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alexdobin

Ready for 2.7.5c .

Aug 17, 2020

aa7bc30 · Aug 17, 2020

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Name		Name	Last commit message	Last commit date
parent directory ..
htslib		htslib
AlignVsTranscript.h		AlignVsTranscript.h
BAMbinSortByCoordinate.cpp		BAMbinSortByCoordinate.cpp
BAMbinSortByCoordinate.h		BAMbinSortByCoordinate.h
BAMbinSortUnmapped.cpp		BAMbinSortUnmapped.cpp
BAMbinSortUnmapped.h		BAMbinSortUnmapped.h
BAMfunctions.cpp		BAMfunctions.cpp
BAMfunctions.h		BAMfunctions.h
BAMoutput.cpp		BAMoutput.cpp
BAMoutput.h		BAMoutput.h
Chain.cpp		Chain.cpp
Chain.h		Chain.h
ChimericAlign.cpp		ChimericAlign.cpp
ChimericAlign.h		ChimericAlign.h
ChimericAlign_chimericJunctionOutput.cpp		ChimericAlign_chimericJunctionOutput.cpp
ChimericAlign_chimericStitching.cpp		ChimericAlign_chimericStitching.cpp
ChimericDetection.cpp		ChimericDetection.cpp
ChimericDetection.h		ChimericDetection.h
ChimericDetection_chimericDetectionMult.cpp		ChimericDetection_chimericDetectionMult.cpp
ChimericSegment.cpp		ChimericSegment.cpp
ChimericSegment.h		ChimericSegment.h
ChimericTranscript.h		ChimericTranscript.h
ErrorWarning.cpp		ErrorWarning.cpp
ErrorWarning.h		ErrorWarning.h
GTF.cpp		GTF.cpp
GTF.h		GTF.h
GTF_superTranscript.cpp		GTF_superTranscript.cpp
GTF_transcriptGeneSJ.cpp		GTF_transcriptGeneSJ.cpp
Genome.cpp		Genome.cpp
Genome.h		Genome.h
Genome_consensusSequence.cpp		Genome_consensusSequence.cpp
Genome_genomeGenerate.cpp		Genome_genomeGenerate.cpp
Genome_genomeLoad.cpp		Genome_genomeLoad.cpp
Genome_genomeOutLoad.cpp		Genome_genomeOutLoad.cpp
Genome_insertSequences.cpp		Genome_insertSequences.cpp
Genome_transformGenome.cpp		Genome_transformGenome.cpp
GlobalVariables.cpp		GlobalVariables.cpp
GlobalVariables.h		GlobalVariables.h
InOutStreams.cpp		InOutStreams.cpp
InOutStreams.h		InOutStreams.h
IncludeDefine.h		IncludeDefine.h
Makefile		Makefile
OutSJ.cpp		OutSJ.cpp
OutSJ.h		OutSJ.h
PackedArray.cpp		PackedArray.cpp
PackedArray.h		PackedArray.h
ParameterInfo.h		ParameterInfo.h
Parameters.cpp		Parameters.cpp
Parameters.h		Parameters.h
ParametersChimeric.h		ParametersChimeric.h
ParametersChimeric_initialize.cpp		ParametersChimeric_initialize.cpp
ParametersGenome.h		ParametersGenome.h
ParametersSolo.cpp		ParametersSolo.cpp
ParametersSolo.h		ParametersSolo.h
Parameters_closeReadsFiles.cpp		Parameters_closeReadsFiles.cpp
Parameters_openReadsFiles.cpp		Parameters_openReadsFiles.cpp
Parameters_readFilesInit.cpp		Parameters_readFilesInit.cpp
Parameters_readSAMheader.cpp		Parameters_readSAMheader.cpp
Quantifications.cpp		Quantifications.cpp
