[med-svn] [python-pysam] 02/03: Merge tag 'upstream/0.8.0'
Andreas Tille
tille at debian.org
Tue Aug 19 19:27:47 UTC 2014
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tille pushed a commit to branch master
in repository python-pysam.
commit 0b21c50e4887f6cec0596c6a5ea5ef2fdf6f548c
Merge: c9e8ef0 547982f
Author: Andreas Tille <tille at debian.org>
Date: Tue Aug 19 21:26:00 2014 +0200
Merge tag 'upstream/0.8.0'
Upstream version 0.8.0
INSTALL | 13 +
MANIFEST.in | 82 +-
PKG-INFO | 4 +-
README.rst | 27 +
doc/api.rst | 3 +-
doc/conf.py | 14 +-
doc/developer.rst | 48 +-
doc/faq.rst | 10 +-
doc/glossary.rst | 4 +-
doc/{contents.rst => index.rst} | 4 +-
doc/release.rst | 26 +
doc/usage.rst | 23 +-
{tabix => htslib}/__init__.py | 0
htslib/bgzf.c | 1085 +
htslib/bgzip.c | 283 +
htslib/config.h | 3 +
htslib/cram/cram.h | 66 +
htslib/cram/cram_codecs.c | 1764 ++
htslib/cram/cram_codecs.h | 155 +
htslib/cram/cram_decode.c | 2138 ++
htslib/cram/cram_decode.h | 112 +
htslib/cram/cram_encode.c | 2630 ++
htslib/cram/cram_encode.h | 105 +
htslib/cram/cram_index.c | 503 +
htslib/cram/cram_index.h | 98 +
htslib/cram/cram_io.c | 3652 +++
htslib/cram/cram_io.h | 532 +
htslib/cram/cram_samtools.c | 144 +
htslib/cram/cram_samtools.h | 97 +
htslib/cram/cram_stats.c | 357 +
htslib/cram/cram_stats.h | 59 +
htslib/cram/cram_structs.h | 752 +
htslib/cram/files.c | 76 +
htslib/cram/mFILE.c | 634 +
htslib/cram/mFILE.h | 88 +
htslib/cram/md5.c | 295 +
htslib/cram/md5.h | 54 +
htslib/cram/misc.h | 110 +
htslib/cram/open_trace_file.c | 386 +
htslib/cram/open_trace_file.h | 115 +
htslib/cram/os.h | 306 +
htslib/cram/pooled_alloc.c | 170 +
htslib/cram/pooled_alloc.h | 56 +
htslib/cram/sam_header.c | 1222 +
htslib/cram/sam_header.h | 452 +
htslib/cram/string_alloc.c | 153 +
htslib/cram/string_alloc.h | 69 +
htslib/cram/thread_pool.c | 713 +
htslib/cram/thread_pool.h | 197 +
htslib/cram/vlen.c | 432 +
htslib/cram/vlen.h | 48 +
htslib/cram/zfio.c | 185 +
htslib/cram/zfio.h | 54 +
htslib/faidx.c | 421 +
htslib/hfile.c | 526 +
htslib/hfile_internal.h | 75 +
htslib/hfile_net.c | 99 +
htslib/hts.c | 1326 +
{tabix => htslib/htslib}/__init__.py | 0
htslib/htslib/bgzf.h | 313 +
htslib/htslib/faidx.h | 112 +
htslib/htslib/hfile.h | 204 +
htslib/htslib/hts.h | 311 +
htslib/htslib/hts_defs.h | 47 +
htslib/htslib/kfunc.h | 49 +
{tabix => htslib/htslib}/khash.h | 339 +-
htslib/htslib/khash_str2int.h | 98 +
{samtools => htslib/htslib}/klist.h | 35 +-
{tabix => htslib/htslib}/knetfile.h | 4 +-
htslib/htslib/kseq.h | 253 +
{tabix => htslib/htslib}/ksort.h | 16 +-
htslib/htslib/kstdint.h | 64 +
htslib/htslib/kstring.h | 270 +
htslib/htslib/sam.h | 399 +
htslib/htslib/synced_bcf_reader.h | 255 +
htslib/htslib/tbx.h | 52 +
htslib/htslib/vcf.h | 823 +
htslib/htslib/vcf_sweep.h | 15 +
htslib/htslib/vcfutils.h | 94 +
htslib/kfunc.c | 254 +
{tabix => htslib}/knetfile.c | 92 +-
htslib/kstring.c | 229 +
htslib/sam.c | 1780 ++
htslib/synced_bcf_reader.c | 1183 +
htslib/tabix.c | 374 +
htslib/tbx.c | 290 +
htslib/vcf.c | 2953 ++
htslib/vcf_sweep.c | 158 +
htslib/vcfutils.c | 642 +
htslib/version.h | 1 +
pysam.egg-info/PKG-INFO | 4 +-
pysam.egg-info/SOURCES.txt | 167 +-
pysam.egg-info/requires.txt | 2 +-
pysam/TabProxies.c | 8374 ++---
pysam/TabProxies.pyx | 46 +-
pysam/__init__.py | 160 +-
pysam/cfaidx.c | 8485 +++++
