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

author	Steffen Moeller <moeller@debian.org>
	Sat, 28 Jul 2018 22:50:40 +0000 (00:50 +0200)
committer	Steffen Moeller <moeller@debian.org>
	Sat, 28 Jul 2018 22:50:40 +0000 (00:50 +0200)
commit	b31915d19be7e34dd1f5d2bebfc257dc2e9ac608
tree	e93ea54418f895665e4316d98125cc90c0956c29	tree \| snapshot
parent	6136085e9b8025bfc1a5e65c5b39d3cd98aceed1	commit \| diff

New upstream version 0.15.0.1+ds

218 files changed:

.travis.yml		diff \| blob \| history
NEWS		diff \| blob \| history
README.rst		diff \| blob \| history
bcftools/LICENSE	[new file with mode: 0644]	blob
bcftools/README	[new file with mode: 0644]	blob
bcftools/bam_sample.c		diff \| blob \| history
bcftools/bam_sample.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/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/filter.c		diff \| blob \| history
bcftools/filter.c.pysam.c		diff \| blob \| history
bcftools/htslib-1.9/LICENSE	[new file with mode: 0644]	blob
bcftools/htslib-1.9/README	[new file with mode: 0644]	blob
bcftools/main.c		diff \| blob \| history
bcftools/main.c.pysam.c		diff \| blob \| history
bcftools/mpileup.c		diff \| blob \| history
bcftools/mpileup.c.pysam.c		diff \| blob \| history
bcftools/plugins/GTisec.c	[new file with mode: 0644]	blob
bcftools/plugins/GTisec.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/GTsubset.c	[new file with mode: 0644]	blob
bcftools/plugins/GTsubset.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/ad-bias.c	[new file with mode: 0644]	blob
bcftools/plugins/ad-bias.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/af-dist.c	[new file with mode: 0644]	blob
bcftools/plugins/af-dist.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/check-ploidy.c	[new file with mode: 0644]	blob
bcftools/plugins/check-ploidy.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/check-sparsity.c	[new file with mode: 0644]	blob
bcftools/plugins/check-sparsity.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/color-chrs.c	[new file with mode: 0644]	blob
bcftools/plugins/color-chrs.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/contrast.c	[new file with mode: 0644]	blob
bcftools/plugins/contrast.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/counts.c	[new file with mode: 0644]	blob
bcftools/plugins/counts.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/dosage.c	[new file with mode: 0644]	blob
bcftools/plugins/dosage.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/fill-AN-AC.c	[new file with mode: 0644]	blob
bcftools/plugins/fill-AN-AC.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/fill-from-fasta.c	[new file with mode: 0644]	blob
bcftools/plugins/fill-from-fasta.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/fill-tags.c	[new file with mode: 0644]	blob
bcftools/plugins/fill-tags.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/fixploidy.c	[new file with mode: 0644]	blob
bcftools/plugins/fixploidy.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/fixref.c	[new file with mode: 0644]	blob
bcftools/plugins/fixref.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/frameshifts.c	[new file with mode: 0644]	blob
bcftools/plugins/frameshifts.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/guess-ploidy.c	[new file with mode: 0644]	blob
bcftools/plugins/guess-ploidy.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/impute-info.c	[new file with mode: 0644]	blob
bcftools/plugins/impute-info.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/isecGT.c	[new file with mode: 0644]	blob
bcftools/plugins/isecGT.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/mendelian.c	[new file with mode: 0644]	blob
bcftools/plugins/mendelian.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/missing2ref.c	[new file with mode: 0644]	blob
bcftools/plugins/missing2ref.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/prune.c	[new file with mode: 0644]	blob
bcftools/plugins/prune.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/setGT.c	[new file with mode: 0644]	blob
bcftools/plugins/setGT.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/smpl-stats.c	[new file with mode: 0644]	blob
