[med-svn] [pysam] branch upstream updated (e1160ac -> fabbcdc)
Charles Plessy
plessy at alioth.debian.org
Fri Aug 9 09:47:34 UTC 2013
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch upstream
in repository pysam.
from e1160ac Imported Upstream version 0.7
new 11d2148 Imported Upstream version 0.7.1
new 51573cd Imported Upstream version 0.7.2
new 14c14ac Imported Upstream version 0.7.3
new 356c1c8 Imported Upstream version 0.7.4
new fabbcdc Imported Upstream version 0.7.5
The 5 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:
MANIFEST.in | 9 +
PKG-INFO | 4 +-
distribute_setup.py | 107 +-
doc/Makefile | 96 +
doc/api.rst | 122 +
doc/conf.py | 204 +
doc/contents.rst | 73 +
doc/developer.rst | 75 +
doc/faq.rst | 40 +
doc/glossary.rst | 73 +
doc/make.bat | 112 +
doc/release.rst | 85 +
doc/usage.rst | 285 +
pysam.egg-info/PKG-INFO | 4 +-
pysam.egg-info/SOURCES.txt | 34 +-
pysam.egg-info/requires.txt | 2 +-
pysam.egg-info/top_level.txt | 9 +-
pysam.py | 1 +
pysam/TabProxies.c | 3890 ++---
pysam/VCF.py | 1087 --
pysam/__init__.py | 35 +-
pysam/csamtools.c |20377 ++++++++++++++-------------
pysam/csamtools.pyx | 56 +-
pysam/ctabix.c | 3770 +++--
pysam/ctabix.pxd | 6 +-
pysam/ctabix.pyx | 3 +
pysam/cvcf.c |14868 +++++++++----------
pysam/cvcf.pyx | 15 +-
KNOWN_BUGS => pysam/include/__init__.py | 0
pysam/pysam_util.c | 19 +-
pysam/tabix_util.h | 6 +
pysam/version.py | 4 +-
KNOWN_BUGS => samtools/__init__.py | 0
samtools/bam.c.pysam.c | 136 +-
samtools/bam.h | 46 +-
samtools/bam2bcf.c.pysam.c | 298 +-
samtools/bam2bcf.h | 26 +-
samtools/bam2bcf_indel.c.pysam.c | 47 +-
samtools/bam2depth.c.pysam.c | 45 +-
samtools/bam_aux.c.pysam.c | 4 +
samtools/bam_cat.c.pysam.c | 9 +-
samtools/bam_color.c.pysam.c | 24 +-
samtools/bam_import.c.pysam.c | 16 +-
samtools/bam_index.c.pysam.c | 9 +-
samtools/bam_mate.c.pysam.c | 82 +-
samtools/bam_md.c.pysam.c | 7 +-
samtools/bam_plcmd.c.pysam.c | 154 +-
samtools/bam_reheader.c.pysam.c | 7 +-
samtools/bam_sort.c.pysam.c | 291 +-
samtools/bam_tview.c.pysam.c | 460 +-
samtools/bam_tview.h | 75 +
samtools/bam_tview_curses.c.pysam.c | 299 +
samtools/bam_tview_html.c.pysam.c | 351 +
samtools/bamshuf.c.pysam.c | 148 +
KNOWN_BUGS => samtools/bcftools/__init__.py | 0
samtools/bcftools/bcf.c.pysam.c | 102 +-
samtools/bcftools/bcf.h | 9 +-
samtools/bcftools/bcfutils.c.pysam.c | 120 +-
samtools/bcftools/call1.c.pysam.c | 101 +-
samtools/bcftools/index.c.pysam.c | 1 +
samtools/bcftools/prob1.c.pysam.c | 470 +-
samtools/bcftools/prob1.h | 7 +
samtools/bcftools/vcf.c.pysam.c | 11 +-
samtools/bedcov.c.pysam.c | 129 +
samtools/bgzf.c.pysam.c | 1072 +-
samtools/bgzf.h | 272 +-
samtools/faidx.c.pysam.c | 5 +
samtools/kprobaln.c.pysam.c | 4 +-
samtools/kseq.h | 55 +-
samtools/ksort.h | 6 +-
samtools/kstring.c.pysam.c | 4 +-
samtools/kstring.h | 56 +-
samtools/misc/ace2sam.c.pysam.c | 251 +
samtools/misc/seqtk.c.pysam.c | 785 --
samtools/padding.c.pysam.c | 481 +
samtools/sam.c.pysam.c | 9 +-
samtools/sam.h | 1 +
samtools/sam_header.c.pysam.c | 78 +-
samtools/sam_header.h | 24 +
samtools/sam_view.c.pysam.c | 83 +-
KNOWN_BUGS => samtools/win32/__init__.py | 0
setup.cfg | 4 +-
setup.py | 92 +-
KNOWN_BUGS => tabix/__init__.py | 0
tabix/{bedidx.c.pysam.c => bedidx.c} | 2 -
tabix/{bgzf.c.pysam.c => bgzf.c} | 2 -
tabix/{bgzip.c.pysam.c => bgzip.c} | 42 +-
tabix/{index.c.pysam.c => index.c} | 32 +-
tabix/{knetfile.c.pysam.c => knetfile.c} | 26 +-
tabix/{kstring.c.pysam.c => kstring.c} | 2 -
tests/Makefile | 12 +-
tests/example_btag.bam | Bin 0 -> 771 bytes
tests/pysam_test.py | 147 +-
tests/tabix_test.py | 114 +-
tests/test_unaligned.bam | Bin 0 -> 514 bytes
95 files changed, 28238 insertions(+), 24378 deletions(-)
create mode 100644 doc/Makefile
create mode 100644 doc/api.rst
create mode 100644 doc/conf.py
create mode 100644 doc/contents.rst
create mode 100644 doc/developer.rst
create mode 100644 doc/faq.rst
create mode 100644 doc/glossary.rst
create mode 100644 doc/make.bat
create mode 100644 doc/release.rst
create mode 100644 doc/usage.rst
create mode 100644 pysam.py
delete mode 100644 pysam/VCF.py
copy KNOWN_BUGS => pysam/include/__init__.py (100%)
create mode 100644 pysam/tabix_util.h
copy KNOWN_BUGS => samtools/__init__.py (100%)
create mode 100644 samtools/bam_tview.h
create mode 100644 samtools/bam_tview_curses.c.pysam.c
create mode 100644 samtools/bam_tview_html.c.pysam.c
create mode 100644 samtools/bamshuf.c.pysam.c
copy KNOWN_BUGS => samtools/bcftools/__init__.py (100%)
create mode 100644 samtools/bedcov.c.pysam.c
create mode 100644 samtools/misc/ace2sam.c.pysam.c
delete mode 100644 samtools/misc/seqtk.c.pysam.c
create mode 100644 samtools/padding.c.pysam.c
copy KNOWN_BUGS => samtools/win32/__init__.py (100%)
copy KNOWN_BUGS => tabix/__init__.py (100%)
copy tabix/{bedidx.c.pysam.c => bedidx.c} (99%)
copy tabix/{bgzf.c.pysam.c => bgzf.c} (99%)
copy tabix/{bgzip.c.pysam.c => bgzip.c} (77%)
copy tabix/{index.c.pysam.c => index.c} (94%)
copy tabix/{knetfile.c.pysam.c => knetfile.c} (95%)
copy tabix/{kstring.c.pysam.c => kstring.c} (99%)
create mode 100644 tests/example_btag.bam
create mode 100644 tests/test_unaligned.bam
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