Quantifications.h		Quantifications.h
ReadAlign.cpp		ReadAlign.cpp
ReadAlign.h		ReadAlign.h
ReadAlignChunk.cpp		ReadAlignChunk.cpp
ReadAlignChunk.h		ReadAlignChunk.h
ReadAlignChunk_mapChunk.cpp		ReadAlignChunk_mapChunk.cpp
ReadAlignChunk_processChunks.cpp		ReadAlignChunk_processChunks.cpp
ReadAlign_CIGAR.cpp		ReadAlign_CIGAR.cpp
ReadAlign_alignBAM.cpp		ReadAlign_alignBAM.cpp
ReadAlign_assignAlignToWindow.cpp		ReadAlign_assignAlignToWindow.cpp
ReadAlign_calcCIGAR.cpp		ReadAlign_calcCIGAR.cpp
ReadAlign_chimericDetection.cpp		ReadAlign_chimericDetection.cpp
ReadAlign_chimericDetectionOld.cpp		ReadAlign_chimericDetectionOld.cpp
ReadAlign_chimericDetectionOldOutput.cpp		ReadAlign_chimericDetectionOldOutput.cpp
ReadAlign_chimericDetectionPEmerged.cpp		ReadAlign_chimericDetectionPEmerged.cpp
ReadAlign_createExtendWindowsWithAlign.cpp		ReadAlign_createExtendWindowsWithAlign.cpp
ReadAlign_mapOneRead.cpp		ReadAlign_mapOneRead.cpp
ReadAlign_mapOneReadSpliceGraph.cpp		ReadAlign_mapOneReadSpliceGraph.cpp
ReadAlign_mappedFilter.cpp		ReadAlign_mappedFilter.cpp
ReadAlign_maxMappableLength2strands.cpp		ReadAlign_maxMappableLength2strands.cpp
ReadAlign_multMapSelect.cpp		ReadAlign_multMapSelect.cpp
ReadAlign_oneRead.cpp		ReadAlign_oneRead.cpp
ReadAlign_outputAlignments.cpp		ReadAlign_outputAlignments.cpp
ReadAlign_outputSpliceGraphSAM.cpp		ReadAlign_outputSpliceGraphSAM.cpp
ReadAlign_outputTranscriptCIGARp.cpp		ReadAlign_outputTranscriptCIGARp.cpp
ReadAlign_outputTranscriptSAM.cpp		ReadAlign_outputTranscriptSAM.cpp
ReadAlign_outputTranscriptSJ.cpp		ReadAlign_outputTranscriptSJ.cpp
ReadAlign_outputVariation.cpp		ReadAlign_outputVariation.cpp
ReadAlign_peOverlapMergeMap.cpp		ReadAlign_peOverlapMergeMap.cpp
ReadAlign_quantTranscriptome.cpp		ReadAlign_quantTranscriptome.cpp
ReadAlign_stitchPieces.cpp		ReadAlign_stitchPieces.cpp
ReadAlign_stitchWindowSeeds.cpp		ReadAlign_stitchWindowSeeds.cpp
ReadAlign_storeAligns.cpp		ReadAlign_storeAligns.cpp
ReadAlign_transformGenome.cpp		ReadAlign_transformGenome.cpp
ReadAlign_waspMap.cpp		ReadAlign_waspMap.cpp
ReadAnnotations.h		ReadAnnotations.h
STAR.cpp		STAR.cpp
SequenceFuns.cpp		SequenceFuns.cpp
SequenceFuns.h		SequenceFuns.h
SharedMemory.cpp		SharedMemory.cpp
SharedMemory.h		SharedMemory.h
SjdbClass.h		SjdbClass.h
Solo.cpp		Solo.cpp
Solo.h		Solo.h
SoloBarcode.cpp		SoloBarcode.cpp
SoloBarcode.h		SoloBarcode.h
SoloBarcode_extractBarcode.cpp		SoloBarcode_extractBarcode.cpp
SoloCommon.h		SoloCommon.h
SoloFeature.cpp		SoloFeature.cpp
SoloFeature.h		SoloFeature.h
SoloFeatureTypes.h		SoloFeatureTypes.h
SoloFeature_addBAMtags.cpp		SoloFeature_addBAMtags.cpp
