[med-svn] [rna-star] branch master updated (b6ba5fd -> c17ebd5)

[Sascha Steinbiss]

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

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

      from  b6ba5fd   Corrected EDAM annotation file
       new  909c70a   New upstream version 2.5.3a+dfsg
       new  439a18d   Merge tag 'upstream/2.5.3a+dfsg'
       new  267ee17   new upstream version
       new  ac200ac   upload to unstable
      adds  f253b49   New upstream version 2.5.3a+dfsg
      adds  5bc6bca   Merge tag 'upstream/2.5.3a+dfsg' into experimental
      adds  947a0b4   new upstream release
       new  c17ebd5   Merge remote-tracking branch 'origin/experimental'

The 5 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 +-
 debian/changelog                         |   12 +
 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 +++++++++++++++---------------
 32 files changed, 2991 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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