[med-svn] [giira] 02/02: Merge branch 'master' of git+ssh://git.debian.org/git/debian-med/giira

[Olivier Sallou]

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osallou pushed a commit to branch master
in repository giira.

commit 59f525c269da92db041ca3c9f6252e33635f003f
Merge: 3102209 b6617fb
Author: Olivier Sallou <olivier.sallou at debian.org>
Date:   Mon Feb 10 14:02:09 2014 +0100

    Merge branch 'master' of git+ssh://git.debian.org/git/debian-med/giira

 debian/changelog                                   |   2 +-
 debian/get-orig-source                             |  19 +-
 debian/patches/fix_non-ascii_characters.patch      |   6 +-
 .../{remove_cplex_code => remove_cplex_code.patch} |  12 +-
 debian/patches/series                              |   2 +-
 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 +-
 20 files changed, 726 insertions(+), 91 deletions(-)

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