[med-svn] [rna-star] 03/07: Merge tag 'upstream/2.5.2a+dfsg'
Andreas Tille
tille at debian.org
Thu May 19 16:16:38 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository rna-star.
commit 3da8d317010c1e14e9ba71d4f987772364d6e3ea
Merge: 38c7b04 834d1b2
Author: Andreas Tille <tille at debian.org>
Date: Thu May 19 17:59:27 2016 +0200
Merge tag 'upstream/2.5.2a+dfsg'
Upstream version 2.5.2a+dfsg
.gitmodules | 3 -
CHANGES.md | 14 +
README.md | 2 +-
RELEASEnotes.md | 2 +-
source/BAMbinSortByCoordinate.cpp | 16 +-
source/BAMbinSortByCoordinate.h | 2 +-
source/BAMbinSortUnmapped.cpp | 8 +-
source/BAMbinSortUnmapped.h | 2 +-
source/BAMfunctions.cpp | 18 +-
source/BAMoutput.cpp | 54 +-
source/BAMoutput.h | 2 +-
source/ErrorWarning.cpp | 2 +-
source/Genome.cpp | 252 +-
source/Genome.h | 8 +-
source/Genome_insertSequences.cpp | 8 +-
source/InOutStreams.cpp | 20 +-
source/InOutStreams.h | 4 +-
source/IncludeDefine.h | 14 +-
source/Makefile | 2 +-
source/OutSJ.cpp | 16 +-
source/OutSJ.h | 26 +-
source/PackedArray.h | 6 +-
source/ParameterInfo.h | 34 +-
source/Parameters.cpp | 632 +--
source/Parameters.h | 150 +-
source/Parameters_openReadsFiles.cpp | 38 +-
source/Quantifications.cpp | 10 +-
source/Quantifications.h | 6 +-
source/ReadAlign.cpp | 62 +-
source/ReadAlign.h | 70 +-
source/ReadAlignChunk.cpp | 40 +-
source/ReadAlignChunk.h | 8 +-
source/ReadAlignChunk_mapChunk.cpp | 44 +-
source/ReadAlignChunk_processChunks.cpp | 70 +-
source/ReadAlign_alignBAM.cpp | 173 +-
source/ReadAlign_assignAlignToWindow.cpp | 44 +-
source/ReadAlign_chimericDetection.cpp | 108 +-
source/ReadAlign_createExtendWindowsWithAlign.cpp | 22 +-
source/ReadAlign_mapOneRead.cpp | 52 +-
source/ReadAlign_maxMappableLength2strands.cpp | 28 +-
source/ReadAlign_multMapSelect.cpp | 50 +-
source/ReadAlign_oneRead.cpp | 40 +-
source/ReadAlign_outputAlignments.cpp | 173 +-
source/ReadAlign_outputTranscriptCIGARp.cpp | 32 +-
source/ReadAlign_outputTranscriptSAM.cpp | 148 +-
source/ReadAlign_outputTranscriptSJ.cpp | 22 +-
source/ReadAlign_quantTranscriptome.cpp | 36 +-
source/ReadAlign_stitchPieces.cpp | 159 +-
source/ReadAlign_stitchWindowSeeds.cpp | 164 +-
source/ReadAlign_storeAligns.cpp | 46 +-
source/STAR.cpp | 194 +-
source/SequenceFuns.cpp | 38 +-
source/SequenceFuns.h | 2 +-
source/SharedMemory.cpp | 24 +-
source/SharedMemory.h | 6 +-
source/SjdbClass.h | 2 +-
source/Stats.cpp | 26 +-
source/Stats.h | 12 +-
source/SuffixArrayFuns.cpp | 162 +-
source/SuffixArrayFuns.h | 2 +-
source/ThreadControl.h | 8 +-
source/Transcript.cpp | 18 +-
source/Transcript.h | 34 +-
source/Transcript_alignScore.cpp | 8 +-
source/Transcriptome.cpp | 32 +-
source/Transcriptome.h | 6 +-
source/Transcriptome_geneCountsAddAlign.cpp | 26 +-
source/Transcriptome_quantAlign.cpp | 28 +-
source/VERSION | 2 +-
source/alignSmithWaterman.cpp | 76 +-
source/bamRemoveDuplicates.cpp | 54 +-
source/binarySearch2.cpp | 8 +-
source/blocksOverlap.cpp | 14 +-
source/extendAlign.cpp | 28 +-
source/funCompareUintAndSuffixes.cpp | 20 +-
source/funCompareUintAndSuffixes.h | 6 +-
source/funCompareUintAndSuffixesMemcmp.cpp | 33 +
source/funCompareUintAndSuffixesMemcmp.h | 10 +
source/genomeGenerate.cpp | 214 +-
source/genomeParametersWrite.cpp | 12 +-
source/genomeSAindex.cpp | 86 +-
source/genomeScanFastaFiles.cpp | 54 +-
source/insertSeqSA.cpp | 141 +-
source/loadGTF.cpp | 80 +-
source/mapThreadsSpawn.cpp | 8 +-
source/outputSJ.cpp | 26 +-
source/parametersDefault | 72 +-
source/parametersDefault.xxd | 4339 +++++++++++----------
source/readLoad.cpp | 66 +-
source/serviceFuns.cpp | 18 +-
source/signalFromBAM.cpp | 54 +-
source/sjSplitAlign.cpp | 2 +-
source/sjdbBuildIndex.cpp | 108 +-
source/sjdbInsertJunctions.cpp | 26 +-
source/sjdbLoadFromFiles.cpp | 6 +-
source/sjdbLoadFromStream.cpp | 2 +-
source/sjdbPrepare.cpp | 58 +-
source/sortSuffixesBucket.cpp | 100 +
source/sortSuffixesBucket.h | 3 +
source/stitchAlignToTranscript.cpp | 124 +-
source/stitchGapIndel.cpp | 28 +-
source/stitchWindowAligns.cpp | 140 +-
source/streamFuns.cpp | 16 +-
source/sysRemoveDir.cpp | 2 +-
104 files changed, 5032 insertions(+), 4574 deletions(-)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/rna-star.git
More information about the debian-med-commit
mailing list