[med-svn] [python-pysam] branch upstream updated (a757e53 -> 547982f)
Andreas Tille
tille at debian.org
Tue Aug 19 19:27:48 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository python-pysam.
from a757e53 Imported Upstream version 0.7.7
new 547982f Imported Upstream version 0.8.0
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
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 +
samtools/faidx.c.pysam.c => htslib/faidx.c | 170 +-
htslib/hfile.c | 526 +
htslib/hfile_internal.h | 75 +
htslib/hfile_net.c | 99 +
htslib/hts.c | 1326 +
{pysam/include => htslib/htslib}/__init__.py | 0
{samtools => htslib/htslib}/bgzf.h | 134 +-
{samtools => htslib/htslib}/faidx.h | 19 +-
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 +-
{samtools => htslib/htslib}/kseq.h | 186 +-
{samtools => htslib/htslib}/ksort.h | 0
htslib/htslib/kstdint.h | 64 +
{samtools => htslib/htslib}/kstring.h | 135 +-
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 +
.../bcftools/kfunc.c.pysam.c => htslib/kfunc.c | 96 +-
{tabix => htslib}/knetfile.c | 92 +-
samtools/kstring.c.pysam.c => htslib/kstring.c | 55 +-
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.pysam.c => kprobaln.c} | 12 +-
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/ksort.h | 271 -
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 -
204 files changed, 127434 insertions(+), 94391 deletions(-)
create mode 100644 README.rst
rename doc/{contents.rst => index.rst} (92%)
rename {tabix => htslib}/__init__.py (100%)
create mode 100644 htslib/bgzf.c
create mode 100644 htslib/bgzip.c
create mode 100644 htslib/config.h
create mode 100644 htslib/cram/cram.h
create mode 100644 htslib/cram/cram_codecs.c
create mode 100644 htslib/cram/cram_codecs.h
create mode 100644 htslib/cram/cram_decode.c
create mode 100644 htslib/cram/cram_decode.h
create mode 100644 htslib/cram/cram_encode.c
create mode 100644 htslib/cram/cram_encode.h
create mode 100644 htslib/cram/cram_index.c
create mode 100644 htslib/cram/cram_index.h
create mode 100644 htslib/cram/cram_io.c
create mode 100644 htslib/cram/cram_io.h
create mode 100644 htslib/cram/cram_samtools.c
create mode 100644 htslib/cram/cram_samtools.h
create mode 100644 htslib/cram/cram_stats.c
create mode 100644 htslib/cram/cram_stats.h
create mode 100644 htslib/cram/cram_structs.h
create mode 100644 htslib/cram/files.c
create mode 100644 htslib/cram/mFILE.c
create mode 100644 htslib/cram/mFILE.h
create mode 100644 htslib/cram/md5.c
create mode 100644 htslib/cram/md5.h
create mode 100644 htslib/cram/misc.h
create mode 100644 htslib/cram/open_trace_file.c
create mode 100644 htslib/cram/open_trace_file.h
create mode 100644 htslib/cram/os.h
create mode 100644 htslib/cram/pooled_alloc.c
create mode 100644 htslib/cram/pooled_alloc.h
create mode 100644 htslib/cram/sam_header.c
create mode 100644 htslib/cram/sam_header.h
create mode 100644 htslib/cram/string_alloc.c
create mode 100644 htslib/cram/string_alloc.h
create mode 100644 htslib/cram/thread_pool.c
create mode 100644 htslib/cram/thread_pool.h
create mode 100644 htslib/cram/vlen.c
create mode 100644 htslib/cram/vlen.h
create mode 100644 htslib/cram/zfio.c
create mode 100644 htslib/cram/zfio.h
copy samtools/faidx.c.pysam.c => htslib/faidx.c (69%)
create mode 100644 htslib/hfile.c
create mode 100644 htslib/hfile_internal.h
create mode 100644 htslib/hfile_net.c
create mode 100644 htslib/hts.c
copy {pysam/include => htslib/htslib}/__init__.py (100%)
copy {samtools => htslib/htslib}/bgzf.h (56%)
copy {samtools => htslib/htslib}/faidx.h (78%)
create mode 100644 htslib/htslib/hfile.h
create mode 100644 htslib/htslib/hts.h
create mode 100644 htslib/htslib/hts_defs.h
create mode 100644 htslib/htslib/kfunc.h
rename {tabix => htslib/htslib}/khash.h (55%)
create mode 100644 htslib/htslib/khash_str2int.h
copy {samtools => htslib/htslib}/klist.h (70%)
rename {tabix => htslib/htslib}/knetfile.h (93%)
copy {samtools => htslib/htslib}/kseq.h (65%)
copy {samtools => htslib/htslib}/ksort.h (100%)
create mode 100644 htslib/htslib/kstdint.h