bcftools/plugins/smpl-stats.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/split.c	[new file with mode: 0644]	blob
bcftools/plugins/split.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/tag2tag.c	[new file with mode: 0644]	blob
bcftools/plugins/tag2tag.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/trio-stats.c	[new file with mode: 0644]	blob
bcftools/plugins/trio-stats.c.pysam.c	[new file with mode: 0644]	blob
bcftools/plugins/trio-switch-rate.c	[new file with mode: 0644]	blob
bcftools/plugins/trio-switch-rate.c.pysam.c	[new file with mode: 0644]	blob
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/tabix.c.pysam.c		diff \| blob \| history
bcftools/test/test-rbuf.c	[new file with mode: 0644]	blob
bcftools/test/test-rbuf.c.pysam.c	[new file with mode: 0644]	blob
bcftools/test/test-regidx.c	[new file with mode: 0644]	blob
bcftools/test/test-regidx.c.pysam.c	[new file with mode: 0644]	blob
bcftools/vcfannotate.c		diff \| blob \| history
bcftools/vcfannotate.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/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/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.h		diff \| blob \| history
benchmark/cython_flagstat.py	[deleted file]	blob \| history
benchmark/python_flagstat.py	[deleted file]	blob \| history
buildwheels.sh	[deleted file]	blob \| history
ci/conda-recipe/build.sh	[deleted file]	blob \| history
ci/conda-recipe/meta.yaml	[deleted file]	blob \| history
ci/install-CGAT-tools.sh	[deleted file]	blob \| history
devtools/buildwheels.sh	[new file with mode: 0755]	blob
devtools/conda-recipe/build.sh	[new file with mode: 0644]	blob
devtools/conda-recipe/meta.yaml	[new file with mode: 0644]	blob
devtools/import.py	[new file with mode: 0644]	blob
devtools/install-CGAT-tools.sh	[new file with mode: 0755]	blob
devtools/run_tests_travis.sh	[new file with mode: 0755]	blob
doc/api.rst		diff \| blob \| history
doc/glossary.rst		diff \| blob \| history
doc/release.rst		diff \| blob \| history
import.py	[deleted file]	blob \| history
import/pysam.c		diff \| blob \| history
import/pysam.h		diff \| blob \| history
pysam/libcalignedsegment.pyx		diff \| blob \| history
pysam/libcalignmentfile.pyx		diff \| blob \| history
pysam/libcbcf.pyx		diff \| blob \| history
pysam/libchtslib.pxd		diff \| blob \| history
pysam/libchtslib.pyx		diff \| blob \| history
pysam/libctabix.pyx		diff \| blob \| history
pysam/libcutils.pxd		diff \| blob \| history
pysam/libcutils.pyx		diff \| blob \| history
pysam/version.py		diff \| blob \| history
run_tests_travis.sh	[deleted file]	blob \| history
samtools/LICENSE		diff \| blob \| history
samtools/README		diff \| blob \| history
samtools/bam.c.pysam.c		diff \| blob \| history
samtools/bam.h		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_lpileup.c		diff \| blob \| history
samtools/bam_lpileup.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_sort.c		diff \| blob \| history
samtools/bam_sort.c.pysam.c		diff \| 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/bedidx.c		diff \| blob \| history
samtools/bedidx.c.pysam.c		diff \| blob \| history
samtools/bedidx.h		diff \| blob \| history
samtools/faidx.c		diff \| blob \| history
samtools/faidx.c.pysam.c		diff \| blob \| history
samtools/htslib-1.9/LICENSE	[new file with mode: 0644]	blob
samtools/htslib-1.9/README	[new file with mode: 0644]	blob
samtools/misc/ace2sam.c.pysam.c		diff \| blob \| history
samtools/phase.c		diff \| blob \| history
samtools/phase.c.pysam.c		diff \| blob \| history
samtools/sam_utils.c		diff \| blob \| history
samtools/sam_utils.c.pysam.c		diff \| blob \| history
samtools/sam_view.c		diff \| blob \| history
samtools/sam_view.c.pysam.c		diff \| blob \| history
samtools/samtools.h		diff \| blob \| history
samtools/samtools.pysam.c		diff \| blob \| history
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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
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tests/pysam_data/example_dash_in_chr.sam	[new file with mode: 0644]	blob
tests/tabix_test.py		diff \| blob \| history

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