last-align (1447-1) unstable; urgency=medium * New upstream version -- Andreas Tille Sun, 05 Feb 2023 21:03:18 +0100 last-align (1420-1) unstable; urgency=medium * Add myself back to uploaders * New upstream version 1420 * Bump Standards-Version to 4.6.2 (no changes needed) -- Nilesh Patra Sat, 31 Dec 2022 17:18:26 +0530 last-align (1418-1) unstable; urgency=medium * New upstream version -- Charles Plessy Wed, 19 Oct 2022 09:29:30 +0900 last-align (1411-1) unstable; urgency=medium * New upstream version -- Andreas Tille Thu, 22 Sep 2022 09:28:20 +0200 last-align (1407-1) unstable; urgency=medium * New upstream version -- Andreas Tille Tue, 23 Aug 2022 16:53:32 +0200 last-align (1406-1) unstable; urgency=medium * New upstream version -- Andreas Tille Thu, 28 Jul 2022 16:49:02 +0200 last-align (1389-1) unstable; urgency=medium * New upstream version -- Andreas Tille Thu, 14 Jul 2022 16:39:54 +0200 last-align (1356-1) unstable; urgency=medium * New upstream version 1356 -- Nilesh Patra Sun, 26 Jun 2022 00:46:20 +0530 last-align (1296-1) unstable; urgency=medium * Team upload. * New upstream version 1296 * Bump Standards-Version to 4.6.1 (no changes needed) -- Nilesh Patra Sun, 29 May 2022 19:12:57 +0530 last-align (1282-1) unstable; urgency=medium * New upstream version 1282 * Refresh patches -- Nilesh Patra Wed, 04 May 2022 15:09:54 +0530 last-align (1268-1) unstable; urgency=medium * New upstream version 1268 -- Nilesh Patra Sat, 26 Feb 2022 23:52:43 +0530 last-align (1260-1) unstable; urgency=medium * Team Upload. * New upstream version 1260 -- Nilesh Patra Wed, 16 Feb 2022 16:40:04 +0530 last-align (1257-2) unstable; urgency=medium * d/rules: + Pass CFLAGS and CXXFLAGS directly to dh_auto_build rather than exporting (Closes: #1003488) + export LC_ALL and LANG to use C.UTF-8 (Closes: #1003489) (Thanks to Vagrant Cascadian for the patches) -- Nilesh Patra Tue, 11 Jan 2022 13:54:19 +0530 last-align (1257-1) unstable; urgency=medium [ Vagrant Cascadian ] * Do not embed cpu-specific features in manpages Closes: #1003379 [ Andreas Tille ] * Re-enable reprotest in Salca-CI to see whether the means above are working properly * New upstream version * Standards-Version: 4.6.0 (routine-update) -- Andreas Tille Mon, 10 Jan 2022 09:53:09 +0100 last-align (1256-1) unstable; urgency=medium * d/watch: Fix fetch URL - last-align has moved to gitlab * New upstream version 1256 * d/p/helpMakefiles.patch: Refresh helpmakefile.patch * d/p/simde: Attempt adapting simde to new upstream * Drop Patches: - Drop d/p/fix-959866.patch: Since the problem has been internally fixed in simde - Drop d/p/2to3.patch: The new upstream is now compatible with both python2 and python3, hence these changes are un-needed. Added d/p/fix-shebang.patch to fix shebang in python script, as a replacement. * d/rules: - Attempt adapting to new upstream version - Add rest manpages - Install all lastdb5 based binaries - Install new fasta+fastq scripts * d/debian/last-align.doc-base.last-align-manual: The manual page has moved to last-cookbook.rst * d/tests/last-test: Add additional tests * d/control: Move python3 to Depends - There are several python3 scripts being vendored, it does make sense to promote python3 to depends * d/salsa-ci.yml: Disable blhc and reprotest * d/lintian-overrides: Add lintian override for maf-cut manpage -- Nilesh Patra Mon, 23 Aug 2021 00:56:44 +0530 last-align (1179-1) unstable; urgency=medium * New upstream version -- Nilesh Patra Mon, 01 Feb 2021 16:02:34 +0530 last-align (1178-1) unstable; urgency=medium * New upstream version -- Nilesh Patra Thu, 28 Jan 2021 17:19:32 +0530 last-align (1170-1) unstable; urgency=medium * New upstream version -- Nilesh Patra Thu, 31 Dec 2020 17:04:25 +0530 last-align (1169-1) unstable; urgency=medium * New upstream version -- Nilesh Patra Wed, 23 Dec 2020 12:13:08 +0530 last-align (1168-1) unstable; urgency=medium * New upstream version -- Nilesh Patra Sat, 19 Dec 2020 16:19:45 +0530 last-align (1167-1) unstable; urgency=medium * Team upload. * New upstream version * Standards-Version: 4.5.1 (routine-update) -- Nilesh Patra Mon, 14 Dec 2020 23:14:25 +0530 last-align (1145-1) unstable; urgency=medium * Team upload. * New upstream version -- Nilesh Patra Wed, 11 Nov 2020 02:58:49 +0530 last-align (1133-1) unstable; urgency=medium * Team upload. * New upstream version -- Nilesh Patra Sat, 17 Oct 2020 13:20:28 +0530 last-align (1111-1) unstable; urgency=medium * Team Upload. * New upstream version 1111 -- Nilesh Patra Sat, 26 Sep 2020 02:11:54 +0530 last-align (1110-1) unstable; urgency=medium * Team upload. * New upstream version * Refreshed patches. -- Steffen Moeller Sun, 20 Sep 2020 16:40:30 +0200 last-align (1080-1) unstable; urgency=medium * New upstream version * Refreshed patches -- Charles Plessy Wed, 12 Aug 2020 11:12:45 +0000 last-align (1066-1) unstable; urgency=medium * Team upload. [ Michael R. Crusoe ] * i386: enable avx2, avx, and sse4.1 specific builds as well * Demote GNU parallel to a recommends; only used by parallel-fasta [ Steffen Moeller ] * New upstream version. * debhelper-compat 13 (routine-update) -- Michael R. Crusoe Sun, 17 May 2020 12:32:51 +0200 last-align (1061-1) unstable; urgency=medium * Team upload. * New upstream version -- Michael R. Crusoe Sun, 10 May 2020 13:57:46 +0200 last-align (1060-5) unstable; urgency=medium * Team upload. * Fix i386 build. -- Michael R. Crusoe Wed, 06 May 2020 21:01:18 +0200 last-align (1060-4) unstable; urgency=medium * Team upload. * Enable cross-building * Fix FTBFS on ppc64el, courtesy of frediz. (Closes: #959866) -- Michael R. Crusoe Wed, 06 May 2020 14:28:21 +0200 last-align (1060-3) unstable; urgency=medium * Team upload. * Use a newer libsimde-dev to fix a bug -- Michael R. Crusoe Sun, 19 Apr 2020 23:38:45 +0200 last-align (1060-2) unstable; urgency=medium * Team upload. * Switch to the libsimde-dev package from an internal copy * Added address of upstream's mailing list as Bug-Submit -- Michael R. Crusoe Sun, 19 Apr 2020 14:21:01 +0200 last-align (1060-1) unstable; urgency=medium * Team upload. * New upstream version * Standards-Version: 4.5.0 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Cleaner clean -- Steffen Moeller Tue, 24 Mar 2020 21:22:27 +0100 last-align (1047-1) unstable; urgency=medium * Team upload. * New upstream version -- Michael R. Crusoe Fri, 24 Jan 2020 16:21:19 +0100 last-align (1045-1) unstable; urgency=medium * Team upload. * New upstream version * Updated simde patches -- Michael R. Crusoe Tue, 31 Dec 2019 08:42:29 +0100 last-align (1044-2) unstable; urgency=medium * Team upload. * Enable building on any architecture via simde. (Closes: #946850) * For any-amd64 and any-i386: compile multiple times with reducing levels of SIMD instruction support and ship a dispatching script to pick the best one for the user at run-time. -- Michael R. Crusoe Sun, 22 Dec 2019 20:19:58 -0700 last-align (1044-1) unstable; urgency=medium * Team upload. * New upstream version * TODO: hope for new upstream version that does not require SSE or AVX to compile. -- Steffen Moeller Sat, 21 Dec 2019 00:28:04 +0100 last-align (1021-2) unstable; urgency=medium * Test-Depends: python3-pil Closes: #946209 -- Andreas Tille Thu, 05 Dec 2019 15:01:59 +0100 last-align (1021-1) unstable; urgency=medium * Team upload. * New upstream version * Fiddling with CFLAGS/CXXFLAGS defaults in Makefile * fixed and minimized 2to3-patches - path for last-train so there is no FTBFS when generating man pages * TODO: Need to work on platform dependencies -- Steffen Moeller Wed, 04 Dec 2019 13:35:17 +0100 last-align (984-2) unstable; urgency=medium * Use 2to3 to port to Python3 Closes: #943148, #943446 * Standards-Version: 4.4.1 * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g -- Andreas Tille Fri, 22 Nov 2019 11:46:43 +0100 last-align (984-1) unstable; urgency=medium * Team upload. * New upstream version * Set fields Upstream-Contact in debian/copyright. * Remove obsolete fields Name, Contact from debian/upstream/metadata. -- Steffen Moeller Wed, 04 Sep 2019 14:05:53 +0200 last-align (983-1) unstable; urgency=medium * Team upload. * New upstream version * debhelper-compat 12 * Standards-Version: 4.4.0 * Updated with no manual changes required by Andreas' routine-update script. -- Steffen Moeller Sat, 27 Jul 2019 12:33:38 +0200 last-align (963-2) unstable; urgency=medium * Example files are not compressed any more - adapt autopkgtest