Sync tophat 2.0.12+dfsg-1 (universe) from Debian unstable (main)

[Jackson Doak]

Please sync tophat 2.0.12+dfsg-1 (universe) from Debian unstable (main)

Explanation of the Ubuntu delta and why it can be dropped:
  * Merge from Debian, remaining changes:
    - Link against boost system.
  * Specify multiarch boost libdir location.
Should be fixed in debian

Changelog entries since current utopic version 2.0.10-1ubuntu1:

tophat (2.0.12+dfsg-1) unstable; urgency=medium

  [ Alexandre Mestiashvili ]
  * d/watch: new url
  * Imported Upstream version 2.0.12+dfsg
  * d/patches/fix_build_w_seqan1.4.patch: patch from Manuel Holtgrewe
    resolving #733352.
     removed const_ness_part1.patch as the new patch solves the problem
     completely
    Closes: #733352
  * debian/patches/fix_includes_path.patch: exclude SeqAn-1.3 from configure.ac

 -- Alexandre Mestiashvili <email address hidden> Thu, 03 Jul 2014 21:06:10 +0200

tophat (2.0.11+dfsg-1) UNRELEASED; urgency=medium

  * New upstream version
  * debian/copyright: Update contact
  * Move debian/upstream to debian/upstream/metadata
  * cme fix dpkg-control
  * debian/rules:
     - Make sure boost libraries will be found
     - some more invocations to help2man

 -- Andreas Tille <email address hidden> Tue, 18 Mar 2014 13:54:41 +0100

[Logan Rosen (logan)]

This bug was fixed in the package tophat - 2.0.12+dfsg-1
Sponsored for Jackson Doak (noskcaj)

---------------
tophat (2.0.12+dfsg-1) unstable; urgency=medium

  [ Alexandre Mestiashvili ]
  * d/watch: new url
  * Imported Upstream version 2.0.12+dfsg
  * d/patches/fix_build_w_seqan1.4.patch: patch from Manuel Holtgrewe
    resolving #733352.
     removed const_ness_part1.patch as the new patch solves the problem
     completely
    Closes: #733352
  * debian/patches/fix_includes_path.patch: exclude SeqAn-1.3 from configure.ac

 -- Alexandre Mestiashvili <email address hidden> Thu, 03 Jul 2014 21:06:10 +0200

tophat (2.0.11+dfsg-1) UNRELEASED; urgency=medium

  * New upstream version
  * debian/copyright: Update contact
  * Move debian/upstream to debian/upstream/metadata
  * cme fix dpkg-control
  * debian/rules:
     - Make sure boost libraries will be found
     - some more invocations to help2man

 -- Andreas Tille <email address hidden> Tue, 18 Mar 2014 13:54:41 +0100