SoloFeature_cellFiltering.cpp		SoloFeature_cellFiltering.cpp
SoloFeature_collapseUMI.cpp		SoloFeature_collapseUMI.cpp
SoloFeature_countCBgeneUMI.cpp		SoloFeature_countCBgeneUMI.cpp
SoloFeature_countSmartSeq.cpp		SoloFeature_countSmartSeq.cpp
SoloFeature_countVelocyto.cpp		SoloFeature_countVelocyto.cpp
SoloFeature_outputResults.cpp		SoloFeature_outputResults.cpp
SoloFeature_processRecords.cpp		SoloFeature_processRecords.cpp
SoloFeature_quantTranscript.cpp		SoloFeature_quantTranscript.cpp
SoloFeature_redistributeReadsByCB.cpp		SoloFeature_redistributeReadsByCB.cpp
SoloFeature_statsOutput.cpp		SoloFeature_statsOutput.cpp
SoloFeature_sumThreads.cpp		SoloFeature_sumThreads.cpp
SoloRead.cpp		SoloRead.cpp
SoloRead.h		SoloRead.h
SoloReadBarcode.cpp		SoloReadBarcode.cpp
SoloReadBarcode.h		SoloReadBarcode.h
SoloReadBarcodeStats.h		SoloReadBarcodeStats.h
SoloReadBarcode_getCBandUMI.cpp		SoloReadBarcode_getCBandUMI.cpp
SoloReadFeature.cpp		SoloReadFeature.cpp
SoloReadFeature.h		SoloReadFeature.h
SoloReadFeatureStats.h		SoloReadFeatureStats.h
SoloReadFeature_inputRecords.cpp		SoloReadFeature_inputRecords.cpp
SoloReadFeature_record.cpp		SoloReadFeature_record.cpp
SoloRead_record.cpp		SoloRead_record.cpp
SpliceGraph.cpp		SpliceGraph.cpp
SpliceGraph.h		SpliceGraph.h
SpliceGraph_findSuperTr.cpp		SpliceGraph_findSuperTr.cpp
SpliceGraph_swScoreSpliced.cpp		SpliceGraph_swScoreSpliced.cpp
SpliceGraph_swTraceBack.cpp		SpliceGraph_swTraceBack.cpp
Stats.cpp		Stats.cpp
Stats.h		Stats.h
SuffixArrayFuns.cpp		SuffixArrayFuns.cpp
SuffixArrayFuns.h		SuffixArrayFuns.h
SuperTranscriptome.cpp		SuperTranscriptome.cpp
SuperTranscriptome.h		SuperTranscriptome.h
Test.hpp		Test.hpp
ThreadControl.cpp		ThreadControl.cpp
ThreadControl.h		ThreadControl.h
TimeFunctions.cpp		TimeFunctions.cpp
TimeFunctions.h		TimeFunctions.h
Transcript.cpp		Transcript.cpp
Transcript.h		Transcript.h
Transcript_alignScore.cpp		Transcript_alignScore.cpp
Transcript_convertGenomeCigar.cpp		Transcript_convertGenomeCigar.cpp
Transcript_generateCigarP.cpp		Transcript_generateCigarP.cpp
Transcript_transformGenome.cpp		Transcript_transformGenome.cpp
Transcript_variationAdjust.cpp		Transcript_variationAdjust.cpp
Transcript_variationOutput.cpp		Transcript_variationOutput.cpp
Transcriptome.cpp		Transcriptome.cpp
Transcriptome.h		Transcriptome.h
Transcriptome_classifyAlign.cpp		Transcriptome_classifyAlign.cpp
Transcriptome_geneCountsAddAlign.cpp		Transcriptome_geneCountsAddAlign.cpp
Transcriptome_geneFullAlignOverlap.cpp		Transcriptome_geneFullAlignOverlap.cpp
Transcriptome_quantAlign.cpp		Transcriptome_quantAlign.cpp
VERSION		VERSION
Variation.cpp		Variation.cpp
Variation.h		Variation.h
