last-align (490-1) unstable; urgency=medium * New upstream version * get-orig-source target now with xz compression * cme fix dpkg-control * Upstream dropped .py suffix - adpapt help2man calls in d/rules -- Andreas Tille Thu, 23 Oct 2014 22:30:48 +0200 last-align (475-1) unstable; urgency=medium * New upstream release. * debian/rules: - removed compression command, as it is now the default. - removed manual page of last-merge-batches.py. * debian/control: suggest GNU parallel. * debian/README.source: removed as conversion from zip is now automagic. -- Charles Plessy Sat, 16 Aug 2014 15:20:37 +0900 last-align (418-1) unstable; urgency=medium * New upstream release * debian/upstream -> debian/upstream/metadata -- Andreas Tille Fri, 21 Mar 2014 14:57:56 +0100 last-align (393-1) unstable; urgency=medium * New upstream release * cme fix dpkg-control * debian/rules: Adapt help2man to the fact that two scripts were deleted from upstream source (no idea how to write manpages for the new parallel-* scripts) * Adapt doc-base control script (text file might be uncompressed) -- Andreas Tille Tue, 28 Jan 2014 17:57:09 +0100 last-align (359-1) unstable; urgency=low * New upstream release. * debian/control: - Removed Pre-Depends on dpkg as Ubuntu LTS is released. - Removed obsolete DM-Upload-Allowed field. - Use canonical VCS URLs. - Normalised with config-model-edit. - Removed version constraint on help2man, satisfied in oldstable. - Mark conformance with Policy version 3.9.4. * debian/watch: updated. * debian/rules: - Restore xz compression of the binary packages. - Produce a manual page for ‘last-split’ with help2man. -- Charles Plessy Sun, 06 Oct 2013 12:16:12 +0900 last-align (199-1) unstable; urgency=low [ Charles Plessy ] * Summarise LAST license in debian/copyright header. [ Andreas Tille ] * New upstream version Closes: #667939 * debian/rules: - switch from cdbs to dh - add help2man call for lastex * debian/install: - removed to use upstream install target (which also installs lastex) * debian/copyright: Make Source field more generic -- Andreas Tille Mon, 07 May 2012 13:28:25 +0200 last-align (198-1) unstable; urgency=low * New upstream version * debian/rules,debian/get-orig-source: Simplified downloading original source * debhelper 9 to enable hardening flags (control+compat, closes: #667939). -- Andreas Tille Mon, 02 Apr 2012 14:16:35 +0200 last-align (193-1) unstable; urgency=low * New upstream version * debian/upstream: Removed duplicate entries for DOI/PMID * debian/control: Standards-Version: 3.9.3 (no changes needed) -- Andreas Tille Thu, 08 Mar 2012 14:34:36 +0100 last-align (189-1) unstable; urgency=low * New upstream release. * Autogenerate a manual page for last-merge-batches (debian/rules). -- Charles Plessy Sat, 22 Oct 2011 18:32:17 +0900 last-align (184-1ubuntu1) precise; urgency=low * Pre-Depends: dpkg (>= 1.15.6) for xz compression support. Needed until after Ubuntu 12.04 LTS. -- Colin Watson Mon, 17 Oct 2011 21:40:04 +0100 last-align (184-1) unstable; urgency=low * New upstream release. * Corrected VCS URLs (debian/control). * Compress source and binary package with xz (debian/get-orig-source, debian/rules). -- Charles Plessy Sat, 17 Sep 2011 20:31:16 +0900 last-align (178-1) unstable; urgency=low * New upstream release changing format of lastal output (r177). -- Charles Plessy Thu, 30 Jun 2011 13:53:03 +0900 last-align (171-1) unstable; urgency=low * New upstream release accepting gcc-4.6.patch (LP: #770770). - Deleted debian/patches and its contents. * Install changelog through CDBS (debian/rules, debian/docs). * Proofread debian/copyright and refreshed DEP-5 format. -- Charles Plessy Mon, 16 May 2011 22:01:53 +0900 last-align (162-1) unstable; urgency=low * New upstream version * Standards-Version: 3.9.2 (no changes needed) * debian/patches/gcc-4.6.patch: Fix gcc-4.6 build error Closes: #625084 -- Andreas Tille Mon, 02 May 2011 15:29:14 +0200 last-align (159-1) unstable; urgency=low * New upstream version * Debhelper 8 (control+compat) * debian/last-align.doc-base.last-align-manual: last-manual seems to have dropped in favour of last-tutorial and other smaller files * debian/rules: Call help2man for new additional script -- Andreas Tille Fri, 11 Mar 2011 23:29:44 +0100 last-align (146-1) unstable; urgency=low * New upstream version * debian/rules: - Maf2html is not any more in the source so we need not to create the manpage - Use help2man to create maf-cull manpage - Remove src/lastex in clean target -- Andreas Tille Thu, 25 Nov 2010 19:46:56 +0100 last-align (139-1) unstable; urgency=low * New upstream version * Standards-Version: 3.9.1 (no changes needed) -- Andreas Tille Wed, 17 Nov 2010 11:22:38 +0100 last-align (128-1) unstable; urgency=low * New upstream version * Standards-Version: 3.9.0 (no changes needed) -- Andreas Tille Fri, 09 Jul 2010 12:12:04 +0200 last-align (119-1) unstable; urgency=low [ Charles Plessy ] * New upstream version. * debian/rules get-orig-source: * Pass --best and --no-name to gzip, for reproductible MD5 sums. * Add ‘.orig’ to the