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

author	Afif Elghraoui <afif@ghraoui.name>
	Sat, 5 Mar 2016 21:41:37 +0000 (13:41 -0800)
committer	Afif Elghraoui <afif@ghraoui.name>
	Sat, 5 Mar 2016 21:41:37 +0000 (13:41 -0800)
commit	364e45ae3dbbca99801346c2e0bb976c5c8d2299
tree	3467d070d92611e021ed0bf08a87dad3b8fd4696	tree \| snapshot
parent	18e49038bca0bc7775fc8f6e3703b207815a4b91	commit \| diff

Imported Upstream version 0.9.0+ds

253 files changed:

.gitignore		diff \| blob \| history
.hgignore	[deleted file]	blob \| history
.hgtags	[deleted file]	blob \| history
.travis.yml		diff \| blob \| history
INSTALL		diff \| blob \| history
KNOWN_BUGS	[deleted file]	blob \| history
MANIFEST.in		diff \| blob \| history
README.rst		diff \| blob \| history
THANKS	[deleted file]	blob \| history
bcftools/HMM.c	[new file with mode: 0644]	blob
bcftools/HMM.c.pysam.c	[new file with mode: 0644]	blob
bcftools/HMM.h	[new file with mode: 0644]	blob
bcftools/bcftools.h	[new file with mode: 0644]	blob
bcftools/call.h	[new file with mode: 0644]	blob
bcftools/ccall.c	[new file with mode: 0644]	blob
bcftools/ccall.c.pysam.c	[new file with mode: 0644]	blob
bcftools/consensus.c	[new file with mode: 0644]	blob
bcftools/consensus.c.pysam.c	[new file with mode: 0644]	blob
bcftools/convert.c	[new file with mode: 0644]	blob
bcftools/convert.c.pysam.c	[new file with mode: 0644]	blob
bcftools/convert.h	[new file with mode: 0644]	blob
bcftools/em.c	[new file with mode: 0644]	blob
bcftools/em.c.pysam.c	[new file with mode: 0644]	blob
bcftools/filter.c	[new file with mode: 0644]	blob
bcftools/filter.c.pysam.c	[new file with mode: 0644]	blob
bcftools/filter.h	[new file with mode: 0644]	blob
bcftools/gvcf.c	[new file with mode: 0644]	blob
bcftools/gvcf.c.pysam.c	[new file with mode: 0644]	blob
bcftools/gvcf.h	[new file with mode: 0644]	blob
bcftools/khash_str2str.h	[new file with mode: 0644]	blob
bcftools/kmin.c	[new file with mode: 0644]	blob
bcftools/kmin.c.pysam.c	[new file with mode: 0644]	blob
bcftools/kmin.h	[new file with mode: 0644]	blob
bcftools/main.c	[new file with mode: 0644]	blob
bcftools/main.c.pysam.c	[new file with mode: 0644]	blob
bcftools/mcall.c	[new file with mode: 0644]	blob
bcftools/mcall.c.pysam.c	[new file with mode: 0644]	blob
bcftools/ploidy.c	[new file with mode: 0644]	blob
bcftools/ploidy.c.pysam.c	[new file with mode: 0644]	blob
bcftools/ploidy.h	[new file with mode: 0644]	blob
bcftools/prob1.c	[new file with mode: 0644]	blob
bcftools/prob1.c.pysam.c	[new file with mode: 0644]	blob
bcftools/prob1.h	[new file with mode: 0644]	blob
bcftools/pysam.h	[new file with mode: 0644]	blob
bcftools/rbuf.h	[new file with mode: 0644]	blob
bcftools/tabix.c	[new file with mode: 0644]	blob
bcftools/tabix.c.pysam.c	[new file with mode: 0644]	blob
bcftools/tsv2vcf.c	[new file with mode: 0644]	blob
bcftools/tsv2vcf.c.pysam.c	[new file with mode: 0644]	blob
bcftools/tsv2vcf.h	[new file with mode: 0644]	blob
bcftools/vcfannotate.c	[new file with mode: 0644]	blob
bcftools/vcfannotate.c.pysam.c	[new file with mode: 0644]	blob
bcftools/vcfcall.c	[new file with mode: 0644]	blob
bcftools/vcfcall.c.pysam.c	[new file with mode: 0644]	blob
bcftools/vcfcnv.c	[new file with mode: 0644]	blob
bcftools/vcfcnv.c.pysam.c	[new file with mode: 0644]	blob
bcftools/vcfconcat.c	[new file with mode: 0644]	blob
bcftools/vcfconcat.c.pysam.c	[new file with mode: 0644]	blob
bcftools/vcfconvert.c	[new file with mode: 0644]	blob
bcftools/vcfconvert.c.pysam.c	[new file with mode: 0644]	blob
bcftools/vcffilter.c	[new file with mode: 0644]	blob
bcftools/vcffilter.c.pysam.c	[new file with mode: 0644]	blob
bcftools/vcfgtcheck.c	[new file with mode: 0644]	blob
bcftools/vcfgtcheck.c.pysam.c	[new file with mode: 0644]	blob
bcftools/vcfindex.c	[new file with mode: 0644]	blob
bcftools/vcfindex.c.pysam.c	[new file with mode: 0644]	blob
bcftools/vcfisec.c	[new file with mode: 0644]	blob
bcftools/vcfisec.c.pysam.c	[new file with mode: 0644]	blob
