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(parent: 3a45c2d) | patch
Imported Upstream version 0.8.1
authorJorge Soares <j.s.soares@gmail.com>
Fri, 28 Nov 2014 09:27:49 +0000 (09:27 +0000)
committerJorge Soares <j.s.soares@gmail.com>
Fri, 28 Nov 2014 09:27:49 +0000 (09:27 +0000)
commite061ec42ab2ce00087c8d1115896ad4196cf5dd6
tree9368e26df36aee3618ea99d33499e1c4477cdda7tree | snapshot
parent3a45c2d0bee0552cff9944988f8e6f4e484b5c51commit | diff
Imported Upstream version 0.8.1
246 files changed:
.gitignore [new file with mode: 0644] blob
.hgignore [new file with mode: 0644] blob
.hgtags [new file with mode: 0644] blob
.travis.yml [new file with mode: 0644] blob
AUTHORS [new file with mode: 0644] blob
PKG-INFO [deleted file] blob | history
benchmark/tabix_bench.py [new file with mode: 0644] blob
benchmark/windows_small.bed [new file with mode: 0644] blob
benchmark/windows_small.bed.gz [new file with mode: 0644] blob
benchmark/windows_small.bed.gz.tbi [new file with mode: 0644] blob
doc/out [deleted file] blob | history
htslib/INSTALL [new file with mode: 0644] blob
htslib/LICENSE [new file with mode: 0644] blob
htslib/Makefile [new file with mode: 0644] blob
htslib/README [new file with mode: 0644] blob
htslib/faidx.5 [new file with mode: 0644] blob
htslib/htslib.mk [new file with mode: 0644] blob
htslib/htslib.pc.in [new file with mode: 0644] blob
htslib/htslib_vars.mk [new file with mode: 0644] blob
htslib/sam.5 [new file with mode: 0644] blob
htslib/tabix.1 [new file with mode: 0644] blob
htslib/test/aux#aux.sam [new file with mode: 0644] blob
htslib/test/aux.fa [new file with mode: 0644] blob
htslib/test/aux.fa.fai [new file with mode: 0644] blob
htslib/test/c1#bounds.sam [new file with mode: 0644] blob
htslib/test/c1#clip.sam [new file with mode: 0644] blob
htslib/test/c1#pad1.sam [new file with mode: 0644] blob
htslib/test/c1#pad2.sam [new file with mode: 0644] blob
htslib/test/c1#pad3.sam [new file with mode: 0644] blob
htslib/test/c1.fa [new file with mode: 0644] blob
htslib/test/c1.fa.fai [new file with mode: 0644] blob
htslib/test/ce#1.sam [new file with mode: 0644] blob
htslib/test/ce#2.sam [new file with mode: 0644] blob
htslib/test/ce#5.sam [new file with mode: 0644] blob
htslib/test/ce#5b.sam [new file with mode: 0644] blob
htslib/test/ce#large_seq.sam [new file with mode: 0644] blob
htslib/test/ce#tag_depadded.sam [new file with mode: 0644] blob
htslib/test/ce#tag_padded.sam [new file with mode: 0644] blob
htslib/test/ce#unmap.sam [new file with mode: 0644] blob
htslib/test/ce#unmap1.sam [new file with mode: 0644] blob
htslib/test/ce#unmap2.sam [new file with mode: 0644] blob
htslib/test/ce.fa [new file with mode: 0644] blob
htslib/test/ce.fa.fai [new file with mode: 0644] blob
htslib/test/compare_sam.pl [new file with mode: 0755] blob
htslib/test/fieldarith.c [new file with mode: 0644] blob
htslib/test/fieldarith.sam [new file with mode: 0644] blob
htslib/test/hfile.c [new file with mode: 0644] blob
htslib/test/sam.c [new file with mode: 0644] blob
htslib/test/test-vcf-api.c [new file with mode: 0644] blob
htslib/test/test-vcf-api.out [new file with mode: 0644] blob
htslib/test/test-vcf-sweep.c [new file with mode: 0644] blob
htslib/test/test-vcf-sweep.out [new file with mode: 0644] blob
htslib/test/test.pl [new file with mode: 0755] blob
htslib/test/test_view.c [new file with mode: 0644] blob
htslib/test/test_view.pl [new file with mode: 0755] blob
htslib/test/xx#blank.sam [new file with mode: 0644] blob
htslib/test/xx#large_aux.sam [new file with mode: 0644] blob
htslib/test/xx#large_aux2.sam [new file with mode: 0644] blob
