package info (click to toggle)
rna-star 2.7.8a%2Bdfsg-2
  • links: PTS, VCS
  • area: main
  • in suites: bullseye
  • size: 3,076 kB
  • sloc: cpp: 20,429; awk: 483; ansic: 470; makefile: 181; sh: 31

Folder: source

d .. (parent)
d d rwxr-xr-x 35 SimpleGoodTuring
d d rwxr-xr-x 64 opal
- - rw-r--r-- 170 AlignVsTranscript.h
- - rw-r--r-- 3,481 BAMbinSortByCoordinate.cpp
- - rw-r--r-- 336 BAMbinSortByCoordinate.h
- - rw-r--r-- 4,012 BAMbinSortUnmapped.cpp
- - rw-r--r-- 303 BAMbinSortUnmapped.h
- - rw-r--r-- 6,736 BAMfunctions.cpp
- - rw-r--r-- 3,264 BAMfunctions.h
- - rw-r--r-- 7,010 BAMoutput.cpp
- - rw-r--r-- 1,217 BAMoutput.h
- - rw-r--r-- 5,014 Chain.cpp
- - rw-r--r-- 716 Chain.h
- - rw-r--r-- 1,427 ChimericAlign.cpp
- - rw-r--r-- 1,297 ChimericAlign.h
- - rw-r--r-- 5,462 ChimericAlign_chimericBAMoutput.cpp
- - rw-r--r-- 1,790 ChimericAlign_chimericJunctionOutput.cpp
- - rw-r--r-- 6,550 ChimericAlign_chimericStitching.cpp
- - rwxr-xr-x 390 ChimericDetection.cpp
- - rwxr-xr-x 772 ChimericDetection.h
- - rw-r--r-- 6,387 ChimericDetection_chimericDetectionMult.cpp
- - rw-r--r-- 1,745 ChimericSegment.cpp
- - rw-r--r-- 546 ChimericSegment.h
- - rw-r--r-- 488 ChimericTranscript.h
- - rw-r--r-- 2,750 ClipCR4.cpp
- - rw-r--r-- 806 ClipCR4.h
- - rw-r--r-- 803 ClipMate.h
- - rw-r--r-- 2,365 ClipMate_clip.cpp
- - rw-r--r-- 1,925 ClipMate_clipChunk.cpp
- - rw-r--r-- 742 ClipMate_initialize.cpp
- - rw-r--r-- 1,305 ErrorWarning.cpp
- - rw-r--r-- 319 ErrorWarning.h
- - rwxr-xr-x 8,211 GTF.cpp
- - rwxr-xr-x 922 GTF.h
- - rwxr-xr-x 11,934 GTF_superTranscript.cpp
- - rwxr-xr-x 8,662 GTF_transcriptGeneSJ.cpp
- - rwxr-xr-x 9,674 Genome.cpp
- - rwxr-xr-x 4,051 Genome.h
- - rwxr-xr-x 18,425 Genome_genomeGenerate.cpp
- - rwxr-xr-x 23,546 Genome_genomeLoad.cpp
- - rwxr-xr-x 2,168 Genome_genomeOutLoad.cpp
- - rw-r--r-- 1,284 Genome_insertSequences.cpp
- - rwxr-xr-x 12,774 Genome_transformGenome.cpp
- - rw-r--r-- 105 GlobalVariables.cpp
- - rw-r--r-- 157 GlobalVariables.h
- - rw-r--r-- 1,015 InOutStreams.cpp
- - rw-r--r-- 540 InOutStreams.h
- - rwxr-xr-x 5,902 IncludeDefine.h
- - rw-r--r-- 8,406 Makefile
- - rw-r--r-- 4,752 OutSJ.cpp
- - rw-r--r-- 1,491 OutSJ.h
- - rw-r--r-- 1,116 PackedArray.cpp
- - rw-r--r-- 788 PackedArray.h
- - rw-r--r-- 3,239 ParameterInfo.h
- - rwxr-xr-x 69,576 Parameters.cpp
- - rwxr-xr-x 11,603 Parameters.h
- - rw-r--r-- 948 ParametersChimeric.h
- - rwxr-xr-x 5,373 ParametersChimeric_initialize.cpp
- - rw-r--r-- 621 ParametersClip.h
- - rw-r--r-- 4,953 ParametersClip_initialize.cpp
- - rw-r--r-- 2,651 ParametersGenome.cpp
- - rwxr-xr-x 1,356 ParametersGenome.h
- - rwxr-xr-x 33,436 ParametersSolo.cpp
