[med-svn] [rna-star] branch master updated (289dd10 -> b375b42)

[Steffen Möller]

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

      from  289dd10   Upload to unstable
       new  5a83665   Preparation for new upstream version.
       new  d874d4b   Imported Upstream version 2.5.1b+dfsg
       new  ad827dd   Merge tag 'upstream/2.5.1b+dfsg'
       new  8b3467a   Adjusted patches for 2.5.1
       new  b375b42   Description of patches, more verbose changelog

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:
 CHANGES.md                                  |   40 +-
 debian/README.source                        |   11 +
 debian/changelog                            |   12 +
 debian/control                              |    2 +-
 debian/patches/compilationstuff.patch       |   52 +-
 debian/patches/donotuse_own_htslib.patch    |   92 +-
 debian/upstream/edam                        |   24 +
 debian/watch                                |    2 +-
 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 +-
 48 files changed, 2628 insertions(+), 2673 deletions(-)
 create mode 100644 debian/upstream/edam
 delete mode 100644 source/STARmanual.tex

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