[med-svn] [python-pysam] branch upstream updated (5128bf9 -> 91c30fd)
Afif Elghraoui
afif-guest at moszumanska.debian.org
Mon Jun 8 08:23:14 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a change to branch upstream
in repository python-pysam.
from 5128bf9 Imported Upstream version 0.8.1
adds 91c30fd Imported Upstream version 0.8.3
No new revisions were added by this update.
Summary of changes:
.gitignore | 2 +-
AUTHORS | 10 +-
INSTALL | 2 +-
MANIFEST.in | 2 +-
doc/api.rst | 13 +-
doc/conf.py | 2 +-
doc/developer.rst | 17 +-
doc/faq.rst | 85 +-
doc/index.rst | 2 +-
doc/release.rst | 61 +-
doc/usage.rst | 14 +-
htslib/INSTALL | 88 +-
htslib/Makefile | 93 +-
htslib/NEWS | 50 +
htslib/bgzf.c | 58 +-
htslib/bgzip.c | 2 +-
htslib/config.mk | 72 +
htslib/config.mk.in | 72 +
htslib/configure | 4012 +++++++++++++++++++++
htslib/configure.ac | 93 +
htslib/cram/cram.h | 9 +-
htslib/cram/cram_codecs.c | 230 +-
htslib/cram/cram_codecs.h | 22 +-
htslib/cram/cram_decode.c | 1339 +++++--
htslib/cram/cram_encode.c | 1994 ++++++----
htslib/cram/cram_index.c | 82 +-
htslib/cram/cram_io.c | 1382 ++++---
htslib/cram/cram_io.h | 98 +-
htslib/cram/cram_samtools.c | 5 +-
htslib/cram/cram_stats.c | 123 +-
htslib/cram/cram_structs.h | 329 +-
htslib/cram/os.h | 2 +
htslib/cram/rANS_byte.h | 336 ++
htslib/cram/rANS_static.c | 841 +++++
htslib/cram/rANS_static.h | 44 +
htslib/cram/sam_header.c | 8 +-
htslib/cram/sam_header.h | 8 -
htslib/cram/thread_pool.c | 178 +-
htslib/cram/thread_pool.h | 15 +-
htslib/cram/vlen.c | 2 +-
htslib/faidx.c | 46 +-
htslib/hfile.c | 23 +-
htslib/hfile_internal.h | 3 +-
htslib/hfile_irods.c | 243 ++
htslib/hts.c | 531 ++-
htslib/htsfile.1 | 71 +
htslib/htsfile.c | 168 +
htslib/htslib.mk | 8 +-
htslib/htslib/bgzf.h | 7 +-
htslib/htslib/faidx.h | 2 +-
htslib/htslib/hfile.h | 10 +-
htslib/htslib/hts.h | 146 +-
htslib/htslib/khash.h | 8 +-
htslib/htslib/khash_str2int.h | 9 +
htslib/htslib/kseq.h | 10 +-
htslib/htslib/regidx.h | 147 +
htslib/htslib/sam.h | 2 +-
htslib/htslib/synced_bcf_reader.h | 15 +-
htslib/htslib/vcf.h | 15 +-
htslib/htslib_vars.mk | 1 +
htslib/knetfile.c | 11 +-
htslib/regidx.c | 338 ++
htslib/sam.c | 134 +-
htslib/synced_bcf_reader.c | 88 +-
htslib/tabix.1 | 121 +-
htslib/tabix.c | 268 +-
htslib/tbx.c | 5 +
htslib/test/{aux#aux.sam => auxf#values.sam} | 0
htslib/test/{aux.fa => auxf.fa} | 0
htslib/test/{aux.fa.fai => auxf.fa.fai} | 0
htslib/test/hfile.c | 4 +-
htslib/test/sam.c | 52 +-
htslib/test/test-regidx.c | 116 +
htslib/test/test-vcf-api.c | 57 +-
htslib/test/test_view.c | 92 +-
htslib/vcf.c | 207 +-
htslib/vcfutils.c | 63 +-
htslib/version.h | 2 +-
install-CGAT-tools.sh | 8 +-
pysam/TabProxies.pyx | 142 +-
pysam/__init__.py | 10 +-
pysam/calignmentfile.pxd | 30 +-
pysam/calignmentfile.pyx | 1109 ++++--
pysam/cbcf.pxd | 158 +
pysam/cbcf.pyx | 2419 +++++++++++++
