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

author	Afif Elghraoui <afif@debian.org>
	Sun, 2 Jul 2017 07:50:19 +0000 (03:50 -0400)
committer	Afif Elghraoui <afif@debian.org>
	Sun, 2 Jul 2017 07:50:19 +0000 (03:50 -0400)
commit	1520aab08562a7f44fd4570ea351a3dbd5db5a35
tree	9a15ae273b85d54ad5f2423a735e7847605bd25e	tree \| snapshot
parent	dadf905780b2c683a23346e1eece6aa56717ca88	commit \| diff

Imported Upstream version 0.11.2.2+ds

210 files changed:

.gitignore		diff \| blob \| history
MANIFEST.in		diff \| blob \| history
bcftools/HMM.c		diff \| blob \| history
bcftools/HMM.c.pysam.c		diff \| blob \| history
bcftools/HMM.h		diff \| blob \| history
bcftools/bam2bcf.c	[new file with mode: 0644]	blob
bcftools/bam2bcf.c.pysam.c	[new file with mode: 0644]	blob
bcftools/bam2bcf.h	[new file with mode: 0644]	blob
bcftools/bam2bcf_indel.c	[new file with mode: 0644]	blob
bcftools/bam2bcf_indel.c.pysam.c	[new file with mode: 0644]	blob
bcftools/bam_sample.c	[new file with mode: 0644]	blob
bcftools/bam_sample.c.pysam.c	[new file with mode: 0644]	blob
bcftools/bam_sample.h	[new file with mode: 0644]	blob
bcftools/bcftools.h		diff \| blob \| history
bcftools/bin.c	[new file with mode: 0644]	blob
bcftools/bin.c.pysam.c	[new file with mode: 0644]	blob
bcftools/bin.h	[new file with mode: 0644]	blob
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	[new file with mode: 0644]	blob
bcftools/csq.c.pysam.c	[new file with mode: 0644]	blob
bcftools/filter.c		diff \| blob \| history
bcftools/filter.c.pysam.c		diff \| blob \| history
bcftools/hclust.c	[new file with mode: 0644]	blob
bcftools/hclust.c.pysam.c	[new file with mode: 0644]	blob
bcftools/hclust.h	[new file with mode: 0644]	blob
bcftools/kheap.h	[new file with mode: 0644]	blob
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	[new file with mode: 0644]	blob
bcftools/mpileup.c.pysam.c	[new file with mode: 0644]	blob
bcftools/mw.h	[new file with mode: 0644]	blob
bcftools/ploidy.c		diff \| blob \| history
bcftools/ploidy.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/regidx.c	[new file with mode: 0644]	blob
bcftools/regidx.c.pysam.c	[new file with mode: 0644]	blob
bcftools/regidx.h	[new file with mode: 0644]	blob
bcftools/smpl_ilist.c	[new file with mode: 0644]	blob
bcftools/smpl_ilist.c.pysam.c	[new file with mode: 0644]	blob
bcftools/smpl_ilist.h	[new file with mode: 0644]	blob
bcftools/tabix.c		diff \| blob \| history
bcftools/tabix.c.pysam.c		diff \| blob \| history
bcftools/tsv2vcf.c		diff \| blob \| history
bcftools/tsv2vcf.c.pysam.c		diff \| blob \| history
bcftools/vcfannotate.c		diff \| blob \| history
bcftools/vcfannotate.c.pysam.c		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/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/vcfroh.c		diff \| blob \| history
bcftools/vcfroh.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/version.h		diff \| blob \| history
buildwheels.sh		diff \| blob \| history
doc/api.rst		diff \| blob \| history
doc/release.rst		diff \| blob \| history
doc/usage.rst		diff \| blob \| history
import.py		diff \| blob \| history
pysam/__init__.py		diff \| blob \| history
pysam/cbcftools_util.h	[new file with mode: 0644]	blob
pysam/csamtools_util.h	[new file with mode: 0644]	blob
pysam/htslib_util.h		diff \| blob \| history
pysam/libcalignedsegment.pxd		diff \| blob \| history
pysam/libcalignedsegment.pyx		diff \| blob \| history
pysam/libcalignmentfile.pyx		diff \| blob \| history
pysam/libcbcf.pxd		diff \| blob \| history
pysam/libcbcf.pyx		diff \| blob \| history
pysam/libcbcftools.pxd	[new file with mode: 0644]	blob
pysam/libcbcftools.pyx	[new file with mode: 0644]	blob
pysam/libcbgzf.pyx		diff \| blob \| history
pysam/libcfaidx.pyx		diff \| blob \| history
pysam/libchtslib.pxd		diff \| blob \| history
pysam/libchtslib.pyx		diff \| blob \| history
pysam/libcsamtools.pxd	[new file with mode: 0644]	blob
pysam/libcsamtools.pyx	[new file with mode: 0644]	blob
pysam/libctabix.pxd		diff \| blob \| history
pysam/libctabix.pyx		diff \| blob \| history
pysam/libctabixproxies.pxd		diff \| blob \| history
pysam/libctabixproxies.pyx		diff \| blob \| history
pysam/libcutils.pxd		diff \| blob \| history
