[med-svn] [giira] 02/04: Merge tag 'upstream/0.0.20140210'

[Andreas Tille]

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tille pushed a commit to branch master
in repository giira.

commit 679bd862ed25d3ac1fe14f96bfd278948c914f4d
Merge: a9bc27b a315672
Author: Andreas Tille <tille at debian.org>
Date:   Mon Feb 10 13:45:16 2014 +0100

    Merge tag 'upstream/0.0.20140210'
    
    Upstream version 0.0.20140210

 src/geneFinder/BWA_Call.java                    |  14 +-
 src/geneFinder/CalculateScores.java             |  10 +-
 src/geneFinder/CigarParser.java                 | 177 ++++++++++
 src/geneFinder/CleanAfterAmbiOpti.java          |   6 +-
 src/geneFinder/GeneFinder.java                  |  18 +-
 src/geneFinder/Giira.java                       |  14 +-
 src/geneFinder/Operon_LP.java                   |   8 +-
 src/geneFinder/OptimizeAmbis.java               |  10 +-
 src/geneFinder/OptimizeAmbis_GLPK.java          | 427 ++++++++++++++++++++++++
 src/geneFinder/PrepareMapping_GF.java           |   4 +-
 src/geneFinder/ProkaryoteExtraction.java        |  13 +-
 src/geneFinder/ReadInParameters_GeneFinder.java |  20 +-
 src/geneFinder/SamParser.java                   |  18 +-
 src/geneFinder/TopHat_Call.java                 |  13 +-
 src/geneFinder/WriteOutput.java                 |  24 +-
 15 files changed, 703 insertions(+), 73 deletions(-)

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