[med-svn] [rna-star] branch upstream updated (16302ab -> 86f7372)

[Andreas Tille]

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

      from  16302ab   Imported Upstream version 2.4.2a+dfsg
       new  86f7372   Imported Upstream version 2.5.0a+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:
 .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 +
 ...awk => sjFromSAMcollapseUandM_inclOverlaps.awk} |   11 +-
 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, 4706 insertions(+), 2415 deletions(-)
 create mode 100644 .travis.yml
 delete mode 100644 CHANGES
 create mode 100644 CHANGES.md
 create mode 100644 Makefile
 delete mode 100644 README
 create mode 100644 README.md
 rename RELEASEnotes => RELEASEnotes.md (75%)
 delete mode 100644 STAR-Fusion-0.1.1/LICENSE
 delete mode 100644 STAR-Fusion-0.1.1/README.md
 delete mode 100755 STAR-Fusion-0.1.1/STAR-Fusion
 delete mode 100644 STAR-Fusion-0.1.1/lib/SAM_entry.pm
 delete mode 100644 STAR-Fusion-0.1.1/lib/SAM_reader.pm
 delete mode 100644 STAR-Fusion-0.1.1/notes
 delete mode 100644 STAR-Fusion-0.1.1/test/Chimeric.out.junction.gz
 delete mode 100644 STAR-Fusion-0.1.1/test/Chimeric.out.sam.gz
 delete mode 100755 STAR-Fusion-0.1.1/test/cleanMe.sh
 delete mode 100755 STAR-Fusion-0.1.1/test/runMe.sh
 create mode 100644 extras/doc-latex/texlive.profile
 create mode 100755 extras/doc-latex/texlive_install.sh
 copy extras/scripts/{sjFromSAMcollapseUandM.awk => sjFromSAMcollapseUandM_inclOverlaps.awk} (83%)
 create mode 100644 source/Genome_insertSequences.cpp
 copy {extras/doc-latex => source}/STARmanual.tex (99%)
 create mode 100644 source/bam_cat.h
 create mode 100644 source/funCompareUintAndSuffixes.cpp
 create mode 100644 source/funCompareUintAndSuffixes.h
 create mode 100644 source/genomeSAindex.cpp
 create mode 100644 source/genomeSAindex.h
 create mode 100644 source/genomeScanFastaFiles.cpp
 create mode 100644 source/genomeScanFastaFiles.h
 create mode 100644 source/insertSeqSA.cpp
 create mode 100644 source/insertSeqSA.h
 create mode 100644 source/parametersDefault.xxd

-- 
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