dgit.raspbian.org Git - python-pysam.git/commit

author	Nilesh Patra <nilesh@debian.org>
	Thu, 14 Oct 2021 19:28:59 +0000 (00:58 +0530)
committer	Nilesh Patra <nilesh@debian.org>
	Thu, 14 Oct 2021 19:28:59 +0000 (00:58 +0530)
commit	0756fadda6074d56d45d8f40268f1342947bb217
tree	8c0edde8baabdf007819694399ba0908cc731434	tree \| snapshot
parent	324a081b63e717816423520cecc55c72a79dbc69	commit \| diff

New upstream version 0.17.0+ds

259 files changed:

.github/workflows/ci.yaml	[new file with mode: 0644]	blob
.github/workflows/release.yaml	[new file with mode: 0644]	blob
.gitignore		diff \| blob \| history
.travis.disabled.yml	[new file with mode: 0644]	blob
.travis.yml	[deleted file]	blob \| history
AUTHORS		diff \| blob \| history
INSTALL		diff \| blob \| history
MANIFEST.in		diff \| blob \| history
NEWS		diff \| blob \| history
README.rst		diff \| blob \| history
bcftools/HMM.c		diff \| blob \| history
bcftools/HMM.c.pysam.c		diff \| blob \| history
bcftools/HMM.h		diff \| blob \| history
bcftools/LICENSE		diff \| blob \| history
bcftools/README		diff \| blob \| history
bcftools/abuf.c	[new file with mode: 0644]	blob
bcftools/abuf.c.pysam.c	[new file with mode: 0644]	blob
bcftools/abuf.h	[new file with mode: 0644]	blob
bcftools/bam2bcf.c		diff \| blob \| history
bcftools/bam2bcf.c.pysam.c		diff \| blob \| history
bcftools/bam2bcf.h		diff \| blob \| history
bcftools/bam2bcf_indel.c		diff \| blob \| history
bcftools/bam2bcf_indel.c.pysam.c		diff \| blob \| history
bcftools/bcftools.h		diff \| blob \| history
bcftools/bcftools.pysam.c		diff \| blob \| history
bcftools/bcftools.pysam.h		diff \| blob \| history
bcftools/bin.c		diff \| blob \| history
bcftools/bin.c.pysam.c		diff \| blob \| history
bcftools/call.h		diff \| blob \| history
bcftools/ccall.c		diff \| blob \| history
bcftools/ccall.c.pysam.c		diff \| blob \| history
bcftools/consensus.c		diff \| blob \| history
bcftools/consensus.c.pysam.c		diff \| blob \| history
bcftools/convert.c		diff \| blob \| history
bcftools/convert.c.pysam.c		diff \| blob \| history
bcftools/csq.c		diff \| blob \| history
bcftools/csq.c.pysam.c		diff \| blob \| history
bcftools/dist.c	[new file with mode: 0644]	blob
bcftools/dist.c.pysam.c	[new file with mode: 0644]	blob
bcftools/dist.h	[new file with mode: 0644]	blob
bcftools/em.c		diff \| blob \| history
bcftools/em.c.pysam.c		diff \| blob \| history
bcftools/extsort.c	[new file with mode: 0644]	blob
bcftools/extsort.c.pysam.c	[new file with mode: 0644]	blob
bcftools/extsort.h	[new file with mode: 0644]	blob
bcftools/filter.c		diff \| blob \| history
bcftools/filter.c.pysam.c		diff \| blob \| history
bcftools/filter.h		diff \| blob \| history
bcftools/hclust.c		diff \| blob \| history
bcftools/hclust.c.pysam.c		diff \| blob \| history
bcftools/htslib-1.10.2/LICENSE	[deleted file]	blob \| history
bcftools/htslib-1.10.2/README	[deleted file]	blob \| history
bcftools/main.c		diff \| blob \| history
bcftools/main.c.pysam.c		diff \| blob \| history
bcftools/mcall.c		diff \| blob \| history
bcftools/mcall.c.pysam.c		diff \| blob \| history
bcftools/mpileup.c		diff \| blob \| history
bcftools/mpileup.c.pysam.c		diff \| blob \| history
bcftools/ploidy.h		diff \| blob \| history
bcftools/prob1.c		diff \| blob \| history
bcftools/prob1.c.pysam.c		diff \| blob \| history
bcftools/prob1.h		diff \| blob \| history
bcftools/rbuf.h		diff \| blob \| history
bcftools/regidx.c		diff \| blob \| history
bcftools/regidx.c.pysam.c		diff \| blob \| history
bcftools/regidx.h		diff \| blob \| history
bcftools/reheader.c		diff \| blob \| history
bcftools/reheader.c.pysam.c		diff \| blob \| history
bcftools/smpl_ilist.c		diff \| blob \| history
bcftools/smpl_ilist.c.pysam.c		diff \| blob \| history
bcftools/str_finder.c	[new file with mode: 0644]	blob
bcftools/str_finder.c.pysam.c	[new file with mode: 0644]	blob
bcftools/str_finder.h	[new file with mode: 0644]	blob
bcftools/utlist.h	[new file with mode: 0644]	blob
bcftools/vcfannotate.c		diff \| blob \| history
bcftools/vcfannotate.c.pysam.c		diff \| blob \| history
