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commit 3da8d317010c1e14e9ba71d4f987772364d6e3ea Merge: 38c7b04 834d1b2 Author: Andreas Tille <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
