[med-svn] [gmap] 03/06: Merge tag 'upstream/2014-07-04'
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Fri Jul 4 09:33:49 UTC 2014
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository gmap.
commit a78521ec799717c62f75362751537b2490e777ac
Merge: 6f22792 536c54f
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Fri Jul 4 09:54:33 2014 +0200
Merge tag 'upstream/2014-07-04'
Upstream version 2014-07-04
ChangeLog | 102 +++
VERSION | 2 +-
configure | 24 +-
debian/changelog | 8 +-
src/access.c | 134 ++--
src/dynprog.c | 9 +-
src/dynprog_end.c | 532 ++++++--------
src/dynprog_simd.c | 40 +-
src/dynprog_simd.h | 2 +-
src/dynprog_single.c | 63 +-
src/genome.c | 14 +-
src/genome.h | 8 +-
src/genome128_hr.c | 367 +++++-----
src/gmap.c | 27 +-
src/gmapindex.c | 23 +-
src/intlist.c | 16 +-
src/intlist.h | 4 +-
src/samprint.c | 10 +-
src/sarray-read.c | 617 ++++++++++------
src/sarray-write.c | 742 ++++++++++++++++++--
src/sarray-write.h | 6 +-
src/splice.c | 1046 ++++++++++++++++++----------
src/splice.h | 57 +-
src/splicetrie.c | 419 +++++------
src/stage1hr.c | 1132 ++++++++++++++++--------------
src/stage3.c | 129 ++--
src/stage3hr.c | 1893 +++++++++++++++++++++++++++++---------------------
src/stage3hr.h | 19 +-
src/substring.c | 316 +++------
src/uint8list.c | 16 +-
src/uint8list.h | 4 +-
src/uintlist.c | 16 +-
src/uintlist.h | 4 +-
33 files changed, 4642 insertions(+), 3159 deletions(-)
diff --cc debian/changelog
index 0a0b815,0000000..d5d1936
mode 100644,000000..100644
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,119 -1,0 +1,125 @@@
++gmap (2014-07-04-1) UNRELEASED; urgency=medium
++
++ * New upstream release
++
++ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de> Fri, 04 Jul 2014 09:59:32 +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> Mon, 30 Jun 2014 13:04:45 +0200
++ -- 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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