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

author	Andreas Tille <tille@debian.org>
	Sat, 17 Feb 2018 13:42:30 +0000 (14:42 +0100)
committer	Andreas Tille <tille@debian.org>
	Sat, 17 Feb 2018 13:42:30 +0000 (14:42 +0100)
commit	5aa6792bd7dd9b57187fe1816f1d1dee7028141e
tree	2674f273189a39dca858cd6e7de3bf230aa7c7fb	tree \| snapshot
parent	f3bd90ac692a53de9dee562e82a11c5cda33b542	commit \| diff

New upstream version 0.14+ds

209 files changed:

.gitignore		diff \| blob \| history
MANIFEST.in		diff \| blob \| history
NEWS		diff \| blob \| history
bcftools/HMM.c.pysam.c		diff \| blob \| history
bcftools/bam2bcf.c.pysam.c		diff \| blob \| history
bcftools/bam2bcf_indel.c.pysam.c		diff \| blob \| history
bcftools/bam_sample.c.pysam.c		diff \| blob \| history
bcftools/bcftools.pysam.c	[new file with mode: 0644]	blob
bcftools/bcftools.pysam.h	[new file with mode: 0644]	blob
bcftools/bin.c.pysam.c		diff \| blob \| history
bcftools/ccall.c.pysam.c		diff \| blob \| history
bcftools/consensus.c.pysam.c		diff \| blob \| history
bcftools/convert.c.pysam.c		diff \| blob \| history
bcftools/csq.c.pysam.c		diff \| blob \| history
bcftools/em.c.pysam.c		diff \| blob \| history
bcftools/filter.c.pysam.c		diff \| blob \| history
bcftools/gvcf.c.pysam.c		diff \| blob \| history
bcftools/hclust.c.pysam.c		diff \| blob \| history
bcftools/kmin.c.pysam.c		diff \| blob \| history
bcftools/main.c.pysam.c		diff \| blob \| history
bcftools/mcall.c.pysam.c		diff \| blob \| history
bcftools/mpileup.c.pysam.c		diff \| blob \| history
bcftools/ploidy.c.pysam.c		diff \| blob \| history
bcftools/prob1.c.pysam.c		diff \| blob \| history
bcftools/pysam.h	[deleted file]	blob \| history
bcftools/regidx.c.pysam.c		diff \| blob \| history
bcftools/reheader.c	[new file with mode: 0644]	blob
bcftools/reheader.c.pysam.c	[new file with mode: 0644]	blob
bcftools/smpl_ilist.c.pysam.c		diff \| blob \| history
bcftools/tabix.c.pysam.c		diff \| blob \| history
bcftools/tsv2vcf.c.pysam.c		diff \| blob \| history
bcftools/vcfannotate.c.pysam.c		diff \| blob \| history
bcftools/vcfbuf.c.pysam.c		diff \| blob \| history
bcftools/vcfcall.c.pysam.c		diff \| blob \| history
bcftools/vcfcnv.c.pysam.c		diff \| blob \| history
bcftools/vcfconcat.c.pysam.c		diff \| blob \| history
bcftools/vcfconvert.c.pysam.c		diff \| blob \| history
bcftools/vcffilter.c.pysam.c		diff \| blob \| history
bcftools/vcfgtcheck.c.pysam.c		diff \| blob \| history
bcftools/vcfindex.c.pysam.c		diff \| blob \| history
bcftools/vcfisec.c.pysam.c		diff \| blob \| history
bcftools/vcfmerge.c.pysam.c		diff \| blob \| history
bcftools/vcfnorm.c.pysam.c		diff \| blob \| history
bcftools/vcfplugin.c.pysam.c		diff \| blob \| history
bcftools/vcfquery.c.pysam.c		diff \| blob \| history
bcftools/vcfroh.c.pysam.c		diff \| blob \| history
bcftools/vcfsom.c.pysam.c		diff \| blob \| history
bcftools/vcfsort.c.pysam.c		diff \| blob \| history
bcftools/vcfstats.c.pysam.c		diff \| blob \| history
bcftools/vcfview.c.pysam.c		diff \| blob \| history
bcftools/vcmp.c.pysam.c		diff \| blob \| history
bcftools/version.c.pysam.c		diff \| blob \| history
benchmark/AlignedSegment_bench.py	[deleted file]	blob \| history
benchmark/tabix_bench.py	[deleted file]	blob \| history
benchmark/windows_small.bed	[deleted file]	blob \| history
