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satta pushed a commit to branch master
in repository rna-star.
commit 41dd97340ac24151c33036f9bb048bf66ca822a0
Merge: 2a4afac 4d28022
Author: Sascha Steinbiss <sa...@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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