[med-svn] [hilive] branch master updated (7a67501 -> 6061b61)

[Andreas Tille]

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tille pushed a change to branch master
in repository hilive.

      from  7a67501   New upstream version
       new  9eef8b7   New upstream version 1.0
       new  0a552c2   Updated version 1.0 from 'upstream/1.0'
       new  6061b61   Adapt patches

The 3 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                        |  67 +--
 CONTRIBUTORS                          |  12 +-
 LICENSE                               |   2 +-
 README.md                             |  80 ++--
 debian/patches/do_not_set_rpath.patch |   2 +-
 debian/patches/use_FindSeQan.patch    |  25 +-
 lib/alignmentSettings.h               | 773 ++++++++++++++++++++++++++++++
 lib/alnread.cpp                       | 874 +++++++++++++++++++++++++---------
 lib/alnread.h                         |  91 +++-
 lib/alnstream.cpp                     | 675 +++++++++++++++-----------
 lib/alnstream.h                       |  39 +-
 lib/argument_parser.cpp               | 778 ++++++++++++++++++++++--------
 lib/argument_parser.h                 | 481 ++++++++++++++++++-
 lib/config.h.in                       |   7 -
 lib/definitions.h                     | 378 ++++++++++-----
 lib/global_variables.h                |   7 +
 lib/headers.h                         |   9 +-
 lib/kindex.cpp                        | 263 +++++-----
 lib/kindex.h                          |  36 +-
 lib/parallel.cpp                      | 183 +++----
 lib/parallel.h                        |  80 +++-
 lib/tools.cpp                         | 296 +++++-------
 lib/tools.h                           | 161 +++++--
 lib/tools_static.cpp                  | 181 +++++++
 lib/tools_static.h                    | 171 +++++++
 tools/build_index.cpp                 | 147 ++----
 tools/hilive.cpp                      | 265 +++++++----
 tools/hilive_out.cpp                  |  66 +++
 28 files changed, 4531 insertions(+), 1618 deletions(-)
 create mode 100644 lib/alignmentSettings.h
 delete mode 100644 lib/config.h.in
 create mode 100644 lib/global_variables.h
 create mode 100644 lib/tools_static.cpp
 create mode 100644 lib/tools_static.h
 create mode 100644 tools/hilive_out.cpp

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