[med-svn] [hilive] 01/02: Merge branch 'master' into debian/jessie-backports

[Andreas Tille]

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tille pushed a commit to branch debian/jessie-backports
in repository hilive.

commit c3173c4b646b1f000eb1290b6e64db6845bd5bde
Merge: 25982b8 419ff2d
Author: Andreas Tille <tille at debian.org>
Date:   Tue Jun 6 16:14:51 2017 +0200

    Merge branch 'master' into debian/jessie-backports

 CMakeLists.txt                        |  102 +++-
 CONTRIBUTORS                          |    8 +
 LICENSE                               |    4 +-
 README                                |   86 ---
 README.md                             |  143 +++++
 debian/changelog                      |   21 +
 debian/compat                         |    2 +-
 debian/control                        |    4 +-
 debian/gbp.conf                       |    3 +
 debian/patches/do_not_set_rpath.patch |   13 +-
 debian/patches/fix_cmath.patch        |   13 -
 debian/patches/series                 |    2 +-
 debian/patches/use_FindSeQan.patch    |   26 +
 debian/watch                          |    6 +-
 lib/alnblock.cpp                      |  359 -----------
 lib/alnblock.h                        |   81 ---
 lib/alnread.cpp                       | 1077 ++++++++++++++++-----------------
 lib/alnread.h                         |   98 +--
 lib/alnstream.cpp                     |  268 +++++---
 lib/alnstream.h                       |   10 +-
 lib/argument_parser.cpp               |  231 +++++++
 lib/argument_parser.h                 |    9 +
 lib/config.h.in                       |    2 +-
 lib/definitions.h                     |  124 ++--
 lib/headers.h                         |    2 +
 lib/kindex.cpp                        |  294 +++------
 lib/kindex.h                          |   31 +-
 lib/tools.cpp                         |  110 ++--
 lib/tools.h                           |   22 +-
 tools/.ann.location                   |    1 -
 tools/build_index.cpp                 |   25 +-
 tools/hilive.cpp                      |  590 +++++-------------
 32 files changed, 1720 insertions(+), 2047 deletions(-)

diff --cc debian/changelog
index e0900dc,741c05b..0aef871
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,23 +1,29 @@@
+ hilive (0.3-2) unstable; urgency=medium
+ 
+   * Adapt path to seqan cmake files
+     Closes: #852850
+ 
+  -- Andreas Tille <tille at debian.org>  Sat, 28 Jan 2017 07:18:15 +0100
+ 
+ hilive (0.3-1) unstable; urgency=medium
+ 
+   [Andreas Tille]
+   * New upstream location with proper tagging, Closes: #833392
+   * debhelper 10
+ 
+   [Gert Wollny] 
+   * d/control: Add libseqan2-dev  and libhts-dev as build dependency 
+   * d/patches/use_...: correct path to cmake modules for FindSeQan
+     an remove forced CXXFLAGS 
+ 
+  -- Andreas Tille <tille at debian.org>  Tue, 06 Dec 2016 09:15:22 +0100
+ 
 +hilive (0.0+20150926-1~bpo8+1) jessie-backports; urgency=medium
 +
 +  * Rebuild for jessie-backports.
 +
 + -- Andreas Tille <tille at debian.org>  Fri, 12 Aug 2016 20:54:18 +0200
 +
  hilive (0.0+20150926-1) unstable; urgency=medium
  
    * Initial release (Closes: #832950)

-- 
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