Closes: #919556 -- Andreas Tille Thu, 17 Jan 2019 11:21:30 +0100 last-align (963-1) unstable; urgency=medium * New upstream version * debhelper 12 * Standards-Version: 4.3.0 * debian/tests/control: Replace needs-recommends by explicitly adding recommended package python-pil to test depends -- Andreas Tille Fri, 11 Jan 2019 22:49:18 +0100 last-align (961-1) unstable; urgency=medium [ Jelmer Vernooij ] * Use secure copyright file specification URI. * Trim trailing whitespace. [ Andreas Tille ] * New upstream version * Remove trailing whitespace in debian/rules -- Andreas Tille Mon, 17 Dec 2018 11:13:03 +0100 last-align (956-1) unstable; urgency=medium * Team upload. * New upstream version. * Standards-Version: 4.2.1 -- Steffen Moeller Tue, 02 Oct 2018 15:07:34 +0200 last-align (938-1) unstable; urgency=medium * New upstream version -- Andreas Tille Wed, 23 May 2018 07:10:11 +0200 last-align (932-1) unstable; urgency=medium * New upstream version * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.4 -- Andreas Tille Thu, 26 Apr 2018 22:27:19 +0200 last-align (921-1) unstable; urgency=medium * New upstream version * make build compatible with -Wl, --as-needed (thanks for the patch to Steve Langasek ) Closes: #889506 * cme fix dpkg-control * debhelper 11 * d/rules: do not parse changelog -- Andreas Tille Mon, 05 Feb 2018 10:39:42 +0100 last-align (885-1) unstable; urgency=medium * New upstream version 885 * debian/rules: re-enable multi-threading. * debian/control: build-depend on zlib1g-dev. -- Charles Plessy Sun, 15 Oct 2017 22:20:19 +0900 last-align (869-1) unstable; urgency=low * Team upload. [ Steffen Moeller ] * [debian/upstream/metadata] Added references to OMICtools, bio.tools, RRID [ Sascha Steinbiss ] * New upstream release. * Use python-pil instead of python-imaging as dependency. Closes: #866438 * Add needs-recommends to d/t/control to fix autopkgtests. -- Sascha Steinbiss Fri, 11 Aug 2017 15:17:15 -0400 last-align (830-2) unstable; urgency=low * Team upload. [ Nadiya Sitdykova ] * Add autopkgtest test-suite -- Nadiya Sitdykova Tue, 06 Jun 2017 01:56:56 -0400 last-align (830-1) unstable; urgency=medium * New upstream version -- Andreas Tille Mon, 23 Jan 2017 08:47:32 +0100 last-align (828-1) unstable; urgency=medium * New upstream version * Manpages for new binaries -- Andreas Tille Mon, 09 Jan 2017 14:16:28 +0100 last-align (809-1) unstable; urgency=medium * New upstream version * debhelper 10 * d/watch: version=4 -- Andreas Tille Wed, 30 Nov 2016 16:04:04 +0100 last-align (759-1) unstable; urgency=medium * New upstream version -- Andreas Tille Tue, 18 Oct 2016 13:43:13 +0200 last-align (755-1) unstable; urgency=medium * New upstream version -- Andreas Tille Sat, 10 Sep 2016 22:37:20 +0200 last-align (752-1) unstable; urgency=medium * New upstream version -- Andreas Tille Tue, 16 Aug 2016 14:35:15 +0200 last-align (746-1) unstable; urgency=medium * New upstream version -- Charles Plessy Fri, 15 Jul 2016 14:24:00 +0900 last-align (737-1) unstable; urgency=medium * New upstream version * cme fix dpkg-control * better hardening -- Andreas Tille Wed, 18 May 2016 18:08:29 +0200 last-align (731-1) unstable; urgency=medium * New upstream version * Fix debian/upstream/metadata * Use xz compression in watch opts * cme fix dpkg-control -- Andreas Tille Sat, 12 Mar 2016 08:01:37 +0100 last-align (712-1) unstable; urgency=medium [ Andreas Tille ] * New upstream version * Moved to Git * Add missing manpages * Depends: parallel (instead of Suggests) [ Julien Lamy ] * debian/rules: - Add missing build flags - Do not try to create manpage for removed tool -- Andreas Tille Thu, 31 Dec 2015 09:18:43 +0100 last-align (658-1) unstable; urgency=medium * New upstream version -- Andreas Tille Thu, 29 Oct 2015 16:23:59 +0100 last-align (621-1) unstable; urgency=medium * New upstream version -- Andreas Tille Thu, 24 Sep 2015 08:53:43 +0200 last-align (588-1) unstable; urgency=medium * New upstream version * Binaries lastex and last-pair-probs do not belong to the package any more * Removed paragraphs from copyright where files are not part of the source any more -- Andreas Tille Mon, 06 Jul 2015 18:00:21 +0200 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