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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