pysam/libcutils.pyx		diff \| blob \| history
pysam/pysam_util.c		diff \| blob \| history
pysam/pysam_util.h		diff \| blob \| history
pysam/samfile_util.c		diff \| blob \| history
pysam/samfile_util.h		diff \| blob \| history
pysam/tabix_util.c		diff \| blob \| history
pysam/utils.py		diff \| blob \| history
pysam/version.py		diff \| blob \| history
samtools/bam.h		diff \| blob \| history
samtools/bam2bcf.c		diff \| blob \| history
samtools/bam2bcf.c.pysam.c		diff \| blob \| history
samtools/bam2bcf.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_cat.c		diff \| blob \| history
samtools/bam_cat.c.pysam.c		diff \| blob \| history
samtools/bam_index.c		diff \| blob \| history
samtools/bam_index.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_quickcheck.c		diff \| blob \| history
samtools/bam_quickcheck.c.pysam.c		diff \| blob \| history
samtools/bam_reheader.c		diff \| blob \| history
samtools/bam_reheader.c.pysam.c		diff \| blob \| history
samtools/bam_rmdup.c		diff \| blob \| history
samtools/bam_rmdup.c.pysam.c		diff \| blob \| history
samtools/bam_sort.c		diff \| blob \| history
samtools/bam_sort.c.pysam.c		diff \| blob \| history
samtools/bam_split.c		diff \| blob \| history
samtools/bam_split.c.pysam.c		diff \| blob \| history
samtools/bam_stat.c		diff \| blob \| history
samtools/bam_stat.c.pysam.c		diff \| blob \| history
samtools/bam_tview.c	[deleted file]	blob \| history
samtools/bam_tview.c.pysam.c	[deleted file]	blob \| history
samtools/bam_tview.h	[deleted file]	blob \| history
samtools/bam_tview_curses.c	[deleted file]	blob \| history
samtools/bam_tview_curses.c.pysam.c	[deleted file]	blob \| history
samtools/bam_tview_html.c	[deleted file]	blob \| history
samtools/bam_tview_html.c.pysam.c	[deleted file]	blob \| history
samtools/bamshuf.c		diff \| blob \| history
samtools/bamshuf.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/cut_target.c		diff \| blob \| history
samtools/cut_target.c.pysam.c		diff \| blob \| history
samtools/errmod.c	[deleted file]	blob \| history
samtools/errmod.c.pysam.c	[deleted file]	blob \| history
samtools/errmod.h	[deleted file]	blob \| history
samtools/faidx.c		diff \| blob \| history
samtools/faidx.c.pysam.c		diff \| blob \| history
samtools/kprobaln.c	[deleted file]	blob \| history
samtools/kprobaln.c.pysam.c	[deleted file]	blob \| history
samtools/kprobaln.h	[deleted file]	blob \| history
samtools/misc/ace2sam.c		diff \| blob \| history
samtools/misc/ace2sam.c.pysam.c		diff \| 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.h		diff \| blob \| history
samtools/sam_opts.c		diff \| blob \| history
samtools/sam_opts.c.pysam.c		diff \| blob \| history
samtools/sam_opts.h		diff \| blob \| history
samtools/sam_utils.c	[new file with mode: 0644]	blob
samtools/sam_utils.c.pysam.c	[new file with mode: 0644]	blob
samtools/sam_view.c		diff \| blob \| history
samtools/sam_view.c.pysam.c		diff \| blob \| history
samtools/stats.c		diff \| blob \| history
samtools/stats.c.pysam.c		diff \| blob \| history
samtools/test/split/test_filter_header_rg.c		diff \| blob \| history
samtools/test/split/test_filter_header_rg.c.pysam.c		diff \| blob \| history
samtools/test/test.c		diff \| blob \| history
samtools/test/test.c.pysam.c		diff \| blob \| history
samtools/version.h		diff \| blob \| history
setup.py		diff \| blob \| history
tests/AlignedSegment_test.py		diff \| blob \| history
tests/AlignmentFile_test.py		diff \| blob \| history
tests/SamFile_test.py	[deleted file]	blob \| history
tests/StreamFiledescriptors_test.py		diff \| blob \| history
tests/TestUtils.py		diff \| blob \| history
tests/VariantFile_test.py		diff \| blob \| history
tests/faidx_test.py		diff \| blob \| history
tests/samtools_test.py		diff \| blob \| history
tests/tabix_data/example.gff2.gz	[new file with mode: 0644]	blob
tests/tabix_data/example.gff2.gz.tbi	[new file with mode: 0644]	blob
tests/tabix_data/example.gff3.gz	[new file with mode: 0644]	blob
tests/tabix_data/example.gff3.gz.tbi	[new file with mode: 0644]	blob
tests/tabix_test.py		diff \| blob \| history
tests/tabixproxies_test.py	[new file with mode: 0644]	blob

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