[med-svn] [rna-star] branch upstream updated (f253b49 -> 4d28022)

[Sascha Steinbiss]

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

      from  f253b49   New upstream version 2.5.3a+dfsg
       new  4d28022   New upstream version 2.5.4a+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:
 CHANGES.md                                         |   18 +
 README.md                                          |   14 +-
 doc/STARmanual.pdf                                 |  Bin 264875 -> 266190 bytes
 extras/doc-latex/convertParDefToLatexTable.awk     |    5 +-
 .../convertParDefToLatexTable.optOptTable.awk      |   46 -
 .../convertParDefToLatexTable.optTable.awk         |   54 -
 extras/doc-latex/parametersDefault.tex             |   52 +-
 extras/doc-latex/texlive.profile                   |   33 -
 extras/doc-latex/texlive_install.sh                |   49 -
 extras/scripts/calcInsertCoverage.awk              |   47 +
 extras/scripts/extractSJfromGTF.sh                 |   10 +
 extras/scripts/mergeLogFinal.awk                   |   34 +
 extras/scripts/mergeSuperContig.awk                |   71 +
 extras/scripts/sjCollapseSamples.awk               |   25 +
 extras/scripts/sjMotif.m                           |   45 +
 extras/scripts/tagXSstrandedData.awk               |   18 +-
 extras/scripts/transcriptTypes.awk                 |   36 +
 extras/scripts/transfragsFromBedGraph.awk          |   26 +
 source/Chain.cpp                                   |    2 +-
 source/Genome.cpp                                  |    6 +-
 source/IncludeDefine.h                             |    4 +-
 source/Makefile                                    |    6 +-
 source/Parameters.cpp                              |   46 +-
 source/Parameters.h                                |   25 +-
 source/Parameters_openReadsFiles.cpp               |   31 +-
 source/Parameters_readSAMheader.cpp                |   37 +
 source/ReadAlign.cpp                               |    1 +
 source/ReadAlign.h                                 |    5 +-
 source/ReadAlignChunk_processChunks.cpp            |   82 +-
 source/ReadAlign_CIGAR.cpp                         |   62 +
 source/ReadAlign_alignBAM.cpp                      |  110 +-
 source/ReadAlign_calcCIGAR.cpp                     |   58 +
 source/ReadAlign_chimericDetection.cpp             |    9 +-
 source/ReadAlign_oneRead.cpp                       |    4 +-
 source/ReadAlign_outputAlignments.cpp              |    2 +
 source/ReadAlign_outputTranscriptSAM.cpp           |   61 +-
 source/ReadAlign_stitchWindowSeeds.cpp             |   32 +-
 source/STAR.cpp                                    |    2 +
 source/SequenceFuns.cpp                            |   43 +
 source/SequenceFuns.h                              |    1 +
 source/VERSION                                     |    2 +-
 source/genomeGenerate.cpp                          |   42 +
 source/parametersDefault                           |   52 +-
 source/parametersDefault.xxd                       | 4625 ++++++++++----------
 source/readLoad.cpp                                |   17 +-
 source/readLoad.h                                  |    2 +-
 source/sjdbPrepare.cpp                             |    2 +-
 source/stitchAlignToTranscript.cpp                 |    4 +-
 source/stitchWindowAligns.cpp                      |   32 +-
 49 files changed, 3363 insertions(+), 2627 deletions(-)
 delete mode 100644 extras/doc-latex/convertParDefToLatexTable.optOptTable.awk
 delete mode 100644 extras/doc-latex/convertParDefToLatexTable.optTable.awk
 delete mode 100644 extras/doc-latex/texlive.profile
 delete mode 100755 extras/doc-latex/texlive_install.sh
 create mode 100644 extras/scripts/calcInsertCoverage.awk
 create mode 100755 extras/scripts/extractSJfromGTF.sh
 create mode 100644 extras/scripts/mergeLogFinal.awk
 create mode 100644 extras/scripts/mergeSuperContig.awk
 create mode 100644 extras/scripts/sjCollapseSamples.awk
 create mode 100644 extras/scripts/sjMotif.m
 create mode 100644 extras/scripts/transcriptTypes.awk
 create mode 100644 extras/scripts/transfragsFromBedGraph.awk
 create mode 100644 source/Parameters_readSAMheader.cpp
 create mode 100644 source/ReadAlign_CIGAR.cpp
 create mode 100644 source/ReadAlign_calcCIGAR.cpp

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