htslib/test/xx#minimal.sam [new file with mode: 0644] blob
htslib/test/xx#pair.sam [new file with mode: 0644] blob
htslib/test/xx#rg.sam [new file with mode: 0644] blob
htslib/test/xx#triplet.sam [new file with mode: 0644] blob
htslib/test/xx#unsorted.sam [new file with mode: 0644] blob
htslib/test/xx.fa [new file with mode: 0644] blob
htslib/test/xx.fa.fai [new file with mode: 0644] blob
htslib/vcf.5 [new file with mode: 0644] blob
install-CGAT-tools.sh [new file with mode: 0755] blob
pysam.egg-info/PKG-INFO [deleted file] blob | history
pysam.egg-info/SOURCES.txt [deleted file] blob | history
pysam.egg-info/dependency_links.txt [deleted file] blob | history
pysam.egg-info/not-zip-safe [deleted file] blob | history
pysam.egg-info/top_level.txt [deleted file] blob | history
pysam/TabProxies.c [deleted file] blob | history
pysam/VCF.py.obsolete [new file with mode: 0644] blob
pysam/alternatives.py.obsolete [new file with mode: 0644] blob
pysam/calignmentfile.c [deleted file] blob | history
pysam/cfaidx.c [deleted file] blob | history
pysam/chtslib.c [deleted file] blob | history
pysam/csamfile.c [deleted file] blob | history
pysam/csamtools.c [deleted file] blob | history
pysam/ctabix.c [deleted file] blob | history
pysam/cvcf.c [deleted file] blob | history
requires.txt [new file with mode: 0644] blob
samtools/bam.c [new file with mode: 0644] blob
samtools/bam2bcf.c [new file with mode: 0644] blob
samtools/bam2bcf_indel.c [new file with mode: 0644] blob
samtools/bam2depth.c [new file with mode: 0644] blob
samtools/bam_aux.c [new file with mode: 0644] blob
samtools/bam_cat.c [new file with mode: 0644] blob
samtools/bam_color.c [new file with mode: 0644] blob
samtools/bam_flags.c [new file with mode: 0644] blob
samtools/bam_import.c [new file with mode: 0644] blob
samtools/bam_index.c [new file with mode: 0644] blob
samtools/bam_lpileup.c [new file with mode: 0644] blob
samtools/bam_mate.c [new file with mode: 0644] blob
samtools/bam_md.c [new file with mode: 0644] blob
samtools/bam_plbuf.c [new file with mode: 0644] blob
samtools/bam_plcmd.c [new file with mode: 0644] blob
samtools/bam_reheader.c [new file with mode: 0644] blob
samtools/bam_rmdup.c [new file with mode: 0644] blob
samtools/bam_rmdupse.c [new file with mode: 0644] blob
samtools/bam_sort.c [new file with mode: 0644] blob
samtools/bam_split.c [new file with mode: 0644] blob
samtools/bam_stat.c [new file with mode: 0644] blob
samtools/bam_tview.c [new file with mode: 0644] blob
samtools/bam_tview_curses.c [new file with mode: 0644] blob
samtools/bam_tview_html.c [new file with mode: 0644] blob
samtools/bamshuf.c [new file with mode: 0644] blob
samtools/bedcov.c [new file with mode: 0644] blob
samtools/bedidx.c [new file with mode: 0644] blob
samtools/cut_target.c [new file with mode: 0644] blob
samtools/errmod.c [new file with mode: 0644] blob
samtools/faidx.c [new file with mode: 0644] blob
samtools/kaln.c [new file with mode: 0644] blob
samtools/misc/ace2sam.c [new file with mode: 0644] blob
samtools/misc/md5.c [new file with mode: 0644] blob
samtools/padding.c [new file with mode: 0644] blob
samtools/phase.c [new file with mode: 0644] blob
samtools/sam.c [new file with mode: 0644] blob
samtools/sam_header.c [new file with mode: 0644] blob
samtools/sam_view.c [new file with mode: 0644] blob
samtools/sample.c [new file with mode: 0644] blob
samtools/stats.c [new file with mode: 0644] blob
samtools/stats_isize.c [new file with mode: 0644] blob
samtools/test/merge/test_bam_translate.c [new file with mode: 0644] blob
