.c
samtools/bam_lpileup.c.pysam.c
samtools/bam_lpileup.h
samtools/bam_markdup.c
samtools/bam_markdup.c.pysam.c
samtools/bam_mate.c
samtools/bam_mate.c.pysam.c
samtools/bam_md.c
samtools/bam_md.c.pysam.c
samtools/bam_plbuf.c
samtools/bam_plbuf.c.pysam.c
samtools/bam_plbuf.h
samtools/bam_plcmd.c
samtools/bam_plcmd.c.pysam.c
samtools/bam_quickcheck.c
samtools/bam_quickcheck.c.pysam.c
samtools/bam_reheader.c
samtools/bam_reheader.c.pysam.c
samtools/bam_rmdup.c
samtools/bam_rmdup.c.pysam.c
samtools/bam_rmdupse.c
samtools/bam_rmdupse.c.pysam.c
samtools/bam_sort.c
samtools/bam_sort.c.pysam.c
samtools/bam_split.c
samtools/bam_split.c.pysam.c
samtools/bam_stat.c
samtools/bam_stat.c.pysam.c
samtools/bamshuf.c
samtools/bamshuf.c.pysam.c
samtools/bamtk.c
samtools/bamtk.c.pysam.c
samtools/bedcov.c
samtools/bedcov.c.pysam.c
samtools/bedidx.c
samtools/bedidx.c.pysam.c
samtools/bedidx.h
samtools/coverage.c [new file with mode: 0644]
samtools/coverage.c.pysam.c [new file with mode: 0644]
samtools/cut_target.c
samtools/cut_target.c.pysam.c
samtools/dict.c
samtools/dict.c.pysam.c
samtools/faidx.c
samtools/faidx.c.pysam.c
samtools/htslib-1.10/LICENSE [new file with mode: 0644]
samtools/htslib-1.10/README [new file with mode: 0644]
samtools/htslib-1.9/LICENSE [deleted file]
samtools/htslib-1.9/README [deleted file]
samtools/misc/ace2sam.c [deleted file]
samtools/misc/ace2sam.c.pysam.c [deleted file]
samtools/padding.c
samtools/padding.c.pysam.c
samtools/phase.c
samtools/phase.c.pysam.c
samtools/sam.c
samtools/sam.c.pysam.c
samtools/sam.h
samtools/sam_header.c [deleted file]
samtools/sam_header.c.pysam.c [deleted file]
samtools/sam_header.h [deleted file]
samtools/sam_opts.c
samtools/sam_opts.c.pysam.c
samtools/sam_opts.h
samtools/sam_utils.c
samtools/sam_utils.c.pysam.c
samtools/sam_view.c
samtools/sam_view.c.pysam.c
samtools/samtools.h
samtools/stats.c
samtools/stats.c.pysam.c
samtools/stats_isize.c
samtools/stats_isize.c.pysam.c
samtools/test/merge/test_bam_translate.c [deleted file]
samtools/test/merge/test_bam_translate.c.pysam.c [deleted file]
samtools/test/merge/test_rtrans_build.c [deleted file]
samtools/test/merge/test_rtrans_build.c.pysam.c [deleted file]
samtools/test/merge/test_trans_tbl_init.c [deleted file]
samtools/test/merge/test_trans_tbl_init.c.pysam.c [deleted file]
samtools/test/split/test_count_rg.c [deleted file]
samtools/test/split/test_count_rg.c.pysam.c [deleted file]
samtools/test/split/test_expand_format_string.c [deleted file]
samtools/test/split/test_expand_format_string.c.pysam.c [deleted file]
samtools/test/split/test_filter_header_rg.c [deleted file]
samtools/test/split/test_filter_header_rg.c.pysam.c [deleted file]
samtools/test/split/test_parse_args.c [deleted file]
samtools/test/split/test_parse_args.c.pysam.c [deleted file]
samtools/test/test.c [deleted file]
samtools/test/test.c.pysam.c [deleted file]
samtools/test/test.h [deleted file]
samtools/test/tview/test_get_rg_sample.c [deleted file]
samtools/test/tview/test_get_rg_sample.c.pysam.c [deleted file]
samtools/tmp_file.c
samtools/tmp_file.c.pysam.c
samtools/tmp_file.h
samtools/version.h [deleted file]
samtools/version.sh [new file with mode: 0755]
samtools/win32/xcurses.h [deleted file]
samtools/win32/zconf.h [deleted file]
samtools/win32/zlib.h [deleted file]
setup.py
tests/00README.txt
tests/AlignmentFile_test.py
tests/faidx_test.py
tests/pysam_data/Makefile
tests/pysam_data/ex3.sam
tests/pysam_data/example_empty_with_header.sam
tests/pysam_data/example_user_header.sam [deleted file]
tests/pysam_data/rg_with_tab.sam
tests/samtools_test.py
tests/test_samtools_python.py