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|
last-align (1179-1) unstable; urgency=medium
* New upstream version
-- Nilesh Patra <npatra974@gmail.com> Mon, 01 Feb 2021 16:02:34 +0530
last-align (1178-1) unstable; urgency=medium
* New upstream version
-- Nilesh Patra <npatra974@gmail.com> Thu, 28 Jan 2021 17:19:32 +0530
last-align (1170-1) unstable; urgency=medium
* New upstream version
-- Nilesh Patra <npatra974@gmail.com> Thu, 31 Dec 2020 17:04:25 +0530
last-align (1169-1) unstable; urgency=medium
* New upstream version
-- Nilesh Patra <npatra974@gmail.com> Wed, 23 Dec 2020 12:13:08 +0530
last-align (1168-1) unstable; urgency=medium
* New upstream version
-- Nilesh Patra <npatra974@gmail.com> 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 <npatra974@gmail.com> Mon, 14 Dec 2020 23:14:25 +0530
last-align (1145-1) unstable; urgency=medium
* Team upload.
* New upstream version
-- Nilesh Patra <npatra974@gmail.com> Wed, 11 Nov 2020 02:58:49 +0530
last-align (1133-1) unstable; urgency=medium
* Team upload.
* New upstream version
-- Nilesh Patra <npatra974@gmail.com> Sat, 17 Oct 2020 13:20:28 +0530
last-align (1111-1) unstable; urgency=medium
* Team Upload.
* New upstream version 1111
-- Nilesh Patra <npatra974@gmail.com> Sat, 26 Sep 2020 02:11:54 +0530
last-align (1110-1) unstable; urgency=medium
* Team upload.
* New upstream version
* Refreshed patches.
-- Steffen Moeller <moeller@debian.org> Sun, 20 Sep 2020 16:40:30 +0200
last-align (1080-1) unstable; urgency=medium
* New upstream version
* Refreshed patches
-- Charles Plessy <plessy@debian.org> 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 <michael.crusoe@gmail.com> Sun, 17 May 2020 12:32:51 +0200
last-align (1061-1) unstable; urgency=medium
* Team upload.
* New upstream version
-- Michael R. Crusoe <michael.crusoe@gmail.com> Sun, 10 May 2020 13:57:46 +0200
last-align (1060-5) unstable; urgency=medium
* Team upload.
* Fix i386 build.
-- Michael R. Crusoe <michael.crusoe@gmail.com> 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 <michael.crusoe@gmail.com> 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 <michael.crusoe@gmail.com> 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 <michael.crusoe@gmail.com> 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 <moeller@debian.org> Tue, 24 Mar 2020 21:22:27 +0100
last-align (1047-1) unstable; urgency=medium
* Team upload.
* New upstream version
-- Michael R. Crusoe <michael.crusoe@gmail.com> 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 <michael.crusoe@gmail.com> 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 <michael.crusoe@gmail.com> 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 <moeller@debian.org> Sat, 21 Dec 2019 00:28:04 +0100
last-align (1021-2) unstable; urgency=medium
* Test-Depends: python3-pil
Closes: #946209
-- Andreas Tille <tille@debian.org> 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 <moeller@debian.org> 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 <tille@debian.org> 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 <moeller@debian.org> 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 <moeller@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <moeller@debian.org> Tue, 02 Oct 2018 15:07:34 +0200
last-align (938-1) unstable; urgency=medium
* New upstream version
-- Andreas Tille <tille@debian.org> 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 <tille@debian.org> 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 <steve.langasek@canonical.com>)
Closes: #889506
* cme fix dpkg-control
* debhelper 11
* d/rules: do not parse changelog
-- Andreas Tille <tille@debian.org> 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 <plessy@debian.org> 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 <satta@debian.org> 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 <rovenskasa@gmail.com> Tue, 06 Jun 2017 01:56:56 -0400
last-align (830-1) unstable; urgency=medium
* New upstream version
-- Andreas Tille <tille@debian.org> Mon, 23 Jan 2017 08:47:32 +0100
last-align (828-1) unstable; urgency=medium
* New upstream version
* Manpages for new binaries
-- Andreas Tille <tille@debian.org> 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 <tille@debian.org> Wed, 30 Nov 2016 16:04:04 +0100
last-align (759-1) unstable; urgency=medium
* New upstream version
-- Andreas Tille <tille@debian.org> Tue, 18 Oct 2016 13:43:13 +0200
last-align (755-1) unstable; urgency=medium
* New upstream version
-- Andreas Tille <tille@debian.org> Sat, 10 Sep 2016 22:37:20 +0200
last-align (752-1) unstable; urgency=medium
* New upstream version
-- Andreas Tille <tille@debian.org> Tue, 16 Aug 2016 14:35:15 +0200
last-align (746-1) unstable; urgency=medium
* New upstream version
-- Charles Plessy <plessy@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> Thu, 31 Dec 2015 09:18:43 +0100
last-align (658-1) unstable; urgency=medium
* New upstream version
-- Andreas Tille <tille@debian.org> Thu, 29 Oct 2015 16:23:59 +0100
last-align (621-1) unstable; urgency=medium
* New upstream version
-- Andreas Tille <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <plessy@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <plessy@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <plessy@debian.org> 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 <cjwatson@ubuntu.com> 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 <plessy@debian.org> 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 <plessy@debian.org> 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 <plessy@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> Mon, 29 Mar 2010 12:29:16 +0200
last-align (99-1) unstable; urgency=low
* New upstream version
-- Andreas Tille <tille@debian.org> 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 <tille@debian.org> Thu, 18 Feb 2010 14:43:15 +0100
last-align (87-1) unstable; urgency=low
* New upstream version
-- Andreas Tille <tille@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <plessy@debian.org> 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 <plessy@debian.org> Mon, 18 May 2009 23:52:24 +0900
last-align (50-1) unstable; urgency=low
* New upstream release (minor changes).
-- Charles Plessy <plessy@debian.org> 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 <plessy@debian.org> 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 <plessy@debian.org> 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 <plessy@debian.org> 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 <plessy@debian.org> Sun, 28 Dec 2008 12:49:05 +0100
last-align (31-1) unstable; urgency=low
* Initial release (Closes: #498562)
-- Charles Plessy <plessy@debian.org> Thu, 13 Nov 2008 15:44:31 +0900
|