[med-svn] [gmap] 02/08: Merge tag 'upstream/2014-11-25'
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Fri Mar 13 09:51:49 UTC 2015
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository gmap.
commit 5a12dccfb677744581287869751cdf8143eacf9e
Merge: fb73380 61cf1e5
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Wed Nov 26 10:11:38 2014 +0100
Merge tag 'upstream/2014-11-25'
Upstream version 2014-11-25
ChangeLog | 141 +++
Makefile.in | 3 +
README | 25 +-
VERSION | 2 +-
acinclude.m4 | 3 +
config/ax_ext.m4 | 4 +-
config/ax_mpi.m4 | 176 ++++
configure | 493 ++++++++++-
configure.ac | 51 +-
debian/changelog | 6 +
src/Makefile.in | 3 +
src/access.c | 42 +-
src/bitpack64-read.c | 30 +-
src/bitpack64-readtwo.c | 6 +-
src/bitpack64-write.c | 14 +-
src/bytecoding.c | 69 +-
src/compress-write.c | 13 +-
src/config.h.in | 3 +
src/genome-write.c | 131 +--
src/genome.c | 32 +-
src/genome_sites.c | 170 ++--
src/get-genome.c | 28 +-
src/gmap.c | 24 +-
src/gmapindex.c | 58 +-
src/gsnap.c | 32 +-
src/iit-read-univ.c | 107 ++-
src/iit-read.c | 200 +++--
src/iit-write-univ.c | 14 +-
src/iit_get.c | 6 +-
src/iit_store.c | 27 +-
src/indel.c | 10 +-
src/indexdb-write.c | 146 ++--
src/indexdb.c | 30 +-
src/indexdb_hr.c | 28 +-
src/mem.c | 62 +-
src/oligoindex_hr.c | 8 +-
src/outbuffer.c | 59 +-
src/pair.c | 706 ++++++++++-----
src/pair.h | 22 +-
src/sam_sort.c | 289 ++++++-
src/samflags.h | 27 +-
src/samheader.c | 4 +-
src/samprint.c | 2214 ++++++++++++++++++++++++++++++++++-------------
src/samprint.h | 9 +-
src/samread.c | 220 ++++-
src/samread.h | 13 +-
src/sarray-read.c | 830 ++++++++++++------
src/snpindex.c | 22 +-
src/splice.c | 38 +-
src/stage1hr.c | 821 ++++++++++--------
src/stage2.c | 22 +-
src/stage3.c | 17 +-
src/stage3hr.c | 1752 +++++++++++++++++++------------------
src/stage3hr.h | 15 +-
src/substring.c | 129 +--
src/substring.h | 14 +-
src/table.c | 20 +-
src/tableuint8.c | 21 +-
src/uniqscan.c | 9 +-
src/univinterval.c | 13 +-
tests/Makefile.in | 3 +
util/Makefile.in | 3 +
util/gmap_build.pl.in | 4 +-
63 files changed, 6332 insertions(+), 3161 deletions(-)
diff --cc debian/changelog
index 5011d19,0000000..b4b682c
mode 100644,000000..100644
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,156 -1,0 +1,162 @@@
++gmap (2014-11-25-1) UNRELEASED; urgency=medium
++
++ * Imported Upstream version 2014-11-25
++
++ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de> Wed, 26 Nov 2014 10:22:52 +0100
++
+gmap (2014-10-22-1) unstable; urgency=medium
+
+ [ Alexandre Mestiashvili ]
+ * build fails due to 2 failing test on i386 for 2014-10-14
+
+ [ Andreas Tille ]
+ * Imported Upstream version 2014-10-22
+
+ [ Alexandre Mestiashvili ]
+ * debian/*.1: updated dates in man pages
+ * d/patches/drop_tests_i386.patch: do not run tests on i386 because they fail.
+ As it is not clear if the program is useful on i386 architecure,
+ let's leave it like that for now.