copy {samtools => htslib/htslib}/kstring.h (55%)
create mode 100644 htslib/htslib/sam.h
create mode 100644 htslib/htslib/synced_bcf_reader.h
create mode 100644 htslib/htslib/tbx.h
create mode 100644 htslib/htslib/vcf.h
create mode 100644 htslib/htslib/vcf_sweep.h
create mode 100644 htslib/htslib/vcfutils.h
copy samtools/bcftools/kfunc.c.pysam.c => htslib/kfunc.c (62%)
rename {tabix => htslib}/knetfile.c (90%)
copy samtools/kstring.c.pysam.c => htslib/kstring.c (85%)
create mode 100644 htslib/sam.c
create mode 100644 htslib/synced_bcf_reader.c
create mode 100644 htslib/tabix.c
create mode 100644 htslib/tbx.c
create mode 100644 htslib/vcf.c
create mode 100644 htslib/vcf_sweep.c
create mode 100644 htslib/vcfutils.c
create mode 100644 htslib/version.h
create mode 100644 pysam/cfaidx.c
create mode 100644 pysam/cfaidx.pxd
create mode 100644 pysam/cfaidx.pyx
create mode 100644 pysam/chtslib.c
create mode 100644 pysam/chtslib.pxd
create mode 100644 pysam/chtslib.pyx
create mode 100644 pysam/csamfile.c
create mode 100644 pysam/csamfile.pxd
create mode 100644 pysam/csamfile.pyx
create mode 100644 pysam/htslib_util.c
create mode 100644 pysam/htslib_util.h
create mode 100644 pysam/pysam_stream.h
create mode 100644 pysam/samfile_util.c
create mode 100644 pysam/samfile_util.h
copy samtools/{kprobaln.c.pysam.c => kprobaln.c} (95%)
delete mode 100644 tabix/bam_endian.h
delete mode 100644 tabix/bedidx.c
delete mode 100644 tabix/bedidx.c.pysam.c
delete mode 100644 tabix/bgzf.c
delete mode 100644 tabix/bgzf.c.pysam.c
delete mode 100644 tabix/bgzf.h
delete mode 100644 tabix/bgzip.c
delete mode 100644 tabix/bgzip.c.pysam.c
delete mode 100644 tabix/index.c
delete mode 100644 tabix/index.c.pysam.c
delete mode 100644 tabix/knetfile.c.pysam.c
delete mode 100644 tabix/kseq.h
delete mode 100644 tabix/ksort.h
delete mode 100644 tabix/kstring.c
delete mode 100644 tabix/kstring.c.pysam.c
delete mode 100644 tabix/kstring.h
delete mode 100644 tabix/pysam.h
delete mode 100644 tabix/tabix.h
delete mode 100644 tests/Makefile
delete mode 100644 tests/ex1.fa
delete mode 100644 tests/ex1.sam.gz
delete mode 100644 tests/ex10.sam
delete mode 100644 tests/ex3.sam
delete mode 100644 tests/ex4.sam
delete mode 100644 tests/ex5.sam
delete mode 100644 tests/ex6.sam
delete mode 100644 tests/ex7.sam
delete mode 100644 tests/ex8.sam
delete mode 100644 tests/ex9_fail.bam
delete mode 100644 tests/ex9_nofail.bam
delete mode 100644 tests/example.bed.gz
delete mode 100644 tests/example.bed.gz.tbi
delete mode 100644 tests/example.gtf.gz
delete mode 100644 tests/example.py
delete mode 100644 tests/example.vcf40
delete mode 100644 tests/example_btag.bam
delete mode 100644 tests/example_btag.sam
delete mode 100644 tests/example_empty_header.bam
delete mode 100644 tests/example_unmapped_reads_no_sq.sam
delete mode 100644 tests/example_user_header.sam
delete mode 100644 tests/issue100.bam
mode change 100755 => 100644 tests/pysam_test.py
delete mode 100755 tests/segfault_tests.py
delete mode 100644 tests/tag_bug.bam
delete mode 100644 tests/test_unaligned.bam
delete mode 100644 tests/vcf-examples/10.vcf
delete mode 100644 tests/vcf-examples/11.vcf
delete mode 100644 tests/vcf-examples/12.vcf
delete mode 100644 tests/vcf-examples/13.vcf
delete mode 100644 tests/vcf-examples/15.vcf
delete mode 100644 tests/vcf-examples/16.vcf
delete mode 100644 tests/vcf-examples/18.vcf
delete mode 100644 tests/vcf-examples/2.vcf
delete mode 100644 tests/vcf-examples/20.vcf
delete mode 100644 tests/vcf-examples/21.vcf
delete mode 100644 tests/vcf-examples/22.vcf
delete mode 100644 tests/vcf-examples/23.vcf
delete mode 100644 tests/vcf-examples/24.vcf
delete mode 100644 tests/vcf-examples/3.vcf
delete mode 100644 tests/vcf-examples/4.vcf
delete mode 100644 tests/vcf-examples/5.vcf
delete mode 100644 tests/vcf-examples/6.vcf
delete mode 100644 tests/vcf-examples/7.vcf
delete mode 100644 tests/vcf-examples/8.vcf
delete mode 100644 tests/vcf-examples/9.vcf
delete mode 100644 tests/vcf-examples/issue85.vcf
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