[med-svn] [rna-star] 02/03: Update upstream source from tag 'upstream/2.5.4a+dfsg'

[Sascha Steinbiss]

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

commit 41dd97340ac24151c33036f9bb048bf66ca822a0
Merge: 2a4afac 4d28022
Author: Sascha Steinbiss <satta at debian.org>
Date:   Fri Jan 26 11:30:24 2018 +0100

    Update upstream source from tag 'upstream/2.5.4a+dfsg'
    
    Update to upstream version '2.5.4a+dfsg'
    with Debian dir 1a6b2ee85b82fee79b1fc3b449fe1c4553660104

 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(-)

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