[med-svn] [pysam] branch master updated (d8131e1 -> 224494d)
Charles Plessy
plessy at alioth.debian.org
Fri Aug 9 09:47:26 UTC 2013
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch master
in repository pysam.
from d8131e1 added python-all-dev dependency to support multiple python versions
new 11d2148 Imported Upstream version 0.7.1
new d3756a4 Merge tag 'upstream/0.7.1'
new 51573cd Imported Upstream version 0.7.2
new 4b62e38 Merge tag 'upstream/0.7.2'
new 14c14ac Imported Upstream version 0.7.3
new f48b0aa Merge tag 'upstream/0.7.3'
new 356c1c8 Imported Upstream version 0.7.4
new 256d533 Merge tag 'upstream/0.7.4'
new fabbcdc Imported Upstream version 0.7.5
new e5648f2 Merge tag 'upstream/0.7.5'
new 0f92ba9 Normalised with config-model-edit.
new 4331ad1 Debhelper 9.
new 224494d Corrected version number.
The 13 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 +-
debian/changelog | 6 +
debian/compat | 2 +-
debian/control | 20 +-
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
98 files changed, 28259 insertions(+), 24385 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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