bowtie (1.1.1-2) unstable; urgency=high

  * Team upload.
  * Install missing commands.  Closes: #776881.

 -- Charles Plessy <plessy@debian.org>  Tue, 03 Feb 2015 10:44:39 +0900

bowtie (1.1.1-1) unstable; urgency=medium

  * New upstream release
  * cme fix dpkg-control
  * Another patch to build with SeqAn 1.4 (Thanks to Gert Wollny)
  * Add Depends: python (also Build-Depends since it is used in tests)

 -- Andreas Tille <tille@debian.org>  Thu, 02 Oct 2014 14:32:50 +0200

bowtie (1.0.1-3) unstable; urgency=medium

  * Drop all architectures except amd64 since there was no success
    in trying to port the code to other architectures.  The portability
    patch introduced in the last revision was droped again
  * debian/copyright: Drop unneeded copyright statements about code that
    was removed from upstream source

 -- Andreas Tille <tille@debian.org>  Mon, 15 Sep 2014 11:00:25 +0200

bowtie (1.0.1-2) unstable; urgency=medium

  * Do not use copy of outdated gcc header file which destroys portability
    to other architectures
    Closes: #756780
  * Add README.Debian informing users about the fact that we ignore copy
    of cpuid.h
  * Add unit tests for build time and autopkgtest
  * Add debian/README.test to explain how to test the package
    Attention: Please take notice of /usr/share/bowtie/README.Debian about
      "Test suite for bowtie created and potential issue with sorting"

 -- Andreas Tille <tille@debian.org>  Wed, 03 Sep 2014 09:50:22 +0200

bowtie (1.0.1-1) unstable; urgency=medium

  * New upstream version (adapted patches)
  * drop debian/get-orig-source but rather remove the SeqAn-1.1 code
    copy via Files-Excluded
  * debian/control: Priority: optional

 -- Andreas Tille <tille@debian.org>  Wed, 30 Jul 2014 13:38:25 +0200

bowtie (1.0.0-6) unstable; urgency=low

  * debian/patches/seqan-popcount.patch: New patch. (Closes: #733398)
  * Version 1.4 of seqan-dev is required now.
  * Standards-Version: 3.9.5 (no changes needed).
  * Updated Vcs-Svn and Vcs-Browse fields as per Debian-Med policy.

 -- Ognyan Kulev <ogi@debian.org>  Sat, 08 Mar 2014 15:13:16 +0200

bowtie (1.0.0-5) unstable; urgency=low

  * Fixed (hopefully) FTBFS by using override_dh_fixperms-indep target
    instead of override_dh_fixperms in debian/rules.

 -- Ognyan Kulev <ogi@debian.org>  Thu, 30 May 2013 09:41:25 +0300

bowtie (1.0.0-4) unstable; urgency=low

  * Lintian fixes:
    - Removed DM-Upload-Allowed field.
    - Standards Version 3.9.4 (no changes needed).
    - Remove execute bits on some files in bowtie-examples.
  * Don't compress *.ebwt index files in bowtie-examples package.
  * Package description now starts with a capital letter.
  
 -- Ognyan Kulev <ogi@debian.org>  Wed, 29 May 2013 22:53:13 +0300

bowtie (1.0.0-3) unstable; urgency=low

  * New patch no_hash_style_both_for_mips.patch.
    This fixes build errors on mips and mipsel.

 -- Ognyan Kulev <ogi@debian.org>  Wed, 24 Apr 2013 15:15:37 +0300

bowtie (1.0.0-2) unstable; urgency=low

  * Requires version 1.3 of SeqAn.
  * Updated README.source about using Debian's SeqAn library.
  * Removed machine_bits_detection.patch and added disable_bits_flag.patch.

 -- Ognyan Kulev <ogi@debian.org>  Wed, 24 Apr 2013 10:49:47 +0300

bowtie (1.0.0-1) unstable; urgency=low

  * New upstream version. (Closes: #705616)
  * Refreshed patches: use_debian_seqan.patch, use-dpkg-buildflags.patch.
  * Removed patch gcc-4.7.patch (fixed upstream).
  * New patch machine_bits_detection.patch.
  * Added build dependancy on seqan-dev.
  * Activated use_debian_seqan.patch and added the following patches:
    - seqan-fix-setBegin-call.patch
    - seqan-rename-ChunkPool.patch
    - seqan-rename-fill-to-resize.patch
  * Added myself to Uploaders control field.

 -- Ognyan Kulev <ogi@debian.org>  Tue, 23 Apr 2013 16:43:49 +0300

bowtie (0.12.7-3) unstable; urgency=low

  * debian/patches/use-dpkg-buildflags.patch: Regard LDFLAGS/CPPFLAGS
    hardening flags (thanks for the patch to Simon Ruderich
    <simon@ruderich.org>)
    Closes: #670230

 -- Andreas Tille <tille@debian.org>  Tue, 24 Apr 2012 13:21:32 +0200

bowtie (0.12.7-2) unstable; urgency=low

  * Do not give a pointer to non existing info pages in manpages
  * debian/control:
     - fixed Vcs fields
     - Standards-Version: 3.9.3 (no changes needed)
  * debian/upstream: Add citation information
  * debian/rules: calculate pkg name instead of setting it
  * debian/copyright: DEP5 verified using
     cme fix dpkg-copyright
  * debian/patches/gcc-4.7.patch: function "reverseInPlace" is declared after
    the function is used
    Thanks to Rodolfo García Peñas <kix@kix.es> and
    gregor herrmann <gregoa@debian.org>
    Closes: #667120
  * debhelper 9 (control+compat)
    Hardening flags were explicitly tested but not enforced in debian/rules

 -- Andreas Tille <tille@debian.org>  Sun, 22 Apr 2012 21:09:05 +0200

bowtie (0.12.7-1) unstable; urgency=low

  * Initial release (Closes: #604940)

 -- Andreas Tille <tille@debian.org>  Wed, 02 Feb 2011 13:47:12 +0100