bcftools/vcfmerge.c	[new file with mode: 0644]	blob
bcftools/vcfmerge.c.pysam.c	[new file with mode: 0644]	blob
bcftools/vcfnorm.c	[new file with mode: 0644]	blob
bcftools/vcfnorm.c.pysam.c	[new file with mode: 0644]	blob
bcftools/vcfplugin.c	[new file with mode: 0644]	blob
bcftools/vcfplugin.c.pysam.c	[new file with mode: 0644]	blob
bcftools/vcfquery.c	[new file with mode: 0644]	blob
bcftools/vcfquery.c.pysam.c	[new file with mode: 0644]	blob
bcftools/vcfroh.c	[new file with mode: 0644]	blob
bcftools/vcfroh.c.pysam.c	[new file with mode: 0644]	blob
bcftools/vcfsom.c	[new file with mode: 0644]	blob
bcftools/vcfsom.c.pysam.c	[new file with mode: 0644]	blob
bcftools/vcfstats.c	[new file with mode: 0644]	blob
bcftools/vcfstats.c.pysam.c	[new file with mode: 0644]	blob
bcftools/vcfview.c	[new file with mode: 0644]	blob
bcftools/vcfview.c.pysam.c	[new file with mode: 0644]	blob
bcftools/vcmp.c	[new file with mode: 0644]	blob
bcftools/vcmp.c.pysam.c	[new file with mode: 0644]	blob
bcftools/vcmp.h	[new file with mode: 0644]	blob
bcftools/version.c	[new file with mode: 0644]	blob
bcftools/version.c.pysam.c	[new file with mode: 0644]	blob
bcftools/version.h	[new file with mode: 0644]	blob
ci/conda-recipe/build.sh	[new file with mode: 0644]	blob
ci/conda-recipe/meta.yaml	[new file with mode: 0644]	blob
ci/install-CGAT-tools.sh	[new file with mode: 0755]	blob
cy_build.py	[new file with mode: 0644]	blob
doc/api.rst		diff \| blob \| history
doc/conf.py		diff \| blob \| history
doc/faq.rst		diff \| blob \| history
doc/index.rst		diff \| blob \| history
doc/installation.rst	[new file with mode: 0644]	blob
doc/release.rst		diff \| blob \| history
doc/usage.rst		diff \| blob \| history
import.py	[new file with mode: 0644]	blob
install-CGAT-tools.sh	[deleted file]	blob \| history
pysam/__init__.py		diff \| blob \| history
pysam/bcftools.py	[new file with mode: 0644]	blob
pysam/calignedsegment.pxd		diff \| blob \| history
pysam/calignedsegment.pyx		diff \| blob \| history
pysam/calignmentfile.pyx		diff \| blob \| history
pysam/cbcf.pxd		diff \| blob \| history
pysam/cbcf.pyx		diff \| blob \| history
pysam/cfaidx.pxd		diff \| blob \| history
pysam/cfaidx.pyx		diff \| blob \| history
pysam/chtslib.pxd		diff \| blob \| history
pysam/csamtools.pxd	[deleted file]	blob \| history
pysam/csamtools.pyx	[deleted file]	blob \| history
pysam/ctabix.pxd		diff \| blob \| history
pysam/ctabix.pyx		diff \| blob \| history
pysam/cutils.pxd		diff \| blob \| history
pysam/cutils.pyx		diff \| blob \| history
pysam/cvcf.pyx		diff \| blob \| history
pysam/htslib_util.h		diff \| blob \| history
pysam/pysam_util.c		diff \| blob \| history
pysam/pysam_util.h		diff \| blob \| history
pysam/samtools.py	[new file with mode: 0644]	blob
pysam/utils.py	[new file with mode: 0644]	blob
pysam/version.py		diff \| blob \| history
run_tests_travis.sh	[new file with mode: 0755]	blob
samtools/bam.c		diff \| blob \| history
samtools/bam.c.pysam.c		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	[new file with mode: 0644]	blob
samtools/bam_addrprg.c.pysam.c	[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_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	[new file with mode: 0644]	blob
samtools/bam_quickcheck.c.pysam.c	[new file with mode: 0644]	blob
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_rmdupse.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		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		diff \| blob \| history
samtools/bam_tview.c.pysam.c		diff \| blob \| history
samtools/bam_tview.h		diff \| blob \| history
samtools/bam_tview_curses.c		diff \| blob \| history
samtools/bam_tview_curses.c.pysam.c		diff \| blob \| history
samtools/bam_tview_html.c		diff \| blob \| history
samtools/bam_tview_html.c.pysam.c		diff \| blob \| history
samtools/bamshuf.c		diff \| blob \| history
samtools/bamshuf.c.pysam.c		diff \| blob \| history
samtools/bamtk.c	[new file with mode: 0644]	blob
samtools/bamtk.c.pysam.c	[new file with mode: 0644]	blob
