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

author	Afif Elghraoui <afif@ghraoui.name>
	Mon, 8 Jun 2015 05:30:02 +0000 (22:30 -0700)
committer	Afif Elghraoui <afif@ghraoui.name>
	Mon, 8 Jun 2015 05:30:02 +0000 (22:30 -0700)
commit	91c30fda77e187b3a1b240064771a90168ab09e6
tree	f5da7dd9863ac0b342f35d1f3deed15e572e782b	tree \| snapshot
parent	5128bf9aedea461752f83632670e1676426bc528	commit \| diff

Imported Upstream version 0.8.3

145 files changed:

.gitignore		diff \| blob \| history
AUTHORS		diff \| blob \| history
INSTALL		diff \| blob \| history
MANIFEST.in		diff \| blob \| history
doc/api.rst		diff \| blob \| history
doc/conf.py		diff \| blob \| history
doc/developer.rst		diff \| blob \| history
doc/faq.rst		diff \| blob \| history
doc/index.rst		diff \| blob \| history
doc/release.rst		diff \| blob \| history
doc/usage.rst		diff \| blob \| history
htslib/INSTALL		diff \| blob \| history
htslib/Makefile		diff \| blob \| history
htslib/NEWS	[new file with mode: 0644]	blob
htslib/bgzf.c		diff \| blob \| history
htslib/bgzip.c		diff \| blob \| history
htslib/config.mk	[new file with mode: 0644]	blob
htslib/config.mk.in	[new file with mode: 0644]	blob
htslib/configure	[new file with mode: 0755]	blob
htslib/configure.ac	[new file with mode: 0644]	blob
htslib/cram/cram.h		diff \| blob \| history
htslib/cram/cram_codecs.c		diff \| blob \| history
htslib/cram/cram_codecs.h		diff \| blob \| history
htslib/cram/cram_decode.c		diff \| blob \| history
htslib/cram/cram_encode.c		diff \| blob \| history
htslib/cram/cram_index.c		diff \| blob \| history
htslib/cram/cram_io.c		diff \| blob \| history
htslib/cram/cram_io.h		diff \| blob \| history
htslib/cram/cram_samtools.c		diff \| blob \| history
htslib/cram/cram_stats.c		diff \| blob \| history
htslib/cram/cram_structs.h		diff \| blob \| history
htslib/cram/os.h		diff \| blob \| history
htslib/cram/rANS_byte.h	[new file with mode: 0644]	blob
htslib/cram/rANS_static.c	[new file with mode: 0644]	blob
htslib/cram/rANS_static.h	[new file with mode: 0644]	blob
htslib/cram/sam_header.c		diff \| blob \| history
htslib/cram/sam_header.h		diff \| blob \| history
htslib/cram/thread_pool.c		diff \| blob \| history
htslib/cram/thread_pool.h		diff \| blob \| history
htslib/cram/vlen.c		diff \| blob \| history
htslib/faidx.c		diff \| blob \| history
htslib/hfile.c		diff \| blob \| history
htslib/hfile_internal.h		diff \| blob \| history
htslib/hfile_irods.c	[new file with mode: 0644]	blob
htslib/hts.c		diff \| blob \| history
htslib/htsfile.1	[new file with mode: 0644]	blob
htslib/htsfile.c	[new file with mode: 0644]	blob
htslib/htslib.mk		diff \| blob \| history
htslib/htslib/bgzf.h		diff \| blob \| history
htslib/htslib/faidx.h		diff \| blob \| history
htslib/htslib/hfile.h		diff \| blob \| history
htslib/htslib/hts.h		diff \| blob \| history
htslib/htslib/khash.h		diff \| blob \| history
htslib/htslib/khash_str2int.h		diff \| blob \| history
htslib/htslib/kseq.h		diff \| blob \| history
htslib/htslib/regidx.h	[new file with mode: 0644]	blob
htslib/htslib/sam.h		diff \| blob \| history
htslib/htslib/synced_bcf_reader.h		diff \| blob \| history
htslib/htslib/vcf.h		diff \| blob \| history
htslib/htslib_vars.mk		diff \| blob \| history
htslib/knetfile.c		diff \| blob \| history
htslib/regidx.c	[new file with mode: 0644]	blob
htslib/sam.c		diff \| blob \| history
htslib/synced_bcf_reader.c		diff \| blob \| history
htslib/tabix.1		diff \| blob \| history
htslib/tabix.c		diff \| blob \| history
htslib/tbx.c		diff \| blob \| history
htslib/test/aux#aux.sam	[deleted file]	blob \| history
htslib/test/aux.fa	[deleted file]	blob \| history
htslib/test/aux.fa.fai	[deleted file]	blob \| history
htslib/test/auxf#values.sam	[new file with mode: 0644]	blob
htslib/test/auxf.fa	[new file with mode: 0644]	blob
htslib/test/auxf.fa.fai	[new file with mode: 0644]	blob
htslib/test/hfile.c		diff \| blob \| history
htslib/test/sam.c		diff \| blob \| history
htslib/test/test-regidx.c	[new file with mode: 0644]	blob
htslib/test/test-vcf-api.c		diff \| blob \| history
htslib/test/test_view.c		diff \| blob \| history
htslib/vcf.c		diff \| blob \| history
htslib/vcfutils.c		diff \| blob \| history
htslib/version.h		diff \| blob \| history
install-CGAT-tools.sh		diff \| blob \| history
pysam/TabProxies.pyx		diff \| blob \| history
pysam/__init__.py		diff \| blob \| history
pysam/calignmentfile.pxd		diff \| blob \| history
pysam/calignmentfile.pyx		diff \| blob \| history
pysam/cbcf.pxd	[new file with mode: 0644]	blob
pysam/cbcf.pyx	[new file with mode: 0644]	blob
pysam/cfaidx.pxd		diff \| blob \| history
pysam/cfaidx.pyx		diff \| blob \| history
pysam/chtslib.pxd		diff \| blob \| history
pysam/chtslib.pyx		diff \| blob \| history
pysam/csamtools.pyx		diff \| blob \| history
pysam/ctabix.pyx		diff \| blob \| history
pysam/cvcf.pyx		diff \| blob \| history
pysam/htslib_util.c		diff \| blob \| history
pysam/htslib_util.h		diff \| blob \| history
pysam/version.py		diff \| blob \| history
requires.txt		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_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/bam_stat.c		diff \| blob \| history
samtools/bam_stat.c.pysam.c		diff \| blob \| history
samtools/errmod.c		diff \| blob \| history
samtools/errmod.c.pysam.c		diff \| blob \| history
samtools/kaln.c	[deleted file]	blob \| history
samtools/kaln.c.pysam.c	[deleted file]	blob \| history
samtools/kaln.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/sam.c		diff \| blob \| history
samtools/sam.c.pysam.c		diff \| blob \| history
samtools/sam.h		diff \| blob \| history
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/merge/test_rtrans_build.c		diff \| blob \| history
samtools/test/merge/test_rtrans_build.c.pysam.c		diff \| 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/version.h		diff \| blob \| history
setup.py		diff \| blob \| history
tests/AlignedSegment_test.py	[new file with mode: 0644]	blob
tests/AlignmentFile_test.py		diff \| blob \| history
tests/SamFile_test.py		diff \| blob \| history
tests/TestUtils.py		diff \| blob \| history
tests/cython_flagstat.py		diff \| blob \| history
tests/pysam_data/Makefile		diff \| blob \| history
tests/python_flagstat.py		diff \| blob \| history
tests/samtools_test.py		diff \| blob \| history
tests/tabix_test.py		diff \| blob \| history

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