[med-svn] [rna-star] 02/06: Merge tag 'upstream/2.5.0a+dfsg'

[Andreas Tille]

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

commit 9114a96bb5da7453771dcaf91b1d41d9d91063a7
Merge: 886ad43 86f7372
Author: Andreas Tille <tille at debian.org>
Date:   Thu Dec 31 12:26:46 2015 +0100

    Merge tag 'upstream/2.5.0a+dfsg'
    
    Upstream version 2.5.0a+dfsg

 .travis.yml                                        |    7 +
 CHANGES                                            |  259 ---
 CHANGES.md                                         |  330 +++
 LICENSE                                            |    2 +-
 Makefile                                           |   24 +
 README                                             |   41 -
 README.md                                          |  128 ++
 RELEASEnotes => RELEASEnotes.md                    |   24 +-
 STAR-Fusion-0.1.1/LICENSE                          |   28 -
 STAR-Fusion-0.1.1/README.md                        |  103 -
 STAR-Fusion-0.1.1/STAR-Fusion                      |  755 -------
 STAR-Fusion-0.1.1/lib/SAM_entry.pm                 |  544 -----
 STAR-Fusion-0.1.1/lib/SAM_reader.pm                |  109 -
 STAR-Fusion-0.1.1/notes                            |    1 -
 STAR-Fusion-0.1.1/test/Chimeric.out.junction.gz    |  Bin 237561 -> 0 bytes
 STAR-Fusion-0.1.1/test/Chimeric.out.sam.gz         |  Bin 507939 -> 0 bytes
 STAR-Fusion-0.1.1/test/cleanMe.sh                  |    4 -
 STAR-Fusion-0.1.1/test/runMe.sh                    |    4 -
 doc/STARmanual.pdf                                 |  Bin 242969 -> 249630 bytes
 extras/doc-latex/STARmanual.tex                    |   32 +-
 extras/doc-latex/parametersDefault.tex             |   56 +-
 extras/doc-latex/texlive.profile                   |   33 +
 extras/doc-latex/texlive_install.sh                |   49 +
 .../sjFromSAMcollapseUandM_inclOverlaps.awk        |   55 +
 source/Genome.cpp                                  |   37 +-
 source/Genome.h                                    |    4 +
 source/Genome_insertSequences.cpp                  |   33 +
 source/GlobalVariables.cpp                         |    5 +-
 source/IncludeDefine.h                             |    9 +-
 source/Makefile                                    |  126 +-
 source/Parameters.cpp                              |  159 +-
 source/Parameters.h                                |   44 +-
 source/ReadAlign.cpp                               |    6 +-
 source/ReadAlign.h                                 |   10 +-
 source/ReadAlignChunk.cpp                          |    2 +-
 source/ReadAlignChunk_processChunks.cpp            |    4 +-
 source/ReadAlign_alignBAM.cpp                      |    2 +-
 source/ReadAlign_chimericDetection.cpp             |    7 +-
 source/ReadAlign_multMapSelect.cpp                 |   72 +-
 source/ReadAlign_outputAlignments.cpp              |   32 +-
 source/ReadAlign_outputTranscriptSAM.cpp           |    2 +-
 source/ReadAlign_stitchWindowSeeds.cpp             |   12 +-
 source/STAR.cpp                                    |   47 +-
 {extras/doc-latex => source}/STARmanual.tex        |    2 +-
 source/SuffixArrayFuns.cpp                         |  200 ++
 source/SuffixArrayFuns.h                           |    4 +-
 source/Transcriptome.cpp                           |   14 +-
 source/VERSION                                     |    2 +-
 source/bam_cat.c                                   |    3 +
 source/bam_cat.h                                   |    8 +
 source/extendAlign.cpp                             |   20 +-
 source/extendAlign.h                               |    3 +-
 source/funCompareUintAndSuffixes.cpp               |   40 +
 source/funCompareUintAndSuffixes.h                 |    7 +
 source/genomeGenerate.cpp                          |  344 +--
 source/genomeParametersWrite.cpp                   |    3 +-
 source/genomeSAindex.cpp                           |  265 +++
 source/genomeSAindex.h                             |   10 +
 source/genomeScanFastaFiles.cpp                    |  100 +
 source/genomeScanFastaFiles.h                      |    9 +
 source/insertSeqSA.cpp                             |  280 +++
 source/insertSeqSA.h                               |   10 +
 source/loadGTF.cpp                                 |   22 +-
 source/parametersDefault                           |   44 +-
 source/parametersDefault.xxd                       | 2305 ++++++++++++++++++++
 source/readLoad.cpp                                |   10 +-
 source/serviceFuns.cpp                             |    2 +
 source/sjSplitAlign.cpp                            |    3 +
 source/sjdbBuildIndex.cpp                          |  157 +-
 source/sjdbInsertJunctions.cpp                     |   26 +-
 source/stitchAlignToTranscript.cpp                 |   11 +-
 source/stitchGapIndel.cpp                          |    3 +
 source/stitchWindowAligns.cpp                      |   37 +-
 source/streamFuns.cpp                              |   14 +-
 source/streamFuns.h                                |    6 +-
 75 files changed, 4751 insertions(+), 2414 deletions(-)

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