[med-svn] [giira] branch upstream updated (979142c -> a315672)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository giira.

      from  979142c   Imported Upstream version 0.0.20131015
       new  a315672   Imported Upstream version 0.0.20140210

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:
 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(-)
 create mode 100755 src/geneFinder/CigarParser.java
 create mode 100755 src/geneFinder/OptimizeAmbis_GLPK.java

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