samtools/test/merge/test_bam_translate.c.pysam.c [new file with mode: 0644] blob
samtools/test/merge/test_pretty_header.c [new file with mode: 0644] blob
samtools/test/merge/test_pretty_header.c.pysam.c [new file with mode: 0644] blob
samtools/test/merge/test_rtrans_build.c [new file with mode: 0644] blob
samtools/test/merge/test_rtrans_build.c.pysam.c [new file with mode: 0644] blob
samtools/test/merge/test_trans_tbl_init.c [new file with mode: 0644] blob
samtools/test/merge/test_trans_tbl_init.c.pysam.c [new file with mode: 0644] blob
samtools/test/split/test_count_rg.c [new file with mode: 0644] blob
samtools/test/split/test_count_rg.c.pysam.c [new file with mode: 0644] blob
samtools/test/split/test_expand_format_string.c [new file with mode: 0644] blob
samtools/test/split/test_expand_format_string.c.pysam.c [new file with mode: 0644] blob
samtools/test/split/test_filter_header_rg.c [new file with mode: 0644] blob
samtools/test/split/test_filter_header_rg.c.pysam.c [new file with mode: 0644] blob
samtools/test/split/test_parse_args.c [new file with mode: 0644] blob
samtools/test/split/test_parse_args.c.pysam.c [new file with mode: 0644] blob
samtools/test/test.c [new file with mode: 0644] blob
samtools/test/tview/test_get_rg_sample.c [new file with mode: 0644] blob
samtools/test/tview/test_get_rg_sample.c.pysam.c [new file with mode: 0644] blob
save/example.py [new file with mode: 0644] blob
save/pysam_bench.py [new file with mode: 0644] blob
save/pysam_test2.6.py [new file with mode: 0755] blob
save/pysam_test_stdin.py [new file with mode: 0644] blob
save/pysam_testpp.py [new file with mode: 0644] blob
save/segfault_tests.py [new file with mode: 0755] blob
save/vcf_test.py [new file with mode: 0644] blob
setup.cfg diff | blob | history
tests/AlignmentFile_test.py [new file with mode: 0644] blob
tests/SamFile_test.py [new file with mode: 0644] blob
tests/TestUtils.py [new file with mode: 0644] blob
tests/_compile_test.pyx [new file with mode: 0644] blob
tests/_compile_test.pyxbld [new file with mode: 0644] blob
tests/_cython_flagstat.pyx [new file with mode: 0644] blob
tests/_cython_flagstat.pyxbld [new file with mode: 0644] blob
tests/compile_test.py [new file with mode: 0644] blob
tests/cython_flagstat.py [new file with mode: 0644] blob
tests/faidx_test.py [new file with mode: 0644] blob
tests/pysam_data/Makefile [new file with mode: 0644] blob
tests/pysam_data/ex1.bed [new file with mode: 0644] blob
tests/pysam_data/ex1.fa [new file with mode: 0644] blob
tests/pysam_data/ex1.fq [new file with mode: 0644] blob
tests/pysam_data/ex1.sam.gz [new file with mode: 0644] blob
tests/pysam_data/ex10.sam [new file with mode: 0644] blob
tests/pysam_data/ex3.sam [new file with mode: 0644] blob
tests/pysam_data/ex4.sam [new file with mode: 0644] blob
tests/pysam_data/ex5.sam [new file with mode: 0644] blob
tests/pysam_data/ex6.sam [new file with mode: 0644] blob
tests/pysam_data/ex7.sam.donottest [new file with mode: 0644] blob
tests/pysam_data/ex8.sam [new file with mode: 0644] blob
tests/pysam_data/ex9_fail.sam [new file with mode: 0644] blob
tests/pysam_data/ex9_nofail.sam [new file with mode: 0644] blob
tests/pysam_data/example_btag.sam [new file with mode: 0644] blob
tests/pysam_data/example_empty_header.sam [new file with mode: 0644] blob
tests/pysam_data/example_unmapped_reads_no_sq.sam [new file with mode: 0644] blob
tests/pysam_data/example_user_header.sam [new file with mode: 0644] blob
tests/pysam_data/issue100.sam [new file with mode: 0644] blob
tests/pysam_data/rg_with_tab.sam [new file with mode: 0644] blob
tests/pysam_data/softclip.sam [new file with mode: 0644] blob
