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(parent: a757e53) | patch
Imported Upstream version 0.8.0
authorAndreas Tille <tille@debian.org>
Tue, 19 Aug 2014 19:25:58 +0000 (21:25 +0200)
committerAndreas Tille <tille@debian.org>
Tue, 19 Aug 2014 19:25:58 +0000 (21:25 +0200)
commit547982fcfe6ce9451856856417591438b3fc9147
tree10be495550c36bae6ee1e96bd27cba1e2eed6e48tree | snapshot
parenta757e53aa364a0816cbebb22c43c9918f08522f8commit | diff
Imported Upstream version 0.8.0
209 files changed:
INSTALL diff | blob | history
MANIFEST.in diff | blob | history
PKG-INFO diff | blob | history
README.rst [new file with mode: 0644] blob
doc/api.rst diff | blob | history
doc/conf.py diff | blob | history
doc/contents.rst [deleted file] blob | history
doc/developer.rst diff | blob | history
doc/faq.rst diff | blob | history
doc/glossary.rst diff | blob | history
doc/index.rst [new file with mode: 0644] blob
doc/release.rst diff | blob | history
doc/usage.rst diff | blob | history
htslib/__init__.py [new file with mode: 0644] blob
htslib/bgzf.c [new file with mode: 0644] blob
htslib/bgzip.c [new file with mode: 0644] blob
htslib/config.h [new file with mode: 0644] blob
htslib/cram/cram.h [new file with mode: 0644] blob
htslib/cram/cram_codecs.c [new file with mode: 0644] blob
htslib/cram/cram_codecs.h [new file with mode: 0644] blob
htslib/cram/cram_decode.c [new file with mode: 0644] blob
htslib/cram/cram_decode.h [new file with mode: 0644] blob
htslib/cram/cram_encode.c [new file with mode: 0644] blob
htslib/cram/cram_encode.h [new file with mode: 0644] blob
htslib/cram/cram_index.c [new file with mode: 0644] blob
htslib/cram/cram_index.h [new file with mode: 0644] blob
htslib/cram/cram_io.c [new file with mode: 0644] blob
htslib/cram/cram_io.h [new file with mode: 0644] blob
htslib/cram/cram_samtools.c [new file with mode: 0644] blob
htslib/cram/cram_samtools.h [new file with mode: 0644] blob
htslib/cram/cram_stats.c [new file with mode: 0644] blob
htslib/cram/cram_stats.h [new file with mode: 0644] blob
htslib/cram/cram_structs.h [new file with mode: 0644] blob
htslib/cram/files.c [new file with mode: 0644] blob
htslib/cram/mFILE.c [new file with mode: 0644] blob
htslib/cram/mFILE.h [new file with mode: 0644] blob
htslib/cram/md5.c [new file with mode: 0644] blob
htslib/cram/md5.h [new file with mode: 0644] blob
htslib/cram/misc.h [new file with mode: 0644] blob
htslib/cram/open_trace_file.c [new file with mode: 0644] blob
htslib/cram/open_trace_file.h [new file with mode: 0644] blob
htslib/cram/os.h [new file with mode: 0644] blob
htslib/cram/pooled_alloc.c [new file with mode: 0644] blob
htslib/cram/pooled_alloc.h [new file with mode: 0644] blob
htslib/cram/sam_header.c [new file with mode: 0644] blob
htslib/cram/sam_header.h [new file with mode: 0644] blob
htslib/cram/string_alloc.c [new file with mode: 0644] blob
htslib/cram/string_alloc.h [new file with mode: 0644] blob
htslib/cram/thread_pool.c [new file with mode: 0644] blob
htslib/cram/thread_pool.h [new file with mode: 0644] blob
htslib/cram/vlen.c [new file with mode: 0644] blob
htslib/cram/vlen.h [new file with mode: 0644] blob
htslib/cram/zfio.c [new file with mode: 0644] blob
htslib/cram/zfio.h [new file with mode: 0644] blob
htslib/faidx.c [new file with mode: 0644] blob
htslib/hfile.c [new file with mode: 0644] blob
htslib/hfile_internal.h [new file with mode: 0644] blob
htslib/hfile_net.c [new file with mode: 0644] blob
htslib/hts.c [new file with mode: 0644] blob
htslib/htslib/__init__.py [new file with mode: 0644] blob
htslib/htslib/bgzf.h [new file with mode: 0644] blob
htslib/htslib/faidx.h [new file with mode: 0644] blob