repacked directory, to conform with the Debian Developer’s Reference (§ 6.7.8.2.4). * Build-depend on help2man (>= 1.36.4+nmu1), since the option --version-string is not available earlier. * Added missing empty line in debian/NEWS. * Gathered information about upstream in debian/upstream-metadata.yaml. [ Andreas Tille ] * debian/last-align.doc-base.last-align-lastex: Upstream documentation evalue-tables.txt was replaced by lastex.txt * debain/rules: Added help2man call for maf-convert -- Andreas Tille Thu, 24 Jun 2010 11:41:46 +0200 last-align (102-1) unstable; urgency=low * New upstream version * debian/rules: scripts/maf2tab.py was removed -> do not try to create manpage for this script * debian/source/format: 3.0 (quilt) -- Andreas Tille Mon, 29 Mar 2010 12:29:16 +0200 last-align (99-1) unstable; urgency=low * New upstream version -- Andreas Tille Thu, 11 Mar 2010 15:38:23 +0100 last-align (96-1) unstable; urgency=low * New upstream version * Standards-Version: 3.8.4 (no changes needed) -- Andreas Tille Thu, 18 Feb 2010 14:43:15 +0100 last-align (87-1) unstable; urgency=low * New upstream version -- Andreas Tille Tue, 03 Nov 2009 10:47:02 +0100 last-align (70-1) unstable; urgency=low * New upstream version * Removed quilt dependency because upstream has applied patches * help2man for all scripts TODO: Write real manpages using the comments inside the scripts. Upstream confirmed that there are no immediate plans for further changes so writing static man pages seems to make sense -- Andreas Tille Mon, 05 Oct 2009 11:56:25 +0200 last-align (62-1) unstable; urgency=low * New upstream version * debian/control: - Added myself to upstream - Standards-Version: 3.8.3 - Build-Depends: help2man, quilt, python-imaging - Recommends: python-imaging * debian/rules: Try to create manpages via help2man wherever possible * debian/patches: Make sure help output goes to stdout as GNU coding style suggests and is needed by help2man -- Andreas Tille Tue, 29 Sep 2009 13:38:57 +0200 last-align (58-1) unstable; urgency=low * New upstream release able to use sequence quality scores. -- Charles Plessy Fri, 19 Jun 2009 20:47:02 +0900 last-align (52-1) unstable; urgency=low * New upstream releases (52 and 51). - Added maf2html.py: converts MAF-format alignments to coloured HTML format. - Made lastal gapped extension faster, by removing an assert (surprising). - Bugfix: made last-dotplot.py not crash on small sequences. -- Charles Plessy Mon, 18 May 2009 23:52:24 +0900 last-align (50-1) unstable; urgency=low * New upstream release (minor changes). -- Charles Plessy Tue, 21 Apr 2009 09:59:54 +0900 last-align (48-1) unstable; urgency=low * New upstream release. - maf-join.py: joins pairwise alignments into multiple alignments. - Changed lastal default gap existence cost for DNA to 7. - Changed lastal default gapped score threshold for DNA to 40. - maf-swap.py: Added -n option to move any sequence to the top. - Allow suffixes K(ibibyte), M(ebibyte), and G(ibibyte) for sizes. - Plus other bugfixes and improvements, please refer Upstream's changelog. * Incremented Standards-Version in debian/control to reflect conformance with Policy 3.8.1 (no changes needed). * Simplified machine-readable debian/copyright file. * last-align.doc-base.last-align-scripts: last-scripts.txt is now compressed. -- Charles Plessy Wed, 08 Apr 2009 19:31:28 +0900 last-align (42-1) unstable; urgency=low * New upstream release: - Corrects an overflow error that made lastal discard some gapped alignments. - Allows lastal options to be set in the score-matrix file. * debian/copyright refreshed and points directly to GPLv3. * Corrected the description in debian/control to not use the first person. -- Charles Plessy Tue, 10 Mar 2009 19:46:32 +0900 last-align (39-1) unstable; urgency=low * New upstream release. - Bugfix: for protein alignments, tyrosine was forbidden in initial matches. - *Old lastdb protein databases won't work properly: you need to re-run lastdb.* * Added debian/NEWS.Debian to indicate the backward incompatibility. * Debian/changelog: removed vanity entries and incremented copyright year. * Transferred informations about packaging practices and repository from README.source to README.Debian. -- Charles Plessy Mon, 02 Feb 2009 12:42:26 +0900 last-align (37-1) unstable; urgency=low * New upstream release. - Updated the documentation, including a table of optimal spaced seeds. - Made lastdb bucket-making code slightly simpler & faster. - Enabled reading & writing of huge files (at least on one system with Linux-2.6.13/x86_64/gcc-4.0.2). - Made lastdb radix sort a bit faster, with the oracle array trick. - Allowed the mismatch score to be zero, due to a request. - Made gaped extension faster for short sequences (e.g. tag mapping). - Bugfix: the sequence names weren't printed correctly for match-counting output (-j 0). - Fixed compiler warnings with gcc 4.3. -- Charles Plessy Sun, 28 Dec 2008 12:49:05 +0100 last-align (31-1) unstable; urgency=low * Initial release (Closes: #498562) -- Charles Plessy Thu, 13 Nov 2008 15:44:31 +0900