bowtie2 (2.3.0-2ubuntu1) zesty; urgency=medium

  * Cherrypick upstream commits to add support for gcc 6 and fix test
    failures when empty tests are run.
  * Refresh existing patch not to run simple_tests.sh for now.

 -- Bhavani Shankar <bhavi@ubuntu.com>  Fri, 10 Feb 2017 09:31:54 +0530

bowtie2 (2.3.0-2) unstable; urgency=medium

  * Team upload.

  [ Sascha Steinbiss ]
  * Skip tests involving simulated reads to avoid use of non-free build-dep
    libmath-random-perl again.
    Closes: #852546
  * Add libclone-perl build dependency.

  [ Alexandre Mestiashvili ]
  * Add patch suppressing -Wmisleading-indentation warnings.

  [ Steffen Moeller ]
  * Adjust EDAM annotations.

 -- Sascha Steinbiss <satta@debian.org>  Wed, 25 Jan 2017 16:27:13 +0100

bowtie2 (2.3.0-1) unstable; urgency=medium

  * Team upload.

  [ Andreas Tille ]
  * New upstream version
  * Code available on Github
  * debhelper 10
  * Remove Carlos Borroto from Uploaders
  * Remove code from test suite that is requiring non-free package
    libmath-random-perl
  * New Build-Depends to run build time test: liblocal-lib-perl

  [ Sascha Steinbiss ]
  * Even more new Build-Depends: libmath-random-perl, libtest-deep-perl
  * Disable rebuilding during tests

 -- Sascha Steinbiss <satta@debian.org>  Sat, 14 Jan 2017 07:50:51 +0000

bowtie2 (2.2.9-4) unstable; urgency=medium

  * Team upload.
  * Make build reproducible by adding compiler flags
    setting -fdebug-prefix-map.

 -- Sascha Steinbiss <satta@debian.org>  Thu, 25 Aug 2016 12:47:33 +0000

bowtie2 (2.2.9-3) unstable; urgency=medium

  * Team upload.
  * Fix building with GCC 6.
    Closes: #831157.

 -- Sascha Steinbiss <satta@debian.org>  Sat, 16 Jul 2016 03:22:51 +0000

bowtie2 (2.2.9-2) unstable; urgency=medium

  * Team upload.
  * Make build reproducible.
    - Remove embedding of build hostname, time and compiler.
    - Fix help2man wrapper heredoc.
    - Sort wildcard expansions in Makefile.
    - Pin down language settings.

 -- Sascha Steinbiss <sascha@steinbiss.name>  Sat, 21 May 2016 17:18:25 +0000

bowtie2 (2.2.9-1) unstable; urgency=medium

  * Imported Upstream version 2.2.9
  * Bump Standards-Version
  * Revert the commit with applied patch
  * Update hardening.patch
  * Cleanup d/rules, remove CPPFLAGS as they are imported anyway

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Thu, 28 Apr 2016 09:26:48 +0200

bowtie2 (2.2.8-1) unstable; urgency=medium

  [ Andreas Tille ]
  * New upstream version repackaged as xz
  * cme fix dpkg-control

  [ Alexandre Mestiashvili ]
  * Imported Upstream version 2.2.8
  * d/rules: export DEB_BUILD_MAINT_OPTIONS = hardening=+all
  * d/copyright: Merge Files: stanzas and update years

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Sat, 12 Mar 2016 15:57:34 +0100

bowtie2 (2.2.6-2) unstable; urgency=medium

  [ Charles Plessy ]
  * d/rules: quote variables contents passed to Makefile, closes: #809076.

 -- Andreas Tille <tille@debian.org>  Mon, 28 Dec 2015 08:23:51 +0100

bowtie2 (2.2.6-1) unstable; urgency=medium

  * Imported Upstream version 2.2.6
  * d/rules: WITH_TBB=1

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Fri, 28 Aug 2015 09:31:45 +0200

bowtie2 (2.2.5-2) unstable; urgency=medium

  * Upload to unstable

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Tue, 28 Apr 2015 18:06:34 +0200

bowtie2 (2.2.5-1) experimental; urgency=medium

  * Imported Upstream version 2.2.5

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Wed, 18 Mar 2015 10:09:35 +0100

bowtie2 (2.2.4-2) unstable; urgency=medium

  * d/control: add python dependency, needed to build bowtie2-build man page
    Closes: #769934
  * d/watch: fix upstream url parsing, see #766878
  * d/rules: remove byte-compiled bowtie2-buildc

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Tue, 18 Nov 2014 23:28:33 +0100

bowtie2 (2.2.4-1) unstable; urgency=medium

  [ Andreas Tille ]
  * d/control: Priority: optional
  * add missing DEP3 description

  [ Alexandre Mestiashvili ]
  * d/test/binary-run: test that binary work 
  * d/test/control: add binary-run

  [ Andreas Tille ]
  * New upstream version
  * do uscan call directly in debian/rules instead of separate script
  * cme fix dpkg-control

