Change log for bwa package in Ubuntu

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 <email address hidden>  Sun, 06 Mar 2022 21:43:27 +0100

Available diffs

• diff from 0.7.17-6 to 0.7.17-7 (750 bytes)

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 <email address hidden>  Thu, 04 Feb 2021 16:16:02 +0100

Available diffs

• diff from 0.7.17-5 to 0.7.17-6 (48.4 KiB)

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 <email address hidden>  Sat, 18 Apr 2020 20:22:35 +0530

Available diffs

• diff from 0.7.17-4 to 0.7.17-5 (1.5 KiB)

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 <email address hidden>  Sat, 14 Dec 2019 11:38:00 +0100

Available diffs

• diff from 0.7.17-3 to 0.7.17-4 (49.2 KiB)

bwa (0.7.17-3~ubuntu0.19.04.1) disco-security; urgency=medium

  * Sync from debian

 -- Mike Salvatore <email address hidden>  Mon, 05 Aug 2019 14:11:34 -0400

Available diffs

• diff from 0.7.17-2 (in Debian) to 0.7.17-3~ubuntu0.19.04.1 (1.2 KiB)

bwa (0.7.17-1ubuntu0.1) bionic-security; urgency=medium

  * SECURITY UPDATE: Stack buffer overflow via a long sequence name in a .alt
    file
    - debian/patches/CVE-2019-10269.patch: exit if .alt is malformatted
    - CVE-2019-10269

 -- Mike Salvatore <email address hidden>  Mon, 05 Aug 2019 11:36:30 -0400

Available diffs

• diff from 0.7.17-1 (in Debian) to 0.7.17-1ubuntu0.1 (1.2 KiB)

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 <email address hidden>  Sat, 30 Mar 2019 15:18:23 +0100

Available diffs

• diff from 0.7.17-2 to 0.7.17-3 (1.3 KiB)

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 <email address hidden>  Fri, 19 Oct 2018 15:05:09 +0200

Available diffs

• diff from 0.7.17-1 to 0.7.17-2 (1.1 KiB)

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 <email address hidden>  Mon, 13 Nov 2017 15:33:11 +0100

Available diffs

• diff from 0.7.16-1 to 0.7.17-1 (3.9 KiB)

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 <email address hidden>  Mon, 07 Aug 2017 16:50:42 +0200

Available diffs

• diff from 0.7.15-5 to 0.7.16-1 (12.0 KiB)

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 <email address hidden>  Fri, 30 Jun 2017 17:37:35 -0400

Available diffs

• diff from 0.7.15-3 to 0.7.15-5 (1.8 KiB)

bwa (0.7.15-3) unstable; urgency=medium

  * bwa/kseq.h is used by SeqLib so include this into libbwa-dev package

 -- Andreas Tille <email address hidden>  Fri, 27 Jan 2017 14:51:16 +0100

Available diffs

• diff from 0.7.15-2 to 0.7.15-3 (387 bytes)

bwa (0.7.15-2) unstable; urgency=medium

  * Team upload
  * Added testsuite
  * debian/examples directory added

 -- Canberk Koç <email address hidden>  Sun, 26 Jun 2016 01:00:42 +0200

Available diffs

• diff from 0.7.15-1 to 0.7.15-2 (929 bytes)

bwa (0.7.15-1) unstable; urgency=medium

  * New upstream version
  * cme fix dpkg-control
  * better hardening

 -- Andreas Tille <email address hidden>  Fri, 03 Jun 2016 17:53:03 +0200

Available diffs

• diff from 0.7.13-1 to 0.7.15-1 (2.1 KiB)

bwa (0.7.13-1) unstable; urgency=medium

  * New upstream version
  * cme fix dpkg-control

 -- Andreas Tille <email address hidden>  Mon, 14 Mar 2016 13:44:35 +0100

Available diffs

• diff from 0.7.12-5 to 0.7.13-1 (14.6 KiB)

bwa (0.7.12-5) unstable; urgency=medium

  * Make a libbwa-dev package for `salmon`.

 -- Michael R. Crusoe <email address hidden>  Sun, 27 Sep 2015 17:16:04 -0700

Available diffs

• diff from 0.7.12-4 to 0.7.12-5 (1.1 KiB)

bwa (0.7.12-4) unstable; urgency=medium

  * Check exact number of arguments of bwtupdate
    Closes: #715703
  * Fix minor spelling issue

 -- Andreas Tille <email address hidden>  Sun, 12 Jul 2015 15:04:54 +0200

Available diffs

• diff from 0.7.12-3 to 0.7.12-4 (1.0 KiB)

bwa (0.7.12-3) unstable; urgency=medium

  * Enable building on freebsd

 -- Andreas Tille <email address hidden>  Fri, 10 Jul 2015 18:24:53 +0200

Available diffs

• diff from 0.7.12-2 to 0.7.12-3 (556 bytes)

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 <email address hidden>  Sat, 04 Jul 2015 13:00:50 +0900

Available diffs

• diff from 0.7.10-1 to 0.7.12-2 (55.8 KiB)

bwa (0.7.10-1) unstable; urgency=medium


  * New upstream version

 -- Andreas Tille <email address hidden>  Thu, 14 Aug 2014 18:31:43 +0200

Available diffs

• diff from 0.7.9a-1 to 0.7.10-1 (3.1 KiB)

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 <email address hidden>  Fri, 06 Jun 2014 21:54:29 +0200

Available diffs

• diff from 0.7.8-1 to 0.7.9a-1 (57.9 KiB)

bwa (0.7.8-1) unstable; urgency=medium


  * New upstream version

 -- Andreas Tille <email address hidden>  Sun, 13 Apr 2014 08:53:07 +0200

Available diffs

• diff from 0.7.5a-2 to 0.7.8-1 (25.2 KiB)

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 <email address hidden>  Tue, 04 Jun 2013 21:51:41 +0300

Available diffs

• diff from 0.6.2-1 to 0.7.5a-2 (116.6 KiB)
• diff from 0.7.5a-1 to 0.7.5a-2 (1.2 KiB)

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 <email address hidden>  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 <email address hidden>  Tue, 26 Jun 2012 09:20:46 +0200

Available diffs

• diff from 0.6.1-1 (in Ubuntu) to 0.6.2-1 (20.4 KiB)

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.

Available diffs

• diff from 0.5.9-2 to 0.6.1-1 (88.1 KiB)

bwa (0.5.9-2) unstable; urgency=low

  * Watchfile should not regard rc releases.
  * Drop cdbs in favour of dh

Available diffs

• diff from 0.5.8c-1 to 0.5.9-2 (22.2 KiB)

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.
 -- Ubuntu Archive Auto-Sync <email address hidden>   Wed,  27 Oct 2010 15:27:20 +0000

Available diffs

• diff from 0.5.8a-1 to 0.5.8c-1 (17.1 KiB)

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).
 -- Ubuntu Archive Auto-Sync <email address hidden>   Fri,  15 Oct 2010 09:25:55 +0000

Available diffs

• diff from 0.5.7-1 to 0.5.8a-1 (20.6 KiB)

bwa (0.5.7-1) unstable; urgency=low

  * New upstream release.

Available diffs

• diff from 0.5.5-1 to 0.5.7-1 (32.9 KiB)

bwa (0.5.5-1) unstable; urgency=low

  * New upstream release.
  * Using Dpkg source format version ‘3.0 (quilt)’ (debian/source/format).
 -- Ubuntu Archive Auto-Sync <email address hidden>   Fri,  18 Dec 2009 06:42:56 +0000

Available diffs

• diff from 0.5.4-1 to 0.5.5-1 (18.3 KiB)

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).