bamRemoveDuplicates.cpp		bamRemoveDuplicates.cpp
bamRemoveDuplicates.h		bamRemoveDuplicates.h
bamSortByCoordinate.cpp		bamSortByCoordinate.cpp
bamSortByCoordinate.h		bamSortByCoordinate.h
bam_cat.c		bam_cat.c
bam_cat.h		bam_cat.h
binarySearch2.cpp		binarySearch2.cpp
binarySearch2.h		binarySearch2.h
blocksOverlap.cpp		blocksOverlap.cpp
blocksOverlap.h		blocksOverlap.h
extendAlign.cpp		extendAlign.cpp
extendAlign.h		extendAlign.h
funCompareUintAndSuffixes.cpp		funCompareUintAndSuffixes.cpp
funCompareUintAndSuffixes.h		funCompareUintAndSuffixes.h
funCompareUintAndSuffixesMemcmp.cpp		funCompareUintAndSuffixesMemcmp.cpp
funCompareUintAndSuffixesMemcmp.h		funCompareUintAndSuffixesMemcmp.h
genomeGenerate.h		genomeGenerate.h
genomeParametersWrite.cpp		genomeParametersWrite.cpp
genomeParametersWrite.h		genomeParametersWrite.h
genomeSAindex.cpp		genomeSAindex.cpp
genomeSAindex.h		genomeSAindex.h
genomeScanFastaFiles.cpp		genomeScanFastaFiles.cpp
genomeScanFastaFiles.h		genomeScanFastaFiles.h
insertSeqSA.cpp		insertSeqSA.cpp
insertSeqSA.h		insertSeqSA.h
mapThreadsSpawn.cpp		mapThreadsSpawn.cpp
mapThreadsSpawn.h		mapThreadsSpawn.h
outputSJ.cpp		outputSJ.cpp
outputSJ.h		outputSJ.h
parametersDefault		parametersDefault
parametersDefault.xxd		parametersDefault.xxd
readLoad.cpp		readLoad.cpp
readLoad.h		readLoad.h
samHeaders.cpp		samHeaders.cpp
samHeaders.h		samHeaders.h
serviceFuns.cpp		serviceFuns.cpp
signalFromBAM.cpp		signalFromBAM.cpp
signalFromBAM.h		signalFromBAM.h
sjAlignSplit.cpp		sjAlignSplit.cpp
sjAlignSplit.h		sjAlignSplit.h
sjdbBuildIndex.cpp		sjdbBuildIndex.cpp
sjdbBuildIndex.h		sjdbBuildIndex.h
sjdbInsertJunctions.cpp		sjdbInsertJunctions.cpp
sjdbInsertJunctions.h		sjdbInsertJunctions.h
sjdbLoadFromFiles.cpp		sjdbLoadFromFiles.cpp
sjdbLoadFromFiles.h		sjdbLoadFromFiles.h
sjdbLoadFromStream.cpp		sjdbLoadFromStream.cpp
sjdbLoadFromStream.h		sjdbLoadFromStream.h
sjdbPrepare.cpp		sjdbPrepare.cpp
sjdbPrepare.h		sjdbPrepare.h
soloInputFeatureUMI.cpp		soloInputFeatureUMI.cpp
soloInputFeatureUMI.h		soloInputFeatureUMI.h
sortSuffixesBucket.h		sortSuffixesBucket.h
stitchAlignToTranscript.cpp		stitchAlignToTranscript.cpp
stitchAlignToTranscript.h		stitchAlignToTranscript.h
stitchGapIndel.cpp		stitchGapIndel.cpp
stitchWindowAligns.cpp		stitchWindowAligns.cpp
stitchWindowAligns.h		stitchWindowAligns.h
streamFuns.cpp		streamFuns.cpp
streamFuns.h		streamFuns.h
stringSubstituteAll.cpp		stringSubstituteAll.cpp
stringSubstituteAll.h		stringSubstituteAll.h
sysRemoveDir.cpp		sysRemoveDir.cpp
sysRemoveDir.h		sysRemoveDir.h
twoPassRunPass1.cpp		twoPassRunPass1.cpp
twoPassRunPass1.h		twoPassRunPass1.h
View all files