[med-svn] [hilive] branch debian/jessie-backports updated (25982b8 -> 9549bea)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

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

      from  25982b8   Rebuild for jessie-backports.
      adds  7c7e152   No working watch file since upstream has no proper versioning
      adds  86233d7   New upstream location with proper tagging
      adds  a0a71e2   Imported Upstream version 0.3
      adds  8b90447   Merge tag 'upstream/0.3'
      adds  a05f984   New upstream version
      adds  a75afba   Adapt patches
      adds  1018f32   Add todo
      adds  ab94565   add a gbp.conf file
      adds  df4205d   d/p/use.. Add patch for correct cmake module path
      adds  5509573   Comment on bug in d/changelog
      adds  05f915d   d/control: Add libhts-dev build dependency
      adds  1cf0055   remove forced CXX flags and add libhts-dev
      adds  6218f47   debhelper 10, upload to unstable
      adds  fec6dc7   Somehow CMakeLists.txt was diverging from upstream branch
      adds  d08efd1   Adapt path to seqan cmake files
      adds  419ff2d   Upload to unstable
       new  c3173c4   Merge branch 'master' into debian/jessie-backports
       new  9549bea   Rebuild for jessie-backports

The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 CMakeLists.txt                        |  102 +++-
 CONTRIBUTORS                          |    8 +
 LICENSE                               |    4 +-
 README                                |   86 ---
 README.md                             |  143 +++++
 debian/changelog                      |   27 +
 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, 1726 insertions(+), 2047 deletions(-)
 create mode 100644 CONTRIBUTORS
 delete mode 100644 README
 create mode 100644 README.md
 create mode 100644 debian/gbp.conf
 delete mode 100644 debian/patches/fix_cmath.patch
 create mode 100644 debian/patches/use_FindSeQan.patch
 delete mode 100644 lib/alnblock.cpp
 delete mode 100644 lib/alnblock.h
 create mode 100644 lib/argument_parser.cpp
 create mode 100644 lib/argument_parser.h
 delete mode 100644 tools/.ann.location

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