benchmark/windows_small.bed.gz	[deleted file]	blob \| history
benchmark/windows_small.bed.gz.tbi	[deleted file]	blob \| history
doc/benchmarking.rst	[new file with mode: 0644]	blob
doc/developer.rst		diff \| blob \| history
doc/index.rst		diff \| blob \| history
doc/release.rst		diff \| blob \| history
import.py		diff \| blob \| history
import/pysam.c	[new file with mode: 0644]	blob
import/pysam.h	[new file with mode: 0644]	blob
pysam/Pileup.py		diff \| blob \| history
pysam/__init__.py		diff \| blob \| history
pysam/htslib_util.c		diff \| blob \| history
pysam/htslib_util.h		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.pxd		diff \| blob \| history
pysam/libcfaidx.pyx		diff \| blob \| history
pysam/libchtslib.pxd		diff \| blob \| history
pysam/libchtslib.pyx		diff \| blob \| history
pysam/libcsamfile.pxd		diff \| blob \| history
pysam/libcsamtools.pxd		diff \| blob \| history
pysam/libctabix.pyx		diff \| blob \| history
pysam/libctabixproxies.pyx		diff \| blob \| history
pysam/libcutils.pxd		diff \| blob \| history
pysam/libcutils.pyx		diff \| blob \| history
pysam/namedtuple.py	[deleted file]	blob \| history
pysam/pysam_util.c		diff \| blob \| history
pysam/pysam_util.h		diff \| blob \| history
pysam/samfile_util.c	[deleted file]	blob \| history
pysam/samfile_util.h	[deleted file]	blob \| history
pysam/tabix_util.c	[deleted file]	blob \| history
pysam/tabix_util.h	[deleted file]	blob \| history
pysam/utils.py		diff \| blob \| history
pysam/version.py		diff \| blob \| history
run_tests_travis.sh		diff \| blob \| history
samtools/LICENSE	[new file with mode: 0644]	blob
samtools/README	[new file with mode: 0644]	blob
samtools/bam.c.pysam.c		diff \| blob \| history
samtools/bam.h		diff \| blob \| history
samtools/bam2bcf.c.pysam.c		diff \| blob \| history
samtools/bam2bcf_indel.c.pysam.c		diff \| blob \| history
samtools/bam2depth.c.pysam.c		diff \| blob \| history
samtools/bam_addrprg.c.pysam.c		diff \| blob \| history
samtools/bam_aux.c.pysam.c		diff \| blob \| history
samtools/bam_cat.c.pysam.c		diff \| blob \| history
samtools/bam_color.c.pysam.c		diff \| blob \| history
samtools/bam_flags.c.pysam.c		diff \| blob \| history
samtools/bam_import.c.pysam.c		diff \| blob \| history
samtools/bam_index.c.pysam.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.pysam.c		diff \| blob \| history
samtools/bam_md.c.pysam.c		diff \| blob \| history
samtools/bam_plbuf.c.pysam.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.pysam.c		diff \| blob \| history
samtools/bam_rmdup.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_split.c.pysam.c		diff \| blob \| history
samtools/bam_stat.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	[new file with mode: 0644]	blob
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.pysam.c		diff \| blob \| history
samtools/lz4/LICENSE	[new file with mode: 0644]	blob
samtools/lz4/lz4.c	[new file with mode: 0644]	blob
samtools/lz4/lz4.c.pysam.c	[new file with mode: 0644]	blob
samtools/lz4/lz4.h	[new file with mode: 0644]	blob
samtools/misc/ace2sam.c.pysam.c		diff \| blob \| history
samtools/padding.c.pysam.c		diff \| blob \| history
samtools/phase.c.pysam.c		diff \| blob \| history
samtools/pysam.h	[deleted file]	blob \| history
samtools/sam.c.pysam.c		diff \| blob \| history
samtools/sam_header.c		diff \| blob \| history