htslib/htslib/hfile.h [new file with mode: 0644] blob
htslib/htslib/hts.h [new file with mode: 0644] blob
htslib/htslib/hts_defs.h [new file with mode: 0644] blob
htslib/htslib/kfunc.h [new file with mode: 0644] blob
htslib/htslib/khash.h [new file with mode: 0644] blob
htslib/htslib/khash_str2int.h [new file with mode: 0644] blob
htslib/htslib/klist.h [new file with mode: 0644] blob
htslib/htslib/knetfile.h [new file with mode: 0644] blob
htslib/htslib/kseq.h [new file with mode: 0644] blob
htslib/htslib/ksort.h [new file with mode: 0644] blob
htslib/htslib/kstdint.h [new file with mode: 0644] blob
htslib/htslib/kstring.h [new file with mode: 0644] blob
htslib/htslib/sam.h [new file with mode: 0644] blob
htslib/htslib/synced_bcf_reader.h [new file with mode: 0644] blob
htslib/htslib/tbx.h [new file with mode: 0644] blob
htslib/htslib/vcf.h [new file with mode: 0644] blob
htslib/htslib/vcf_sweep.h [new file with mode: 0644] blob
htslib/htslib/vcfutils.h [new file with mode: 0644] blob
htslib/kfunc.c [new file with mode: 0644] blob
htslib/knetfile.c [new file with mode: 0644] blob
htslib/kstring.c [new file with mode: 0644] blob
htslib/sam.c [new file with mode: 0644] blob
htslib/synced_bcf_reader.c [new file with mode: 0644] blob
htslib/tabix.c [new file with mode: 0644] blob
htslib/tbx.c [new file with mode: 0644] blob
htslib/vcf.c [new file with mode: 0644] blob
htslib/vcf_sweep.c [new file with mode: 0644] blob
htslib/vcfutils.c [new file with mode: 0644] blob
htslib/version.h [new file with mode: 0644] blob
pysam.egg-info/PKG-INFO diff | blob | history
pysam.egg-info/SOURCES.txt diff | blob | history
pysam.egg-info/requires.txt diff | blob | history
pysam/TabProxies.c diff | blob | history
pysam/TabProxies.pyx diff | blob | history
pysam/__init__.py diff | blob | history
pysam/cfaidx.c [new file with mode: 0644] blob
pysam/cfaidx.pxd [new file with mode: 0644] blob
pysam/cfaidx.pyx [new file with mode: 0644] blob
pysam/chtslib.c [new file with mode: 0644] blob
pysam/chtslib.pxd [new file with mode: 0644] blob
pysam/chtslib.pyx [new file with mode: 0644] blob
pysam/csamfile.c [new file with mode: 0644] blob
pysam/csamfile.pxd [new file with mode: 0644] blob
pysam/csamfile.pyx [new file with mode: 0644] blob
pysam/csamtools.c diff | blob | history
pysam/csamtools.pxd diff | blob | history
pysam/csamtools.pyx diff | blob | history
pysam/ctabix.c diff | blob | history
pysam/ctabix.pxd diff | blob | history
pysam/ctabix.pyx diff | blob | history
pysam/cvcf.c diff | blob | history
pysam/cvcf.pxd diff | blob | history
pysam/cvcf.pyx diff | blob | history
pysam/htslib_util.c [new file with mode: 0644] blob
pysam/htslib_util.h [new file with mode: 0644] blob
pysam/pysam_stream.h [new file with mode: 0644] blob
pysam/pysam_util.c diff | blob | history
pysam/pysam_util.h diff | blob | history
pysam/samfile_util.c [new file with mode: 0644] blob
pysam/samfile_util.h [new file with mode: 0644] blob
pysam/tabix_util.h diff | blob | history
pysam/version.py diff | blob | history
samtools/bam.h diff | blob | history
samtools/bam_endian.h diff | blob | history
samtools/bam_lpileup.c.pysam.c diff | blob | history
samtools/bam_mate.c.pysam.c diff | blob | history
samtools/bam_pileup.c.pysam.c diff | blob | history
samtools/bamshuf.c.pysam.c diff | blob | history
samtools/bcftools/bcf.h diff | blob | history
samtools/bgzf.c.pysam.c diff | blob | history
samtools/khash.h diff | blob | history
samtools/klist.h diff | blob | history
samtools/kprobaln.c [new file with mode: 0644] blob
samtools/razf.c.pysam.c diff | blob | history
setup.cfg diff | blob | history
setup.py diff | blob | history