tests/pysam_data/tag_bug.sam [new file with mode: 0644] blob
tests/pysam_data/test.gtf [new file with mode: 0644] blob
tests/pysam_data/test.gtf.gz [new file with mode: 0644] blob
tests/pysam_data/test_unaligned.sam [new file with mode: 0644] blob
tests/python_flagstat.py [new file with mode: 0644] blob
tests/refactoring.pl [new file with mode: 0644] blob
tests/refactoring.txt [new file with mode: 0644] blob
tests/samtools_test.py [new file with mode: 0644] blob
tests/tabix_data/example.bed.gz [new file with mode: 0644] blob
tests/tabix_data/example.bed.gz.tbi [new file with mode: 0644] blob
tests/tabix_data/example.gtf.gz [new file with mode: 0644] blob
tests/tabix_data/example.gtf.gz.tbi [new file with mode: 0644] blob
tests/tabix_data/example.sam.gz [new file with mode: 0644] blob
tests/tabix_data/example.sam.gz.tbi [new file with mode: 0644] blob
tests/tabix_data/example.vcf.gz [new file with mode: 0644] blob
tests/tabix_data/example.vcf.gz.tbi [new file with mode: 0644] blob
tests/tabix_data/example.vcf40 [new file with mode: 0644] blob
tests/tabix_data/example_badcomments.bed.gz [new file with mode: 0644] blob
tests/tabix_data/example_badcomments.bed.gz.tbi [new file with mode: 0644] blob
tests/tabix_data/example_badcomments.gtf.gz [new file with mode: 0644] blob
tests/tabix_data/example_badcomments.gtf.gz.tbi [new file with mode: 0644] blob
tests/tabix_data/example_badcomments.sam.gz [new file with mode: 0644] blob
tests/tabix_data/example_badcomments.sam.gz.tbi [new file with mode: 0644] blob
tests/tabix_data/example_badcomments.vcf.gz [new file with mode: 0644] blob
tests/tabix_data/example_badcomments.vcf.gz.tbi [new file with mode: 0644] blob
tests/tabix_data/example_comments.bed.gz [new file with mode: 0644] blob
tests/tabix_data/example_comments.bed.gz.tbi [new file with mode: 0644] blob
tests/tabix_data/example_comments.gtf.gz [new file with mode: 0644] blob
tests/tabix_data/example_comments.gtf.gz.tbi [new file with mode: 0644] blob
tests/tabix_data/example_comments.sam.gz [new file with mode: 0644] blob
tests/tabix_data/example_comments.sam.gz.tbi [new file with mode: 0644] blob
tests/tabix_data/example_comments.vcf.gz [new file with mode: 0644] blob
tests/tabix_data/example_comments.vcf.gz.tbi [new file with mode: 0644] blob
tests/tabix_data/example_unicode.vcf [new file with mode: 0644] blob
tests/tabix_data/gtf_toofew_fields.gtf.gz [new file with mode: 0644] blob
tests/tabix_data/gtf_toomany_fields.gtf.gz [new file with mode: 0644] blob
tests/tabix_data/gtf_wrong_fields.gtf.gz [new file with mode: 0644] blob
tests/tabix_data/vcf/10.vcf [new file with mode: 0644] blob
tests/tabix_data/vcf/11.vcf [new file with mode: 0644] blob
tests/tabix_data/vcf/12.vcf [new file with mode: 0644] blob
tests/tabix_data/vcf/13.vcf [new file with mode: 0644] blob
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tests/tabix_data/vcf/2.vcf [new file with mode: 0644] blob
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tests/tabix_data/vcf/7.vcf [new file with mode: 0644] blob
tests/tabix_data/vcf/8.vcf [new file with mode: 0644] blob
tests/tabix_data/vcf/9.vcf [new file with mode: 0644] blob
tests/tabix_data/vcf/README.txt [new file with mode: 0644] blob
tests/tabix_data/vcf/issue85.vcf [new file with mode: 0644] blob
tests/tabix_test.py [new file with mode: 0644] blob
win32/getopt.c [new file with mode: 0644] blob
win32/getopt.h [new file with mode: 0644] blob
win32/stdint.h [new file with mode: 0644] blob
win32/unistd.h [new file with mode: 0644] blob
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