[med-svn] [hilive] branch upstream updated (a0a71e2 -> 9eef8b7)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository hilive.

      from  a0a71e2   Imported Upstream version 0.3
       new  9eef8b7   New upstream version 1.0

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
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Summary of changes:
 CMakeLists.txt          |  67 ++--
 CONTRIBUTORS            |  12 +-
 LICENSE                 |   2 +-
 README.md               |  80 +++--
 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 ++++
 26 files changed, 4518 insertions(+), 1604 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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