[med-svn] [hilive] branch upstream updated (da4bbd3 -> a0a71e2)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository hilive.

      from  da4bbd3   Imported Upstream version 0.0+20150926
       new  a0a71e2   Imported Upstream version 0.3

The 1 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 +++++++
 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 ++++++++------------------
 23 files changed, 1655 insertions(+), 2022 deletions(-)
 create mode 100644 CONTRIBUTORS
 delete mode 100644 README
 create mode 100644 README.md
 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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