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htslib
BAMbinSortByCoordinate.cpp
BAMbinSortByCoordinate.h
BAMbinSortUnmapped.cpp
BAMbinSortUnmapped.h
BAMfunctions.cpp
BAMfunctions.h
BAMoutput.cpp
BAMoutput.h
Chain.cpp
Chain.h
ChimericAlign.cpp
ChimericAlign.h
ChimericAlign_chimericJunctionOutput.cpp
ChimericAlign_chimericStitching.cpp
ChimericDetection.cpp
ChimericDetection.h
ChimericDetection_chimericDetectionMult.cpp
ChimericSegment.cpp
ChimericSegment.h
ChimericTranscript.h
ErrorWarning.cpp
ErrorWarning.h
Genome.cpp
Genome.h
Genome_genomeGenerate.cpp
Genome_insertSequences.cpp
GlobalVariables.cpp
GlobalVariables.h
InOutStreams.cpp
InOutStreams.h
IncludeDefine.h
Makefile
OutSJ.cpp
OutSJ.h
PackedArray.cpp
PackedArray.h
ParameterInfo.h
Parameters.cpp
Parameters.h
ParametersChimeric.h
ParametersGenome.h
Parameters_closeReadsFiles.cpp
Parameters_openReadsFiles.cpp
Parameters_readSAMheader.cpp
Quantifications.cpp
Quantifications.h
ReadAlign.cpp
ReadAlign.h
ReadAlignChunk.cpp
ReadAlignChunk.h
ReadAlignChunk_mapChunk.cpp
ReadAlignChunk_processChunks.cpp
ReadAlign_CIGAR.cpp
ReadAlign_alignBAM.cpp
ReadAlign_assignAlignToWindow.cpp
ReadAlign_calcCIGAR.cpp
ReadAlign_chimericDetection.cpp
ReadAlign_chimericDetectionOld.cpp
ReadAlign_chimericDetectionOldOutput.cpp
ReadAlign_chimericDetectionPEmerged.cpp
ReadAlign_createExtendWindowsWithAlign.cpp
ReadAlign_mapOneRead.cpp
ReadAlign_mappedFilter.cpp
ReadAlign_maxMappableLength2strands.cpp
ReadAlign_multMapSelect.cpp
ReadAlign_oneRead.cpp
ReadAlign_outputAlignments.cpp
ReadAlign_outputTranscriptCIGARp.cpp
ReadAlign_outputTranscriptSAM.cpp
ReadAlign_outputTranscriptSJ.cpp
ReadAlign_outputVariation.cpp
ReadAlign_peOverlapMergeMap.cpp
ReadAlign_quantTranscriptome.cpp
ReadAlign_stitchPieces.cpp
ReadAlign_stitchWindowSeeds.cpp
ReadAlign_storeAligns.cpp
ReadAlign_waspMap.cpp
STAR.cpp
SequenceFuns.cpp
SequenceFuns.h
SharedMemory.cpp
SharedMemory.h
SjdbClass.h
Stats.cpp
Stats.h
SuffixArrayFuns.cpp
SuffixArrayFuns.h
ThreadControl.cpp
ThreadControl.h
TimeFunctions.cpp
TimeFunctions.h
Transcript.cpp
Transcript.h
Transcript_alignScore.cpp
Transcript_generateCigarP.cpp
Transcript_variationAdjust.cpp
Transcript_variationOutput.cpp
Transcriptome.cpp
Transcriptome.h
Transcriptome_geneCountsAddAlign.cpp
Transcriptome_quantAlign.cpp
VERSION
Variation.cpp
Variation.h
alignSmithWaterman.cpp
alignSmithWaterman.h
bamRemoveDuplicates.cpp
bamRemoveDuplicates.h
bam_cat.c
bam_cat.h
binarySearch2.cpp
binarySearch2.h
blocksOverlap.cpp
blocksOverlap.h
extendAlign.cpp
extendAlign.h
funCompareUintAndSuffixes.cpp
funCompareUintAndSuffixes.h
funCompareUintAndSuffixesMemcmp.cpp
funCompareUintAndSuffixesMemcmp.h
genomeGenerate.h
genomeParametersWrite.cpp
genomeParametersWrite.h
genomeSAindex.cpp
genomeSAindex.h
genomeScanFastaFiles.cpp
genomeScanFastaFiles.h
insertSeqSA.cpp
insertSeqSA.h
loadGTF.cpp
loadGTF.h
mapThreadsSpawn.cpp
mapThreadsSpawn.h
outputSJ.cpp
outputSJ.h
parametersDefault
parametersDefault.xxd
readLoad.cpp
readLoad.h
serviceFuns.cpp
signalFromBAM.cpp
signalFromBAM.h
sjAlignSplit.cpp
sjdbBuildIndex.cpp
sjdbBuildIndex.h
sjdbInsertJunctions.cpp
sjdbInsertJunctions.h
sjdbLoadFromFiles.cpp
sjdbLoadFromFiles.h
sjdbLoadFromStream.cpp
sjdbLoadFromStream.h
sjdbPrepare.cpp
sjdbPrepare.h
sortSuffixesBucket.h
stitchAlignToTranscript.cpp
stitchAlignToTranscript.h
stitchGapIndel.cpp
stitchWindowAligns.cpp
stitchWindowAligns.h
streamFuns.cpp
streamFuns.h
stringSubstituteAll.cpp
stringSubstituteAll.h
sysRemoveDir.cpp
sysRemoveDir.h