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- htslib
- AlignVsTranscript.h
- 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
- GTF.cpp
- GTF.h
- GTF_superTranscript.cpp
- GTF_transcriptGeneSJ.cpp
- Genome.cpp
- Genome.h
- Genome_consensusSequence.cpp
- Genome_genomeGenerate.cpp
- Genome_genomeLoad.cpp
- Genome_genomeOutLoad.cpp
- Genome_insertSequences.cpp
- Genome_transformGenome.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
- ParametersChimeric_initialize.cpp
- ParametersGenome.h
- ParametersSolo.cpp
- ParametersSolo.h
- Parameters_closeReadsFiles.cpp
- Parameters_openReadsFiles.cpp
- Parameters_readFilesInit.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_mapOneReadSpliceGraph.cpp
- ReadAlign_mappedFilter.cpp
- ReadAlign_maxMappableLength2strands.cpp
- ReadAlign_multMapSelect.cpp
- ReadAlign_oneRead.cpp
- ReadAlign_outputAlignments.cpp
- ReadAlign_outputSpliceGraphSAM.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_transformGenome.cpp
- ReadAlign_waspMap.cpp
- ReadAnnotations.h
- STAR.cpp
- SequenceFuns.cpp
- SequenceFuns.h
- SharedMemory.cpp
- SharedMemory.h
- SjdbClass.h
- Solo.cpp
- Solo.h
- SoloBarcode.cpp
- SoloBarcode.h
- SoloBarcode_extractBarcode.cpp
- SoloCommon.h
- SoloFeature.cpp
- SoloFeature.h
- SoloFeatureTypes.h
- SoloFeature_addBAMtags.cpp
- SoloFeature_cellFiltering.cpp
- SoloFeature_collapseUMI.cpp
- SoloFeature_countCBgeneUMI.cpp
- SoloFeature_countSmartSeq.cpp
- SoloFeature_countVelocyto.cpp
- SoloFeature_outputResults.cpp
- SoloFeature_processRecords.cpp
- SoloFeature_quantTranscript.cpp
- SoloFeature_redistributeReadsByCB.cpp
- SoloFeature_statsOutput.cpp
- SoloFeature_sumThreads.cpp
- SoloRead.cpp
- SoloRead.h
- SoloReadBarcode.cpp
- SoloReadBarcode.h
- SoloReadBarcodeStats.h
- SoloReadBarcode_getCBandUMI.cpp
- SoloReadFeature.cpp
- SoloReadFeature.h
- SoloReadFeatureStats.h
- SoloReadFeature_inputRecords.cpp
- SoloReadFeature_record.cpp
- SoloRead_record.cpp
- SpliceGraph.cpp
- SpliceGraph.h
- SpliceGraph_findSuperTr.cpp
- SpliceGraph_swScoreSpliced.cpp
- SpliceGraph_swTraceBack.cpp
- Stats.cpp
- Stats.h
- SuffixArrayFuns.cpp
- SuffixArrayFuns.h
- SuperTranscriptome.cpp
- SuperTranscriptome.h
- Test.hpp
- ThreadControl.cpp
- ThreadControl.h
- TimeFunctions.cpp
- TimeFunctions.h
- Transcript.cpp
- Transcript.h
- Transcript_alignScore.cpp
- Transcript_convertGenomeCigar.cpp
- Transcript_generateCigarP.cpp
- Transcript_transformGenome.cpp
- Transcript_variationAdjust.cpp
- Transcript_variationOutput.cpp
- Transcriptome.cpp
- Transcriptome.h
- Transcriptome_classifyAlign.cpp
- Transcriptome_geneCountsAddAlign.cpp
- Transcriptome_geneFullAlignOverlap.cpp
- Transcriptome_quantAlign.cpp
- VERSION
- Variation.cpp
- Variation.h
- bamRemoveDuplicates.cpp
- bamRemoveDuplicates.h
- bamSortByCoordinate.cpp
- bamSortByCoordinate.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
- mapThreadsSpawn.cpp
- mapThreadsSpawn.h
- outputSJ.cpp
- outputSJ.h
- parametersDefault
- parametersDefault.xxd
- readLoad.cpp
- readLoad.h
- samHeaders.cpp
- samHeaders.h
- serviceFuns.cpp
- signalFromBAM.cpp
- signalFromBAM.h
- sjAlignSplit.cpp
- sjAlignSplit.h
- sjdbBuildIndex.cpp
- sjdbBuildIndex.h
- sjdbInsertJunctions.cpp
- sjdbInsertJunctions.h
- sjdbLoadFromFiles.cpp
- sjdbLoadFromFiles.h
- sjdbLoadFromStream.cpp
- sjdbLoadFromStream.h
- sjdbPrepare.cpp
- sjdbPrepare.h
- soloInputFeatureUMI.cpp
- soloInputFeatureUMI.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
- twoPassRunPass1.cpp
- twoPassRunPass1.h
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funCompareUintAndSuffixes.h

New sorting routine for inserting sequence into the genome - fixes th…

May 6, 2016

d93cd79 · May 6, 2016