pysam/cfaidx.pxd | 32 +
pysam/cfaidx.pyx | 340 +
pysam/chtslib.c | 3162 ++
pysam/chtslib.pxd | 854 +
pysam/chtslib.pyx | 94 +
pysam/csamfile.c | 44792 ++++++++++++++++++++++++++
pysam/csamfile.pxd | 200 +
pysam/csamfile.pyx | 3464 +++
pysam/csamtools.c | 51700 +++----------------------------
pysam/csamtools.pxd | 578 +-
pysam/csamtools.pyx | 3989 +--
pysam/ctabix.c | 14944 ++++-----
pysam/ctabix.pxd | 260 +-
pysam/ctabix.pyx | 860 +-
pysam/cvcf.c | 24327 +++++++--------
pysam/cvcf.pxd | 1 +
pysam/cvcf.pyx | 59 +-
pysam/htslib_util.c | 143 +
pysam/htslib_util.h | 90 +
pysam/pysam_stream.h | 12 +
pysam/pysam_util.c | 408 +-
pysam/pysam_util.h | 70 +-
pysam/samfile_util.c | 186 +
pysam/samfile_util.h | 11 +
pysam/tabix_util.h | 7 +-
pysam/version.py | 4 +-
samtools/bam.h | 4 +-
samtools/bam_endian.h | 2 +-
samtools/bam_lpileup.c.pysam.c | 2 +-
samtools/bam_mate.c.pysam.c | 2 +-
samtools/bam_pileup.c.pysam.c | 2 +-
samtools/bamshuf.c.pysam.c | 3 +-
samtools/bcftools/bcf.h | 2 +-
samtools/bgzf.c.pysam.c | 2 +-
samtools/khash.h | 4 +-
samtools/klist.h | 4 +-
samtools/kprobaln.c | 280 +
samtools/razf.c.pysam.c | 2 +-
setup.cfg | 4 +-
setup.py | 437 +-
tabix/bam_endian.h | 42 -
tabix/bedidx.c | 156 -
tabix/bedidx.c.pysam.c | 158 -
tabix/bgzf.c | 555 -
tabix/bgzf.c.pysam.c | 557 -
tabix/bgzf.h | 193 -
tabix/bgzip.c | 206 -
tabix/bgzip.c.pysam.c | 208 -
tabix/index.c | 967 -
tabix/index.c.pysam.c | 969 -
tabix/knetfile.c.pysam.c | 634 -
tabix/kseq.h | 227 -
tabix/kstring.c | 165 -
tabix/kstring.c.pysam.c | 167 -
tabix/kstring.h | 68 -
tabix/pysam.h | 5 -
tabix/tabix.h | 145 -
tests/Makefile | 52 -
tests/ex1.fa | 56 -
tests/ex1.sam.gz | Bin 113194 -> 0 bytes
tests/ex10.sam | 19 -
tests/ex3.sam | 13 -
tests/ex4.sam | 9 -
tests/ex5.sam | 5 -
tests/ex6.sam | 5 -
tests/ex7.sam | 2 -
tests/ex8.sam | 3 -
tests/ex9_fail.bam | Bin 10280 -> 0 bytes
tests/ex9_nofail.bam | Bin 10270 -> 0 bytes
tests/example.bed.gz | Bin 879 -> 0 bytes
tests/example.bed.gz.tbi | Bin 245 -> 0 bytes
tests/example.gtf.gz | Bin 3825 -> 0 bytes
tests/example.py | 79 -
tests/example.vcf40 | 23 -
tests/example_btag.bam | Bin 771 -> 0 bytes
tests/example_btag.sam | 6 -
tests/example_empty_header.bam | Bin 7554 -> 0 bytes
tests/example_unmapped_reads_no_sq.sam | 3 -
tests/example_user_header.sam | 8 -
tests/issue100.bam | Bin 4344 -> 0 bytes
tests/pysam_test.py | 2540 +-
tests/segfault_tests.py | 37 -
tests/tabix_test.py | 951 +-
tests/tag_bug.bam | Bin 383 -> 0 bytes
tests/test_unaligned.bam | Bin 514 -> 0 bytes
tests/vcf-examples/10.vcf | 84 -
tests/vcf-examples/11.vcf | 216 -
tests/vcf-examples/12.vcf | 1000 -
tests/vcf-examples/13.vcf | 220 -
tests/vcf-examples/15.vcf | 317 -
tests/vcf-examples/16.vcf | 369 -
tests/vcf-examples/18.vcf | 1000 -
tests/vcf-examples/2.vcf | 334 -
tests/vcf-examples/20.vcf | 307 -
tests/vcf-examples/21.vcf | 310 -
tests/vcf-examples/22.vcf | 1000 -
tests/vcf-examples/23.vcf | 419 -
tests/vcf-examples/24.vcf | 724 -
tests/vcf-examples/3.vcf | 1000 -
tests/vcf-examples/4.vcf | 318 -
tests/vcf-examples/5.vcf | 1000 -
tests/vcf-examples/6.vcf | 278 -
tests/vcf-examples/7.vcf | 317 -
tests/vcf-examples/8.vcf | 84 -
tests/vcf-examples/9.vcf | 1000 -
tests/vcf-examples/issue85.vcf | 26 -
203 files changed, 129018 insertions(+), 93877 deletions(-)
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