[med-svn] [rna-star] branch upstream updated (86f7372 -> d874d4b)

[Steffen Möller]

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

      from  86f7372   Imported Upstream version 2.5.0a+dfsg
      adds  d874d4b   Imported Upstream version 2.5.1b+dfsg

No new revisions were added by this update.

Summary of changes:
 CHANGES.md                                  |   40 +-
 doc/STARmanual.pdf                          |  Bin 249630 -> 251507 bytes
 extras/doc-latex/STARmanual.tex             |    9 +-
 extras/doc-latex/parametersDefault.tex      |   32 +-
 source/BAMbinSortByCoordinate.cpp           |   14 +-
 source/BAMbinSortByCoordinate.h             |    2 +-
 source/BAMfunctions.cpp                     |    2 +-
 source/Genome.cpp                           |   23 +-
 source/Genome.h                             |    4 +-
 source/Genome_insertSequences.cpp           |    2 +-
 source/Makefile                             |    3 +
 source/Parameters.cpp                       |   52 +-
 source/Parameters.h                         |   11 +-
 source/ReadAlign_alignBAM.cpp               |   30 +-
 source/ReadAlign_chimericDetection.cpp      |   35 +-
 source/ReadAlign_mapOneRead.cpp             |    5 +-
 source/ReadAlign_multMapSelect.cpp          |   81 +-
 source/ReadAlign_outputAlignments.cpp       |  141 +-
 source/ReadAlign_outputTranscriptSAM.cpp    |   34 +-
 source/ReadAlign_quantTranscriptome.cpp     |    3 +
 source/ReadAlign_stitchPieces.cpp           |    2 +-
 source/ReadAlign_stitchWindowSeeds.cpp      |   15 +-
 source/STAR.cpp                             |    7 +-
 source/STARmanual.tex                       |  451 ---
 source/Stats.cpp                            |   12 +-
 source/Stats.h                              |    4 +-
 source/SuffixArrayFuns.cpp                  |   10 +-
 source/SuffixArrayFuns.h                    |    1 -
 source/Transcriptome_geneCountsAddAlign.cpp |    2 +-
 source/Transcriptome_quantAlign.cpp         |    3 +-
 source/VERSION                              |    2 +-
 source/bamRemoveDuplicates.cpp              |    4 +-
 source/blocksOverlap.cpp                    |    2 +-
 source/extendAlign.cpp                      |    4 +-
 source/genomeGenerate.cpp                   |   67 +-
 source/genomeSAindex.cpp                    |   13 +-
 source/parametersDefault                    |   30 +-
 source/parametersDefault.xxd                | 3940 ++++++++++++++-------------
 source/signalFromBAM.cpp                    |    8 +-
 source/sjdbBuildIndex.cpp                   |    2 +
 source/stitchAlignToTranscript.cpp          |    4 +-
 41 files changed, 2502 insertions(+), 2604 deletions(-)
 delete mode 100644 source/STARmanual.tex

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