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commit 5a12dccfb677744581287869751cdf8143eacf9e Merge: fb73380 61cf1e5 Author: Alexandre Mestiashvili <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> Sat, 11 Oct 2014 08:17:29 +0200 + +gmap (2014-07-28-1) unstable; urgency=medium + + * Imported Upstream version 2014-07-28 + + -- Alexandre Mestiashvili <[email protected]> Wed, 30 Jul 2014 09:55:12 +0200 + +gmap (2014-07-04-1) unstable; urgency=medium + + * New upstream release + + -- Alexandre Mestiashvili <[email protected]> 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 <[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
