bwa (0.7.18-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.6.2 (routine-update) Use secure URI in Homepage field. * Removed 2 patches applied upstream (CVE-2019-10269, gcc10). Removed no-longer-needed SIMDe patch. -- Michael R. Crusoe Sat, 07 Sep 2024 13:58:12 +0200 bwa (0.7.17-7) unstable; urgency=medium * Team upload * Installing all header files in /usr/include/bwa * Standards-Version: 4.6.0 (routine-update) [ Steffen Möller ] * Update metadata - ref to guix -- Pierre Gruet Sun, 06 Mar 2022 21:43:27 +0100 bwa (0.7.17-6) unstable; urgency=medium [ Michael R. Crusoe ] * debian/patches/hurd: define PATH_MAX, if needed (fixes FTBFS on hurd-*) * Switch to libsimde-dev from our code copy * Build libbwa.a with -fPIC for uncalled [ Andreas Tille ] * Drop redundant debian/gbp.conf * Demote perl from Depends to Recommends [ Michael R. Crusoe ] * Forward many patches upstream * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) * watch file standard 4 (routine-update) -- Michael R. Crusoe Thu, 04 Feb 2021 16:16:02 +0100 bwa (0.7.17-5) unstable; urgency=medium [ Nilesh Patra ] * Team upload. * Add patch to build with gcc-10 Closes: #957059 [ Andreas Tille ] * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 12 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * mv debian/NEWS.Debian debian/NEWS -- Nilesh Patra Sat, 18 Apr 2020 20:22:35 +0530 bwa (0.7.17-4) unstable; urgency=medium * debian/control: update my email address * debian/patches/spelling: fix a few typos * Enable for all architectures using simde -- Michael R. Crusoe Sat, 14 Dec 2019 11:38:00 +0100 bwa (0.7.17-3) unstable; urgency=medium * Team upload. [ Dylan Aïssi ] * Add patch from upstream to fix CVE-2019-10269. (Closes: #926014) [ Jelmer Vernooij ] * Trim trailing whitespace. -- Dylan Aïssi Sat, 30 Mar 2019 15:18:23 +0100 bwa (0.7.17-2) unstable; urgency=medium * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 * Secure URI in copyright format * Fix wrong-path-for-interpreter -- Andreas Tille Fri, 19 Oct 2018 15:05:09 +0200 bwa (0.7.17-1) unstable; urgency=medium * debian/upstream/metadata: RRID -> SciCrunch [ Pointed out by John Marshall ] * debian/patches/series: - check_for_nan.patch superseded by upstream's bcb475cd033b3641d2de19ad6fb70da7bdd54f77 - commenting issue behind fix_heap_block_overrun is analysed in https://github.com/lh3/bwa/issues/146 [ Andreas Tille ] * debhelper 10 * Standards-Version: 4.1.1 -- Andreas Tille Mon, 13 Nov 2017 15:33:11 +0100 bwa (0.7.16-1) unstable; urgency=medium * Team upload. * debian/control: Policy bump tp 4.1.0 * debian/upstream/metadata: Add references to registries. -- Steffen Moeller Mon, 07 Aug 2017 16:50:42 +0200 bwa (0.7.15-5) unstable; urgency=medium * Team upload. [Nadiya Sitdykova] * Add patch to fix heap block overrun * Add patch with workaround for incorrect implicit type casting (resolves upstream issue #108) * Remove patch with workaround for issue #108 * Add patch that checks computed avg and std for nan (straitforward fix for upstream issue #108) Closes: #853859 * Add patch that fixes printing of unsigned counts [Steffen Moeller] * debian/upstream/metadata: Added bio.tools entry -- Nadiya Sitdykova Fri, 30 Jun 2017 17:37:35 -0400 bwa (0.7.15-4) UNRELEASED; urgency=medium * Debugging (see deactivated patch debian/patches/debug.patch that tries to track down upstream issue #108) ==> Any