bcftools/vcfbuf.c		diff \| blob \| history
bcftools/vcfbuf.c.pysam.c		diff \| blob \| history
bcftools/vcfbuf.h		diff \| blob \| history
bcftools/vcfcall.c		diff \| blob \| history
bcftools/vcfcall.c.pysam.c		diff \| blob \| history
bcftools/vcfcnv.c		diff \| blob \| history
bcftools/vcfcnv.c.pysam.c		diff \| blob \| history
bcftools/vcfconcat.c		diff \| blob \| history
bcftools/vcfconcat.c.pysam.c		diff \| blob \| history
bcftools/vcfconvert.c		diff \| blob \| history
bcftools/vcfconvert.c.pysam.c		diff \| blob \| history
bcftools/vcffilter.c		diff \| blob \| history
bcftools/vcffilter.c.pysam.c		diff \| blob \| history
bcftools/vcfgtcheck.c		diff \| blob \| history
bcftools/vcfgtcheck.c.pysam.c		diff \| blob \| history
bcftools/vcfindex.c		diff \| blob \| history
bcftools/vcfindex.c.pysam.c		diff \| blob \| history
bcftools/vcfisec.c		diff \| blob \| history
bcftools/vcfisec.c.pysam.c		diff \| blob \| history
bcftools/vcfmerge.c		diff \| blob \| history
bcftools/vcfmerge.c.pysam.c		diff \| blob \| history
bcftools/vcfnorm.c		diff \| blob \| history
bcftools/vcfnorm.c.pysam.c		diff \| blob \| history
bcftools/vcfplugin.c		diff \| blob \| history
bcftools/vcfplugin.c.pysam.c		diff \| blob \| history
bcftools/vcfquery.c		diff \| blob \| history
bcftools/vcfquery.c.pysam.c		diff \| blob \| history
bcftools/vcfroh.c		diff \| blob \| history
bcftools/vcfroh.c.pysam.c		diff \| blob \| history
bcftools/vcfsom.c		diff \| blob \| history
bcftools/vcfsom.c.pysam.c		diff \| blob \| history
bcftools/vcfsort.c		diff \| blob \| history
bcftools/vcfsort.c.pysam.c		diff \| blob \| history
bcftools/vcfstats.c		diff \| blob \| history
bcftools/vcfstats.c.pysam.c		diff \| blob \| history
bcftools/vcfview.c		diff \| blob \| history
bcftools/vcfview.c.pysam.c		diff \| blob \| history
bcftools/vcmp.c		diff \| blob \| history
bcftools/vcmp.c.pysam.c		diff \| blob \| history
bcftools/vcmp.h		diff \| blob \| history
bcftools/version.c		diff \| blob \| history
bcftools/version.c.pysam.c		diff \| blob \| history
bcftools/version.sh		diff \| blob \| history
cy_build.py		diff \| blob \| history
devtools/import.py		diff \| blob \| history
devtools/install-CGAT-tools.sh		diff \| blob \| history
devtools/run_tests_travis.sh		diff \| blob \| history
doc/api.rst		diff \| blob \| history
doc/benchmarking.rst		diff \| blob \| history
doc/conf.py		diff \| blob \| history
doc/developer.rst		diff \| blob \| history
doc/faq.rst		diff \| blob \| history
doc/glossary.rst		diff \| blob \| history
doc/index.rst		diff \| blob \| history
doc/installation.rst		diff \| blob \| history
doc/release.rst		diff \| blob \| history
doc/usage.rst		diff \| blob \| history
import/pysam.c		diff \| blob \| history
import/pysam.h		diff \| blob \| history
pysam.py	[deleted file]	blob \| history
pysam/__init__.py		diff \| blob \| history
pysam/libcalignedsegment.pxd		diff \| blob \| history
pysam/libcalignedsegment.pyx		diff \| blob \| history
pysam/libcalignmentfile.pxd		diff \| blob \| history
pysam/libcalignmentfile.pyx		diff \| blob \| history
pysam/libcbcf.pyx		diff \| blob \| history
pysam/libcbcftools.pxd		diff \| blob \| history
pysam/libcfaidx.pyx		diff \| blob \| history
pysam/libchtslib.pxd		diff \| blob \| history
pysam/libchtslib.pyx		diff \| blob \| history
pysam/libcsamtools.pxd		diff \| blob \| history
pysam/libctabix.pyx		diff \| blob \| history
pysam/libcutils.pxd		diff \| blob \| history
pysam/libcutils.pyx		diff \| blob \| history
pysam/samtools.py		diff \| blob \| history
pysam/version.h		diff \| blob \| history
pysam/version.py		diff \| blob \| history
samtools/LICENSE		diff \| blob \| history
samtools/README		diff \| blob \| history
samtools/amplicon_stats.c	[new file with mode: 0644]	blob
samtools/amplicon_stats.c.pysam.c	[new file with mode: 0644]	blob
samtools/bam.c		diff \| blob \| history
samtools/bam.c.pysam.c		diff \| blob \| history
samtools/bam.h		diff \| blob \| history
samtools/bam2bcf_indel.c		diff \| blob \| history
samtools/bam2bcf_indel.c.pysam.c		diff \| blob \| history
