[med-svn] [rna-star] branch upstream updated (060cffa -> f253b49)

[Sascha Steinbiss]

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

satta pushed a change to branch upstream
in repository rna-star.

      from  060cffa   Imported Upstream version 2.5.2b+dfsg
       new  f253b49   New upstream version 2.5.3a+dfsg

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:
 .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(-)
 create mode 100644 extras/scripts/tagXSstrandedData.awk
 create mode 100644 source/Chain.cpp
 create mode 100644 source/Chain.h

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