help would be welcome! * debian/upstream/metadata: Added RRID and SEQwiki entries (Steffen Moeller) -- Andreas Tille Thu, 16 Mar 2017 09:12:09 +0100 bwa (0.7.15-3) unstable; urgency=medium * bwa/kseq.h is used by SeqLib so include this into libbwa-dev package -- Andreas Tille Fri, 27 Jan 2017 14:51:16 +0100 bwa (0.7.15-2) unstable; urgency=medium * Team upload * Added testsuite * debian/examples directory added -- Canberk Koç Sun, 26 Jun 2016 01:00:42 +0200 bwa (0.7.15-1) unstable; urgency=medium * New upstream version * cme fix dpkg-control * better hardening -- Andreas Tille Fri, 03 Jun 2016 17:53:03 +0200 bwa (0.7.13-1) unstable; urgency=medium * New upstream version * cme fix dpkg-control -- Andreas Tille Mon, 14 Mar 2016 13:44:35 +0100 bwa (0.7.12-5) unstable; urgency=medium * Make a libbwa-dev package for `salmon`. -- Michael R. Crusoe Sun, 27 Sep 2015 17:16:04 -0700 bwa (0.7.12-4) unstable; urgency=medium * Check exact number of arguments of bwtupdate Closes: #715703 * Fix minor spelling issue -- Andreas Tille Sun, 12 Jul 2015 15:04:54 +0200 bwa (0.7.12-3) unstable; urgency=medium * Enable building on freebsd -- Andreas Tille Fri, 10 Jul 2015 18:24:53 +0200 bwa (0.7.12-2) unstable; urgency=medium * Upload to Unstable. * Install bash completion script in /usr/share/bash-completion/completions. * Also distribute README-alt.md. * Watch GitHub instead of SourceForge. -- Charles Plessy Sat, 04 Jul 2015 13:00:50 +0900 bwa (0.7.12-1) experimental; urgency=medium * New upstream version * simplified watch file * cme fix dpkg-control -- Andreas Tille Tue, 27 Jan 2015 08:46:44 +0100 bwa (0.7.10-1) unstable; urgency=medium * New upstream version -- Andreas Tille Thu, 14 Aug 2014 18:31:43 +0200 bwa (0.7.9a-1) unstable; urgency=medium * New upstream version * debian/copyright: Add Upstream-Contact * debian/rules: Install NEWS.md as upstream changelog -- Andreas Tille Fri, 06 Jun 2014 21:54:29 +0200 bwa (0.7.8-1) unstable; urgency=medium * New upstream version -- Andreas Tille Sun, 13 Apr 2014 08:53:07 +0200 bwa (0.7.7-1) unstable; urgency=medium * New upstream version * Move debian/upstream to debian/upstream/metadata -- Andreas Tille Tue, 18 Mar 2014 13:45:44 +0100 bwa (0.7.6a-1) unstable; urgency=medium * New upstream version * cme fix dpkg-control -- Andreas Tille Fri, 21 Feb 2014 12:32:04 +0100 bwa (0.7.5a-2) unstable; urgency=low * Fixed FTBFS: SSE2 is required so require amd64-based architecture for now. (9284b99) * Updated Vcs-* fields. (521828c) * New package description taken from homepage. (0ad135b) * Standards-Version: 3.9.4 (3ce8e1a) -- Ognyan Kulev Tue, 04 Jun 2013 21:51:41 +0300 bwa (0.7.5a-1) unstable; urgency=low [ Charles Plessy ] - Imported Upstream version 0.7.0 (947c814) - solid2fastq.pl was removed upstream. (4d08b81) - Bash completion. (ad07300) - Updated list of BWA's commands. (c330e89) [ Ognyan Kulev ] - Imported upstream version 0.7.5a (ec16902, Closes: #710682) - README is renamed to README.md by upstream. (f42f5c0) - Standards-Version: 3.9.4 (no changes needed) - Removed DM-Upload-Allowed field. (78af085) - Added myself as uploader. (86455dc) -- Ognyan Kulev Tue, 04 Jun 2013 08:51:31 +0300 bwa (0.6.2-1) unstable; urgency=low [ Carlos Borroto ] * New upstream release [ Andreas Tille ] * debian/control: - versioned Build-Depends debhelper >= 9 - Standards-Version: 3.9.3 (no changes needed) - Add