[med-svn] [subread] 04/14: Merge tag 'upstream/1.5.0-p2+dfsg'

[Alex Mestiashvili]

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

malex-guest pushed a commit to branch master
in repository subread.

commit 0d7e546abb14186ac7776f4fc3a2c0824baa8189
Merge: 5e128f5 8b7078e
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Fri Apr 22 15:54:25 2016 +0200

    Merge tag 'upstream/1.5.0-p2+dfsg'
    
    Upstream version 1.5.0-p2+dfsg

 doc/SubreadUsersGuide.tex                          |   20 +-
 src/HelperFunctions.c                              |  148 +++
 src/HelperFunctions.h                              |    1 +
 src/Makefile                                       |    2 +-
 src/Makefile.Linux                                 |    8 +-
 src/SNPCalling.c                                   |   20 +-
 src/core-bigtable.c                                |   40 +-
 src/core-indel.c                                   |   19 +-
 src/core-interface-aligner.c                       |    2 +
 src/core-interface-subjunc.c                       |   20 +-
 src/core-junction.c                                | 1166 ++++++++++++++++----
 src/core.c                                         |  222 ++--
 src/core.h                                         |    3 +-
 src/coverage_calc.c                                |    4 +-
 src/gene-algorithms.c                              |   20 +-
 src/gene-algorithms.h                              |    2 +-
 src/gene-value-index.c                             |   16 +-
 src/global-reassembly.c                            |    5 +-
 src/index-builder.c                                |    2 +
 src/input-files.c                                  |   62 +-
 src/input-files.h                                  |    5 +-
 src/makefile.version                               |    6 +-
 src/propmapped.c                                   |    8 +-
 src/read-repair.c                                  |    6 +-
 src/readSummary.c                                  |  282 +++--
 src/removeDupReads.c                               |    6 +-
 src/sambam-file.c                                  |    6 +
 src/sambam-file.h                                  |    1 +
 src/subread.h                                      |    2 +-
 src/subtools.c                                     |    5 +-
 test/featureCounts/data/corner-EXON-ONLY.ora       |    9 +
 .../data/test-minimum-dup.ora.summary              |   12 -
 test/featureCounts/test_corner_cases.sh            |    1 +
 33 files changed, 1668 insertions(+), 463 deletions(-)

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