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/dict.c	[new file with mode: 0644]	blob
samtools/dict.c.pysam.c	[new file with mode: 0644]	blob
samtools/errmod.c		diff \| blob \| history
samtools/errmod.c.pysam.c		diff \| blob \| history
samtools/misc/md5.c	[deleted file]	blob \| history
samtools/misc/md5.c.pysam.c	[deleted file]	blob \| history
samtools/misc/md5.h	[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.c		diff \| blob \| history
samtools/sam.c.pysam.c		diff \| blob \| history
samtools/sam.h		diff \| blob \| history
samtools/sam_opts.c	[new file with mode: 0644]	blob
samtools/sam_opts.c.pysam.c	[new file with mode: 0644]	blob
samtools/sam_opts.h	[new file with mode: 0644]	blob
samtools/sam_view.c		diff \| blob \| history
samtools/sam_view.c.pysam.c		diff \| blob \| history
samtools/samtools.h		diff \| blob \| history
samtools/stats.c		diff \| blob \| history
samtools/stats.c.pysam.c		diff \| blob \| history
samtools/test/merge/test_bam_translate.c		diff \| blob \| history
samtools/test/merge/test_bam_translate.c.pysam.c		diff \| blob \| history
samtools/test/merge/test_pretty_header.c	[deleted file]	blob \| history
samtools/test/merge/test_pretty_header.c.pysam.c	[deleted file]	blob \| history
samtools/test/merge/test_trans_tbl_init.c		diff \| blob \| history
samtools/test/merge/test_trans_tbl_init.c.pysam.c		diff \| blob \| history
samtools/test/split/test_count_rg.c		diff \| blob \| history
samtools/test/split/test_count_rg.c.pysam.c		diff \| blob \| history
samtools/test/split/test_expand_format_string.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		diff \| blob \| history
samtools/test/split/test_parse_args.c.pysam.c		diff \| blob \| history
samtools/version.h		diff \| blob \| history
setup.cfg	[deleted file]	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		diff \| blob \| history
tests/TestUtils.py		diff \| blob \| history
tests/VariantFile_test.py	[new file with mode: 0644]	blob
tests/cbcf_data/Makefile	[new file with mode: 0644]	blob
tests/cbcf_data/example_empty.vcf	[new file with mode: 0644]	blob
tests/cbcf_data/example_vcf40.vcf	[new file with mode: 0644]	blob
tests/cbcf_data/example_vcf42.vcf	[new file with mode: 0644]	blob
tests/cbcf_data/example_vcf42_only_header.vcf	[new file with mode: 0644]	blob
tests/cbcf_data/example_vcf42_withcontigs.vcf	[new file with mode: 0644]	blob
tests/cbcf_data/missing_genotypes.vcf	[new file with mode: 0644]	blob
tests/faidx_test.py		diff \| blob \| history
tests/pysam_data/Makefile		diff \| blob \| history
tests/pysam_data/ex1.vcf.gz	[new file with mode: 0644]	blob
tests/pysam_data/ex1.vcf.gz.tbi	[new file with mode: 0644]	blob
tests/pysam_data/example_aligned_pairs.sam	[new file with mode: 0644]	blob
tests/pysam_data/example_empty_with_header.sam	[new file with mode: 0644]	blob
tests/pysam_data/faidx_empty_seq.fq	[new file with mode: 0644]	blob
tests/pysam_data/test_mapped_unmapped.sam	[new file with mode: 0644]	blob
tests/pysam_data/test_query_position.sam	[new file with mode: 0644]	blob
tests/samtools_test.py		diff \| blob \| history
tests/tabix_data/empty.bed.gz	[new file with mode: 0644]	blob
tests/tabix_data/empty.bed.gz.tbi	[new file with mode: 0644]	blob
tests/tabix_data/example_0v23.bed.gz	[new file with mode: 0644]	blob
tests/tabix_data/example_0v23.bed.gz.tbi	[new file with mode: 0644]	blob
tests/tabix_data/example_0v23.vcf.gz	[new file with mode: 0644]	blob
tests/tabix_data/example_0v23.vcf.gz.tbi	[new file with mode: 0644]	blob
tests/tabix_data/example_0v26.bed.gz	[new file with mode: 0644]	blob
tests/tabix_data/example_0v26.bed.gz.tbi	[new file with mode: 0644]	blob
tests/tabix_data/example_0v26.vcf.gz	[new file with mode: 0644]	blob
tests/tabix_data/example_0v26.vcf.gz.tbi	[new file with mode: 0644]	blob
tests/tabix_data/vcf/vcf_v42.vcf	[new file with mode: 0644]	blob
tests/tabix_test.py		diff \| blob \| history

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

RSS Atom