Carlos Borroto as uploader to make sure a package with his changes is not considered as NMU * debian/docs: Add NEWS.Debian * debian/watch: Use SF redirector as suggested by lintian -- Andreas Tille Tue, 26 Jun 2012 09:20:46 +0200 bwa (0.6.1-1) unstable; urgency=low [b794564] New upstream release. [fc9894b] Pass -D_NO_SSE2 everywhere except on amd64 (Closes: #648803). [52312b6] Corrected changelog: 0.6.0-1 was actually uploaded to unstable. -- Charles Plessy Wed, 30 Nov 2011 19:36:04 +0900 bwa (0.6.0-1) unstable; urgency=low [9ce640c] New upstream release (not to use in a production pipeline). [e641dd6] Corrected the name of the file downloaded by uscan. [4ada685] Pass Dpkg build flags to the compiler through Debhelper 9. Thanks, Niels Thykier! -- Charles Plessy Mon, 14 Nov 2011 19:28:44 +0900 bwa (0.5.10-1) unstable; urgency=low [a01f6ca] New upstream release. [6d7bc7f] Conforms with Debian Policy version 3.9.2. [125c73d] Corrected Vcs-Git URL. [37f43c9] Normalised machine-readable copyright file with config-edit. [4e2e0d0] Distribute xa2multi.pl in ‘usr/share/bwa’. [b106d64] Removed redundant ChangeLog file, already installed by Debhelper. -- Charles Plessy Mon, 14 Nov 2011 13:12:50 +0900 bwa (0.5.9-2) unstable; urgency=low * Watchfile should not regard rc releases. * Drop cdbs in favour of dh -- Andreas Tille Fri, 11 Mar 2011 22:49:07 +0100 bwa (0.5.9-1) unstable; urgency=low * New usptream release - Upstream moved to GitHub (debian/upstream-metadata.yaml). - Checked copyright; one file was removed (debian/copyright). * Migrated the Debian source package to Git (debian/control). * Use Debhelper 8 (debian/control, debian/compat). -- Charles Plessy Tue, 08 Feb 2011 16:11:12 +0900 bwa (0.5.8c-1) unstable; urgency=low * Bug fix release, reverting the scoring system back to the one used in 0.5.7. 0.5.8a/b may produce a CIGAR like 10M2I10M4D2M which should not happen in principle. Such wrong cigars also incur errors in indel calling when samtools is in use (Closes: #601568). * Incremented Standards-Version to reflect conformance with Policy 3.9.1 (debian/control, no changes needed). * debian/copyright updated and reformatted. -- Charles Plessy Wed, 27 Oct 2010 21:14:34 +0900 bwa (0.5.8a-1) unstable; urgency=low * New upstream release. * Use the more convenient viewsvn as VCS-Broswer (debian/control). * Incremented Standards-Version to reflect conformance with Policy 3.9.0 (debian/control, no changes needed). -- Charles Plessy Wed, 30 Jun 2010 10:44:30 +0900 bwa (0.5.7-1) unstable; urgency=low * New upstream release. -- Charles Plessy Tue, 02 Mar 2010 23:33:06 +0900 bwa (0.5.6-1) unstable; urgency=low * New upstream release. * Incremented Standards-Version to reflect conformance with Policy 3.8.4 (debian/control). -- Charles Plessy Wed, 17 Feb 2010 12:48:57 +0900 bwa (0.5.5-1) unstable; urgency=low * New upstream release. * Using Dpkg source format version ‘3.0 (quilt)’ (debian/source/format). -- Charles Plessy Wed, 11 Nov 2009 23:05:19 +0900 bwa (0.5.4-1) unstable; urgency=low * New upstream release, see ‘/usr/share/doc/bwa/NEWS.gz’. * Refreshed debian/copyright. * Reflected the rename of dBWT-Sw to BWA-SW in the package's description (debian/control). -- Charles Plessy Mon, 19 Oct 2009 13:59:42 +0900 bwa (0.5.3-1) unstable; urgency=low * Initial release (Closes: #548719) -- Charles Plessy Thu, 08 Oct 2009 19:20:41 +0900