samtools/bam2depth.c		diff \| blob \| history
samtools/bam2depth.c.pysam.c		diff \| blob \| history
samtools/bam_addrprg.c		diff \| blob \| history
samtools/bam_addrprg.c.pysam.c		diff \| blob \| history
samtools/bam_ampliconclip.c	[new file with mode: 0644]	blob
samtools/bam_ampliconclip.c.pysam.c	[new file with mode: 0644]	blob
samtools/bam_ampliconclip.h	[new file with mode: 0644]	blob
samtools/bam_aux.c		diff \| blob \| history
samtools/bam_aux.c.pysam.c		diff \| blob \| history
samtools/bam_cat.c		diff \| blob \| history
samtools/bam_cat.c.pysam.c		diff \| blob \| history
samtools/bam_color.c		diff \| blob \| history
samtools/bam_color.c.pysam.c		diff \| blob \| history
samtools/bam_fastq.c		diff \| blob \| history
samtools/bam_fastq.c.pysam.c		diff \| blob \| history
samtools/bam_flags.c		diff \| blob \| history
samtools/bam_flags.c.pysam.c		diff \| blob \| history
samtools/bam_import.c	[new file with mode: 0644]	blob
samtools/bam_import.c.pysam.c	[new file with mode: 0644]	blob
samtools/bam_index.c.pysam.c		diff \| blob \| history
samtools/bam_markdup.c		diff \| blob \| history
samtools/bam_markdup.c.pysam.c		diff \| blob \| history
samtools/bam_mate.c		diff \| blob \| history
samtools/bam_mate.c.pysam.c		diff \| blob \| history
samtools/bam_md.c		diff \| blob \| history
samtools/bam_md.c.pysam.c		diff \| blob \| history
samtools/bam_plcmd.c		diff \| blob \| history
samtools/bam_plcmd.c.pysam.c		diff \| blob \| history
samtools/bam_reheader.c.pysam.c		diff \| blob \| history
samtools/bam_rmdupse.c.pysam.c		diff \| blob \| history
samtools/bam_sort.c		diff \| blob \| history
samtools/bam_sort.c.pysam.c		diff \| blob \| history
samtools/bam_stat.c		diff \| blob \| history
samtools/bam_stat.c.pysam.c		diff \| blob \| history
samtools/bamtk.c		diff \| blob \| history
samtools/bamtk.c.pysam.c		diff \| blob \| history
samtools/bedcov.c		diff \| blob \| history
samtools/bedcov.c.pysam.c		diff \| blob \| history
samtools/bedidx.c		diff \| blob \| history
samtools/bedidx.c.pysam.c		diff \| blob \| history
samtools/coverage.c		diff \| blob \| history
samtools/coverage.c.pysam.c		diff \| blob \| history
samtools/cut_target.c		diff \| blob \| history
samtools/cut_target.c.pysam.c		diff \| blob \| history
samtools/dict.c		diff \| blob \| history
samtools/dict.c.pysam.c		diff \| blob \| history
samtools/faidx.c		diff \| blob \| history
samtools/faidx.c.pysam.c		diff \| blob \| history
samtools/htslib-1.10/LICENSE	[deleted file]	blob \| history
samtools/htslib-1.10/README	[deleted file]	blob \| history
samtools/padding.c		diff \| blob \| history
samtools/padding.c.pysam.c		diff \| blob \| history
samtools/phase.c		diff \| blob \| history
samtools/phase.c.pysam.c		diff \| blob \| history
samtools/sam_view.c		diff \| blob \| history
samtools/sam_view.c.pysam.c		diff \| blob \| history
samtools/samtools.pysam.c		diff \| blob \| history
samtools/samtools.pysam.h		diff \| blob \| history
samtools/stats.c		diff \| blob \| history
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samtools/stats_isize.c.pysam.c		diff \| blob \| history
samtools/tmp_file.h		diff \| blob \| history
samtools/version.sh		diff \| blob \| history
setup.py		diff \| blob \| history
tests/AlignedSegment_test.py		diff \| blob \| history
tests/AlignmentFileHeader_test.py		diff \| blob \| history
tests/AlignmentFilePileup_test.py		diff \| blob \| history
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tests/StreamFiledescriptors_test.py		diff \| blob \| history
tests/TestUtils.py		diff \| blob \| history
tests/VariantFile_test.py		diff \| blob \| history
tests/VariantRecord_test.py		diff \| blob \| history
tests/cbcf_data/Makefile		diff \| blob \| history
tests/compile_test.py		diff \| blob \| history
tests/faidx_test.py		diff \| blob \| history
tests/pysam_data/0example_no_seq_in_header.bam	[new file with mode: 0644]	blob
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tests/test_samtools_python.py		diff \| blob \| history

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