tabix/__init__.py [deleted file] blob | history
tabix/bam_endian.h [deleted file] blob | history
tabix/bedidx.c [deleted file] blob | history
tabix/bedidx.c.pysam.c [deleted file] blob | history
tabix/bgzf.c [deleted file] blob | history
tabix/bgzf.c.pysam.c [deleted file] blob | history
tabix/bgzf.h [deleted file] blob | history
tabix/bgzip.c [deleted file] blob | history
tabix/bgzip.c.pysam.c [deleted file] blob | history
tabix/index.c [deleted file] blob | history
tabix/index.c.pysam.c [deleted file] blob | history
tabix/khash.h [deleted file] blob | history
tabix/knetfile.c [deleted file] blob | history
tabix/knetfile.c.pysam.c [deleted file] blob | history
tabix/knetfile.h [deleted file] blob | history
tabix/kseq.h [deleted file] blob | history
tabix/ksort.h [deleted file] blob | history
tabix/kstring.c [deleted file] blob | history
tabix/kstring.c.pysam.c [deleted file] blob | history
tabix/kstring.h [deleted file] blob | history
tabix/pysam.h [deleted file] blob | history
tabix/tabix.h [deleted file] blob | history
tests/Makefile [deleted file] blob | history
tests/ex1.fa [deleted file] blob | history
tests/ex1.sam.gz [deleted file] blob | history
tests/ex10.sam [deleted file] blob | history
tests/ex3.sam [deleted file] blob | history
tests/ex4.sam [deleted file] blob | history
tests/ex5.sam [deleted file] blob | history
tests/ex6.sam [deleted file] blob | history
tests/ex7.sam [deleted file] blob | history
tests/ex8.sam [deleted file] blob | history
tests/ex9_fail.bam [deleted file] blob | history
tests/ex9_nofail.bam [deleted file] blob | history
tests/example.bed.gz [deleted file] blob | history
tests/example.bed.gz.tbi [deleted file] blob | history
tests/example.gtf.gz [deleted file] blob | history
tests/example.py [deleted file] blob | history
tests/example.vcf40 [deleted file] blob | history
tests/example_btag.bam [deleted file] blob | history
tests/example_btag.sam [deleted file] blob | history
tests/example_empty_header.bam [deleted file] blob | history
tests/example_unmapped_reads_no_sq.sam [deleted file] blob | history
tests/example_user_header.sam [deleted file] blob | history
tests/issue100.bam [deleted file] blob | history
tests/pysam_test.py [changed mode: 0755->0644] diff | blob | history
tests/segfault_tests.py [deleted file] blob | history
tests/tabix_test.py diff | blob | history
tests/tag_bug.bam [deleted file] blob | history
tests/test_unaligned.bam [deleted file] blob | history
tests/vcf-examples/10.vcf [deleted file] blob | history
tests/vcf-examples/11.vcf [deleted file] blob | history
tests/vcf-examples/12.vcf [deleted file] blob | history
tests/vcf-examples/13.vcf [deleted file] blob | history
tests/vcf-examples/15.vcf [deleted file] blob | history
tests/vcf-examples/16.vcf [deleted file] blob | history
tests/vcf-examples/18.vcf [deleted file] blob | history
tests/vcf-examples/2.vcf [deleted file] blob | history
tests/vcf-examples/20.vcf [deleted file] blob | history
tests/vcf-examples/21.vcf [deleted file] blob | history
tests/vcf-examples/22.vcf [deleted file] blob | history
tests/vcf-examples/23.vcf [deleted file] blob | history
tests/vcf-examples/24.vcf [deleted file] blob | history
tests/vcf-examples/3.vcf [deleted file] blob | history
tests/vcf-examples/4.vcf [deleted file] blob | history
tests/vcf-examples/5.vcf [deleted file] blob | history
tests/vcf-examples/6.vcf [deleted file] blob | history
tests/vcf-examples/7.vcf [deleted file] blob | history
tests/vcf-examples/8.vcf [deleted file] blob | history
tests/vcf-examples/9.vcf [deleted file] blob | history
tests/vcf-examples/issue85.vcf [deleted file] blob | history
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