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commit a78521ec799717c62f75362751537b2490e777ac Merge: 6f22792 536c54f Author: Alexandre Mestiashvili <[email protected]> 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 <[email protected]> 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 <[email protected]> Mon, 30 Jun 2014 13:04:45 +0200 ++ -- Alexandre Mestiashvili <[email protected]> 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 <[email protected]> Fri, 02 Aug 2013 15:09:36 +0200 + +gmap (2012-06-12-1) unstable; urgency=low + + * New upstream release + + -- Shaun Jackman <[email protected]> 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 <[email protected]> Sun, 01 Apr 2012 09:53:26 +0200 + +gmap (2011-12-28-1) unstable; urgency=low + + * New upstream release. + + -- Shaun Jackman <[email protected]> Thu, 29 Dec 2011 12:32:19 -0800 + +gmap (2011-11-30-1) unstable; urgency=low + + * New upstream release. + + -- Shaun Jackman <[email protected]> Wed, 07 Dec 2011 10:46:12 -0800 + +gmap (2011-10-16-1) unstable; urgency=low + + * New upstream release. + + -- Shaun Jackman <[email protected]> Wed, 19 Oct 2011 15:40:36 -0700 + +gmap (2011-09-14-1) unstable; urgency=low + + * New upstream release. + + -- Shaun Jackman <[email protected]> Thu, 15 Sep 2011 14:36:34 -0700 + +gmap (2011-09-09-1) unstable; urgency=low + + * New upstream release. + + -- Shaun Jackman <[email protected]> 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 <[email protected]> Tue, 23 Aug 2011 10:45:46 -0700 + +gmap (2011-03-11-1) unstable; urgency=low + + * New upstream release. + + -- Shaun Jackman <[email protected]> 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 <[email protected]> Fri, 06 Aug 2010 10:12:23 -0700 + +gmap (2010-07-21-1) unstable; urgency=low + + * New upstream release. + + -- Shaun Jackman <[email protected]> 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 <[email protected]> Wed, 21 Jul 2010 11:07:28 -0700 + +gmap (2010-03-09-1) unstable; urgency=low + + * Initial release. Closes: #580277. + + -- Shaun Jackman <[email protected]> Wed, 28 Apr 2010 11:55:31 -0700 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/gmap.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