pysam/cfaidx.pxd | 9 +-
pysam/cfaidx.pyx | 39 +-
pysam/chtslib.pxd | 891 ++++-
pysam/chtslib.pyx | 2 +-
pysam/csamtools.pyx | 2 +
pysam/ctabix.pyx | 4 +-
pysam/cvcf.pyx | 2 +-
pysam/htslib_util.c | 18 +
pysam/htslib_util.h | 20 +-
pysam/version.py | 6 +-
requires.txt | 2 +-
samtools/bam.h | 2 +-
samtools/bam2bcf_indel.c | 40 +-
samtools/bam2bcf_indel.c.pysam.c | 40 +-
samtools/bam2depth.c | 16 +-
samtools/bam2depth.c.pysam.c | 16 +-
samtools/bam_mate.c | 3 +-
samtools/bam_mate.c.pysam.c | 3 +-
samtools/bam_md.c | 1 -
samtools/bam_md.c.pysam.c | 1 -
samtools/bam_plcmd.c | 45 +-
samtools/bam_plcmd.c.pysam.c | 45 +-
samtools/bam_sort.c | 61 +-
samtools/bam_sort.c.pysam.c | 61 +-
samtools/bam_stat.c | 40 +-
samtools/bam_stat.c.pysam.c | 40 +-
samtools/errmod.c | 7 +-
samtools/errmod.c.pysam.c | 7 +-
samtools/kaln.c | 486 ---
samtools/kaln.c.pysam.c | 488 ---
samtools/kaln.h | 67 -
samtools/misc/ace2sam.c | 2 +-
samtools/misc/ace2sam.c.pysam.c | 2 +-
samtools/padding.c | 2 +-
samtools/padding.c.pysam.c | 2 +-
samtools/sam.c | 8 +-
samtools/sam.c.pysam.c | 8 +-
samtools/sam.h | 3 +-
samtools/sam_view.c | 27 +-
samtools/sam_view.c.pysam.c | 27 +-
samtools/stats.c | 21 +-
samtools/stats.c.pysam.c | 21 +-
samtools/test/merge/test_rtrans_build.c | 4 +-
samtools/test/merge/test_rtrans_build.c.pysam.c | 4 +-
samtools/test/merge/test_trans_tbl_init.c | 2 +-
samtools/test/merge/test_trans_tbl_init.c.pysam.c | 2 +-
samtools/version.h | 2 +-
setup.py | 169 +-
tests/AlignedSegment_test.py | 447 +++
tests/AlignmentFile_test.py | 1387 +++----
tests/SamFile_test.py | 14 +-
tests/TestUtils.py | 72 +-
tests/cython_flagstat.py | 1 -
tests/pysam_data/Makefile | 13 +-
tests/python_flagstat.py | 2 -
tests/samtools_test.py | 45 +-
tests/tabix_test.py | 7 +-
142 files changed, 18515 insertions(+), 4939 deletions(-)
create mode 100644 htslib/NEWS
create mode 100644 htslib/config.mk
create mode 100644 htslib/config.mk.in
create mode 100755 htslib/configure
create mode 100644 htslib/configure.ac
create mode 100644 htslib/cram/rANS_byte.h
create mode 100644 htslib/cram/rANS_static.c
create mode 100644 htslib/cram/rANS_static.h
create mode 100644 htslib/hfile_irods.c
create mode 100644 htslib/htsfile.1
create mode 100644 htslib/htsfile.c
create mode 100644 htslib/htslib/regidx.h
create mode 100644 htslib/regidx.c
rename htslib/test/{aux#aux.sam => auxf#values.sam} (100%)
rename htslib/test/{aux.fa => auxf.fa} (100%)
rename htslib/test/{aux.fa.fai => auxf.fa.fai} (100%)
create mode 100644 htslib/test/test-regidx.c
create mode 100644 pysam/cbcf.pxd
create mode 100644 pysam/cbcf.pyx
delete mode 100644 samtools/kaln.c
delete mode 100644 samtools/kaln.c.pysam.c
delete mode 100644 samtools/kaln.h
create mode 100644 tests/AlignedSegment_test.py
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