[med-svn] [pysam] 10/13: Merge tag 'upstream/0.7.5'

[Charles Plessy]

This is an automated email from the git hooks/post-receive script.

plessy pushed a commit to branch master
in repository pysam.

commit e5648f2c4ff8982ad47c94db9c8a5fcb86106bd8
Merge: 256d533 fabbcdc
Author: Charles Plessy <plessy at debian.org>
Date:   Fri Aug 9 18:34:41 2013 +0900

    Merge tag 'upstream/0.7.5'
    
    Upstream version 0.7.5
    
    # gpg: Signature made Fri 09 Aug 2013 18:34:40 JST using RSA key ID 2295D502
    # gpg: Good signature from "Charles Plessy <plessy at debian.org>"

 MANIFEST.in                          |    6 +
 PKG-INFO                             |    2 +-
 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              |    2 +-
 pysam.egg-info/SOURCES.txt           |   21 +-
 pysam.py                             |    1 +
 pysam/TabProxies.c                   | 3888 ++---
 pysam/__init__.py                    |    4 +
 pysam/csamtools.c                    |27233 +++++++++++++++++++---------------
 pysam/csamtools.pyx                  |   48 +-
 pysam/ctabix.c                       | 1970 ++-
 pysam/ctabix.pxd                     |    6 +-
 pysam/ctabix.pyx                     |    2 +-
 pysam/cvcf.c                         |13214 +++++++++--------
 pysam/cvcf.pyx                       |   19 +-
 pysam/pysam_util.c                   |   19 +-
 pysam/tabix_util.h                   |    6 +
 pysam/version.py                     |    4 +-
 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 +
 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 +-
 setup.py                             |   18 +-
 tests/Makefile                       |   12 +-
 tests/pysam_test.py                  |  139 +-
 tests/tabix_test.py                  |  114 +-
 tests/test_unaligned.bam             |  Bin 0 -> 514 bytes
 78 files changed, 31105 insertions(+), 23458 deletions(-)

-- 
Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/pysam.git