+ * d/README.Debian: note that embeded tests are skipped for i386
+
+ -- Andreas Tille <tille at debian.org> Sun, 26 Oct 2014 08:20:42 +0100
+
+gmap (2014-10-09-1) unstable; urgency=medium
+
+ * New upstream version
+ * cme fix dpkg-control
+ * DEP5 fix
+
+ -- Andreas Tille <tille at debian.org> Sat, 11 Oct 2014 08:17:29 +0200
+
+gmap (2014-07-28-1) unstable; urgency=medium
+
+ * Imported Upstream version 2014-07-28
+
+ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de> Wed, 30 Jul 2014 09:55:12 +0200
+
+gmap (2014-07-04-1) unstable; urgency=medium
+
+ * New upstream release
+
+ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de> Fri, 04 Jul 2014 10:49:40 +0200
+
+gmap (2014-06-10-1) UNRELEASED; urgency=medium
+
+ * New upstream release
+ * debian/patches/install-data-local: refreshed
+ * d/control: use canonical Vcs fields
+ - updated Standards-Version
+ - added help2man to Build-Depends:
+ - remove trailing slash from Homepage
+ - added myself to Uploaders:
+ * d/rules: install symlinks for gmap,gsnap and gmap_build in /usr/bin
+ - use as bindir /usr/lib/gmap
+ * d/install: removed as all files are installed in /usr/lib/gmap
+ * d/copyright:
+ - refresh copyright, add not mentioned before files
+ - add Comment that code was influenced by another software
+ * debian/*.1: updated man pages
+ * d/docs: install NOTICE
+
+ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de> Fri, 04 Jul 2014 09:59:32 +0200
+
+gmap (2013-07-20-1) unstable; urgency=low
+
+ * New upstream version
+ * debian/control:
+ - cme fix dpkg-control
+ - debhelper 9
+
+ -- Andreas Tille <tille at debian.org> Fri, 02 Aug 2013 15:09:36 +0200
+
+gmap (2012-06-12-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Shaun Jackman <sjackman at debian.org> Tue, 12 Jun 2012 15:06:22 -0700
+
+gmap (2012-03-23-1) UNRELEASED; urgency=low
+
+ * New upstream release
+ * debian/control:
+ - Added myself to Uploaders
+ - Standards-Version: 3.9.3 (no changes needed)
+ * debhelper 8 (control+compat)
+ * debian/upstream: Add citation information
+ * debian/copyright: Fixed some DEP5 issues and verified using
+ cme fix dpkg-copyright
+ * debian/install: gsnap_tally is not builded any more in this version
+ * debian/rules: really use autotools-dev to enable building twice in
+ a row
+
+ -- Andreas Tille <tille at debian.org> Sun, 01 Apr 2012 09:53:26 +0200
+
+gmap (2011-12-28-1) unstable; urgency=low
+
+ * New upstream release.
+
+ -- Shaun Jackman <sjackman at debian.org> Thu, 29 Dec 2011 12:32:19 -0800
+
+gmap (2011-11-30-1) unstable; urgency=low
+
+ * New upstream release.
+
+ -- Shaun Jackman <sjackman at debian.org> Wed, 07 Dec 2011 10:46:12 -0800
+
+gmap (2011-10-16-1) unstable; urgency=low
+
+ * New upstream release.
+
+ -- Shaun Jackman <sjackman at debian.org> Wed, 19 Oct 2011 15:40:36 -0700
+
+gmap (2011-09-14-1) unstable; urgency=low
+
+ * New upstream release.
+
+ -- Shaun Jackman <sjackman at debian.org> Thu, 15 Sep 2011 14:36:34 -0700
+
+gmap (2011-09-09-1) unstable; urgency=low
+
+ * New upstream release.
+
+ -- Shaun Jackman <sjackman at debian.org> Wed, 14 Sep 2011 17:09:21 -0700
+
+gmap (2011-08-15-1) unstable; urgency=low
+
+ * New upstream release.
+ * Bump Standards-Version to 3.9.2.
+
+ -- Shaun Jackman <sjackman at debian.org> Tue, 23 Aug 2011 10:45:46 -0700
+
+gmap (2011-03-11-1) unstable; urgency=low
+
+ * New upstream release.
+
+ -- Shaun Jackman <sjackman at debian.org> Wed, 23 Mar 2011 10:16:38 -0700
+
+gmap (2010-07-27-1) unstable; urgency=low
+
+ * New upstream release.
+ * Bump Standards-Version to 3.9.1.
+
+ -- Shaun Jackman <sjackman at debian.org> Fri, 06 Aug 2010 10:12:23 -0700
+
+gmap (2010-07-21-1) unstable; urgency=low
+
+ * New upstream release.
+
+ -- Shaun Jackman <sjackman at debian.org> Thu, 22 Jul 2010 11:36:34 -0700
+
+gmap (2010-07-20-1) unstable; urgency=low
+
+ * New upstream release.
+ * Bump Standards-Version to 3.9.0.
+
+ -- Shaun Jackman <sjackman at debian.org> Wed, 21 Jul 2010 11:07:28 -0700
+
+gmap (2010-03-09-1) unstable; urgency=low
+
+ * Initial release. Closes: #580277.
+
+ -- Shaun Jackman <sjackman at debian.org> Wed, 28 Apr 2010 11:55:31 -0700
--
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