samtools/sam_header.c.pysam.c		diff \| blob \| history
samtools/sam_opts.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/sample.c.pysam.c		diff \| blob \| history
samtools/samtools.h		diff \| blob \| history
samtools/samtools.pysam.c	[new file with mode: 0644]	blob
samtools/samtools.pysam.h	[new file with mode: 0644]	blob
samtools/stats.c.pysam.c		diff \| blob \| history
samtools/stats_isize.c.pysam.c		diff \| blob \| history
samtools/test/merge/test_bam_translate.c.pysam.c		diff \| blob \| history
samtools/test/merge/test_rtrans_build.c.pysam.c		diff \| blob \| history
samtools/test/merge/test_trans_tbl_init.c.pysam.c		diff \| blob \| history
samtools/test/split/test_count_rg.c.pysam.c		diff \| blob \| history
samtools/test/split/test_expand_format_string.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/split/test_parse_args.c.pysam.c		diff \| blob \| history
samtools/test/test.c		diff \| blob \| history
samtools/test/test.c.pysam.c		diff \| blob \| history
samtools/test/tview/test_get_rg_sample.c.pysam.c		diff \| blob \| history
samtools/tmp_file.c	[new file with mode: 0644]	blob
samtools/tmp_file.c.pysam.c	[new file with mode: 0644]	blob
samtools/tmp_file.h	[new file with mode: 0644]	blob
samtools/version.h		diff \| blob \| history
setup.cfg		diff \| blob \| history
setup.py		diff \| blob \| history
tests/AlignedSegment_bench.py	[new file with mode: 0644]	blob
tests/AlignedSegment_test.py		diff \| blob \| history
tests/AlignmentFileFetchTestUtils.py	[new file with mode: 0644]	blob
tests/AlignmentFileFetch_bench.py	[new file with mode: 0644]	blob
tests/AlignmentFileHeader_test.py	[new file with mode: 0644]	blob
tests/AlignmentFilePileup_bench.py	[new file with mode: 0644]	blob
tests/AlignmentFilePileup_test.py	[new file with mode: 0644]	blob
tests/AlignmentFile_bench.py	[new file with mode: 0644]	blob
tests/AlignmentFile_test.py		diff \| blob \| history
tests/PileupTestUtils.py	[new file with mode: 0644]	blob
tests/StreamFiledescriptors_test.py		diff \| blob \| history
tests/TestUtils.py		diff \| blob \| history
tests/VariantFileFetchTestUtils.py	[new file with mode: 0644]	blob
tests/VariantFile_bench.py	[new file with mode: 0644]	blob
tests/VariantFile_test.py		diff \| blob \| history
tests/cbcf_data/gnomad.vcf	[new file with mode: 0644]	blob
tests/cbcf_data/gnomad_fixed.vcf	[new file with mode: 0644]	blob
tests/compile_test.py		diff \| blob \| history
tests/faidx_bench.py	[new file with mode: 0644]	blob
tests/faidx_test.py		diff \| blob \| history
tests/linking_test.py		diff \| blob \| history
tests/pysam_data/Makefile		diff \| blob \| history
tests/pysam_data/example_no_seq_in_header.bam	[new file with mode: 0644]	blob
tests/samtools_test.py		diff \| blob \| history
tests/tabix_bench.py	[new file with mode: 0644]	blob
tests/tabix_data/example.bed	[new file with mode: 0644]	blob
tests/tabix_data/example_large.bed	[new file with mode: 0644]	blob
tests/tabix_data/example_large.bed.gz	[new file with mode: 0644]	blob
tests/tabix_data/example_large.bed.gz.tbi	[new file with mode: 0644]	blob
tests/tabix_test.py		diff \| blob \| history
tests/tabixproxies_test.py		diff \| blob \| history
tests/test_samtools_python.py		diff \| blob \| history

Unnamed repository; edit this file 'description' to name the repository.

RSS Atom