 -- Andreas Tille <tille@debian.org>  Sun, 26 Oct 2014 07:08:46 +0100

bowtie2 (2.2.3-1) unstable; urgency=medium

  * Imported Upstream version 2.2.3

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Tue, 03 Jun 2014 16:13:47 +0200

bowtie2 (2.2.2-1) unstable; urgency=medium

  * Imported Upstream version 2.2.2

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Tue, 15 Apr 2014 13:40:01 +0200

bowtie2 (2.2.1-1) unstable; urgency=medium

  * Imported Upstream version 2.2.1
  * d/changelog: updated Copyright years

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Fri, 07 Mar 2014 09:37:13 +0100

bowtie2 (2.2.0-1) unstable; urgency=medium

  [ Alexandre Mestiashvili ]
  * Imported Upstream version 2.2.0

  [ James McCoy ]
  * Move debian/upstream to debian/upstream/metadata

  [ Alexandre Mestiashvili ]
  * refreshed patches, dropped fix_makefile_machine_detection.patch
  * d/control: bump Standards-Version
    Architecture: amd64 kfreebsd-amd64, starting from this version
    bowtie2 works on amd64 only
    added python to Depends:  
  * d/rules: remove i386 related fixes,rules for new binaries  
  * d/bowtie2.install: added new binaries introduced by the new version  

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Thu, 20 Feb 2014 13:29:58 +0100

bowtie2 (2.1.0-2) unstable; urgency=low

  * Closes: #713000 
  * d/control: fixed description for bowtie2-examples,
     bumped Standards-Version,
     removed DM-Upload-Allowed,
     use canonical vcs
  * d/tests/: underscore are not allowed for tests

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Tue, 25 Jun 2013 13:58:18 +0200

bowtie2 (2.1.0-1) unstable; urgency=low

  * - d/help2man-wrapper: as kindly suggested by Andreas Tille 
    Closes: #701686
    - d/rules: use help2man-wrapper instead of help2man to generate man pages
  * Imported Upstream version 2.1.0
  * refreshed patches

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Wed, 27 Feb 2013 15:58:40 +0100

bowtie2 (2.0.6-1) unstable; urgency=low

  * Imported Upstream version 2.0.6

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Tue, 19 Feb 2013 17:30:42 +0100

bowtie2 (2.0.5-1) unstable; urgency=low

  * Imported Upstream version 2.0.5

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Fri, 11 Jan 2013 11:19:34 +0100

bowtie2 (2.0.4-1) unstable; urgency=low

  * Imported Upstream version 2.0.4

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Thu, 27 Dec 2012 17:33:36 +0100

bowtie2 (2.0.2-1) unstable; urgency=low

  [ Carlos Borroto ]
  * Imported Upstream version 2.0.2
  * bowtie2_gcc4.7.patch no longer needed

  [ Alexandre Mestiashvili ]
  * added autopkgtest testsuite
  * updated Uploaders field

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Mon, 19 Nov 2012 16:31:02 +0100

bowtie2 (2.0.0-beta7-1) unstable; urgency=low

  [ Alexandre Mestiashvili ]
  * debian/control force architcures to i386/amd64 kfreebsd-i386/amd64 and 
    hurd-i386 SSE is not availbale on others. Closes: #668123 
  * debhelper version 9
  * debian/rules forced hardening flags
  * hardening.patch to inject hardening CPPFLAGS
  * Imported Upstream version 2.0.0-beta7
  * debian/bowtie2.lintian-overrides to avoid lintian's waring
    to be fixed by using epochs and tilda in upstream version 

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Mon, 30 Jul 2012 13:51:31 +0200

bowtie2 (2.0.0-beta6-3) unstable; urgency=low

  * normalized architecture detection.
    For example kfreebsd-amd64 is detected as an amd64 architecture 
    and msse flag is set.(Previous commit was wrong) (Closes: #673159)

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Fri, 01 Jun 2012 21:58:49 +0200

bowtie2 (2.0.0-beta6-2) unstable; urgency=low

  * debian/rules normalized output of dpkg-architecture,  
    so for example kfreebsd-amd64 is detected as an amd64 architecture 
    and sse flags are enabled for it.

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Thu, 31 May 2012 19:22:56 +0200

bowtie2 (2.0.0-beta6-1) unstable; urgency=low

  * updated debian/watch and get-orig-source to track -source suffix
  * Imported Upstream version 2.0.0-beta6
  * debian/patches/fix_makefile_machine_detection.patch
    use -msse2 only for Intel architectures, Closes: #672526

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Fri, 11 May 2012 08:41:59 +0200

bowtie2 (2.0.0-beta5-2) unstable; urgency=low

  [ Alexandre Mestiashvili ]
  * file sse_util.h has missing copyright header. 
    The Author (Benjamin Langmead) has
    confirmed that the file is distributed under GPL3 license.

  [ Andreas Tille ]
  * debian/upstream: Added publication
  * debian/patches/fix_makefile_machine_detection.patch + debian/rules:
    prevent -mXX and -msse2 switches for non Intel architectures

  [ Alexandre Mestiashvili ]
  * debian/patches/bowtie2_gcc4.7.patch Closes: #672090
  * updated DEP3 headers
  * bumperd Standards-Version to 3.9.3
  * uname -m doesn't detect 32 bit chroot env - updated patcH

 -- Andreas Tille <tille@debian.org>  Thu, 26 Apr 2012 13:59:54 +0200

bowtie2 (2.0.0-beta5-1) unstable; urgency=low

  [ Alexandre Mestiashvili ]
  * Initial release (Closes: #660762)

 -- Alexandre Mestiashvili <alex@biotec.tu-dresden.de>  Wed, 22 Feb 2012 11:03:03 +0100
