[med-svn] [rna-star] branch upstream updated (d874d4b -> 834d1b2)
Andreas Tille
tille at debian.org
Thu May 19 16:16:39 UTC 2016
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tille pushed a change to branch upstream
in repository rna-star.
from d874d4b Imported Upstream version 2.5.1b+dfsg
new 834d1b2 Imported Upstream version 2.5.2a+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:
.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(-)
create mode 100644 source/funCompareUintAndSuffixesMemcmp.cpp
create mode 100644 source/funCompareUintAndSuffixesMemcmp.h
create mode 100644 source/sortSuffixesBucket.cpp
create mode 100644 source/sortSuffixesBucket.h
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