[med-svn] [giira] branch master updated (a9bc27b -> b6617fb)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository giira.

      from  a9bc27b   Merge branch 'master' of git+ssh://git.debian.org/git/debian-med/giira
       new  a315672   Imported Upstream version 0.0.20140210
       new  679bd86   Merge tag 'upstream/0.0.20140210'
       new  c9154d3   Inject new upstream source
       new  b6617fb   Consistent naming of patches; refreshed patch

The 4 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:
 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(-)
 rename debian/patches/{remove_cplex_code => remove_cplex_code.patch} (93%)
 create mode 100755 src/geneFinder/CigarParser.java
 create mode 100755 src/geneFinder/OptimizeAmbis_GLPK.java

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/giira.git