[med-svn] [rna-star] 01/02: Merge tag 'upstream/2.5.3a+dfsg' into experimental

[Sascha Steinbiss]

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satta pushed a commit to branch experimental
in repository rna-star.

commit 5bc6bcade343cc4f8ea77dc6a26cf55b1c81b2b7
Merge: b6ba5fd f253b49
Author: Sascha Steinbiss <satta at debian.org>
Date:   Wed May 31 17:41:15 2017 +0200

    Merge tag 'upstream/2.5.3a+dfsg' into experimental
    
    Upstream version 2.5.3a+dfsg

 .travis.yml                              |   11 +
 CHANGES.md                               |   13 +
 README.md                                |   18 +-
 doc/STARmanual.pdf                       |  Bin 251507 -> 264875 bytes
 extras/doc-latex/STARmanual.tex          |   32 +-
 extras/doc-latex/parametersDefault.tex   |   79 +-
 extras/scripts/tagXSstrandedData.awk     |   35 +
 source/BAMbinSortByCoordinate.cpp        |    2 +-
 source/BAMbinSortUnmapped.cpp            |    2 +-
 source/Chain.cpp                         |  126 +
 source/Chain.h                           |   30 +
 source/Genome.cpp                        |   42 +-
 source/Genome.h                          |    2 +-
 source/IncludeDefine.h                   |    3 +-
 source/Makefile                          |    2 +-
 source/Parameters.cpp                    |  134 +-
 source/Parameters.h                      |   34 +-
 source/ReadAlign_alignBAM.cpp            |   14 +-
 source/ReadAlign_chimericDetection.cpp   |   82 +-
 source/ReadAlign_multMapSelect.cpp       |    5 +-
 source/ReadAlign_outputAlignments.cpp    |    2 +-
 source/ReadAlign_outputTranscriptSAM.cpp |    3 +
 source/STAR.cpp                          |   49 +-
 source/SharedMemory.cpp                  |   10 +-
 source/SharedMemory.h                    |    2 +-
 source/VERSION                           |    2 +-
 source/bamRemoveDuplicates.cpp           |   37 +-
 source/genomeGenerate.cpp                |   11 +-
 source/genomeParametersWrite.cpp         |    6 +
 source/parametersDefault                 |   27 +-
 source/parametersDefault.xxd             | 4548 +++++++++++++++---------------
 31 files changed, 2979 insertions(+), 2384 deletions(-)

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