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 <[email protected]> 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 <[email protected]>" 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