- - rwxr-xr-x 5,094 ParametersSolo.h
- - rw-r--r-- 400 Parameters_closeReadsFiles.cpp
- - rw-r--r-- 5,090 Parameters_openReadsFiles.cpp
- - rw-r--r-- 8,835 Parameters_readFilesInit.cpp
- - rw-r--r-- 1,816 Parameters_readSAMheader.cpp
- - rw-r--r-- 10,883 Parameters_samAttributes.cpp
- - rw-r--r-- 1,126 Quantifications.cpp
- - rw-r--r-- 662 Quantifications.h
- - rwxr-xr-x 4,558 ReadAlign.cpp
- - rwxr-xr-x 9,182 ReadAlign.h
- - rw-r--r-- 5,917 ReadAlignChunk.cpp
- - rw-r--r-- 1,525 ReadAlignChunk.h
- - rw-r--r-- 6,173 ReadAlignChunk_mapChunk.cpp
- - rwxr-xr-x 17,284 ReadAlignChunk_processChunks.cpp
- - rw-r--r-- 2,752 ReadAlign_CIGAR.cpp
- - rwxr-xr-x 25,793 ReadAlign_alignBAM.cpp
- - rw-r--r-- 5,297 ReadAlign_assignAlignToWindow.cpp
- - rw-r--r-- 2,299 ReadAlign_calcCIGAR.cpp
- - rw-r--r-- 1,922 ReadAlign_chimericDetection.cpp
- - rw-r--r-- 14,081 ReadAlign_chimericDetectionOld.cpp
- - rw-r--r-- 3,654 ReadAlign_chimericDetectionOldOutput.cpp
- - rw-r--r-- 1,084 ReadAlign_chimericDetectionPEmerged.cpp
- - rw-r--r-- 3,562 ReadAlign_createExtendWindowsWithAlign.cpp
- - rw-r--r-- 5,255 ReadAlign_mapOneRead.cpp
- - rwxr-xr-x 1,151 ReadAlign_mapOneReadSpliceGraph.cpp
- - rw-r--r-- 901 ReadAlign_mappedFilter.cpp
- - rw-r--r-- 4,546 ReadAlign_maxMappableLength2strands.cpp
- - rw-r--r-- 3,930 ReadAlign_multMapSelect.cpp
- - rwxr-xr-x 4,377 ReadAlign_oneRead.cpp
- - rwxr-xr-x 15,120 ReadAlign_outputAlignments.cpp
- - rwxr-xr-x 5,728 ReadAlign_outputSpliceGraphSAM.cpp
- - rw-r--r-- 2,786 ReadAlign_outputTranscriptCIGARp.cpp
- - rwxr-xr-x 14,615 ReadAlign_outputTranscriptSAM.cpp
- - rw-r--r-- 3,265 ReadAlign_outputTranscriptSJ.cpp
- - rw-r--r-- 163 ReadAlign_outputVariation.cpp
- - rw-r--r-- 12,450 ReadAlign_peOverlapMergeMap.cpp
- - rw-r--r-- 4,424 ReadAlign_quantTranscriptome.cpp
- - rwxr-xr-x 13,936 ReadAlign_stitchPieces.cpp
- - rwxr-xr-x 12,229 ReadAlign_stitchWindowSeeds.cpp
- - rw-r--r-- 5,747 ReadAlign_storeAligns.cpp
- - rwxr-xr-x 2,844 ReadAlign_transformGenome.cpp
- - rw-r--r-- 3,457 ReadAlign_waspMap.cpp
- - rw-r--r-- 748 ReadAnnotations.h
- - rwxr-xr-x 9,941 STAR.cpp
- - rw-r--r-- 14,326 SequenceFuns.cpp
- - rw-r--r-- 1,539 SequenceFuns.h
- - rw-r--r-- 6,435 SharedMemory.cpp
- - rw-r--r-- 3,504 SharedMemory.h
- - rw-r--r-- 264 SjdbClass.h
- - rwxr-xr-x 2,813 Solo.cpp
- - rw-r--r-- 556 Solo.h
- - rw-r--r-- 936 SoloBarcode.cpp
- - rw-r--r-- 913 SoloBarcode.h
- - rwxr-xr-x 1,131 SoloBarcode_extractBarcode.cpp
- - rw-r--r-- 323 SoloCommon.h
- - rwxr-xr-x 1,001 SoloFeature.cpp
- - rwxr-xr-x 3,539 SoloFeature.h
- - rw-r--r-- 552 SoloFeatureTypes.h
- - rw-r--r-- 791 SoloFeature_addBAMtags.cpp
- - rw-r--r-- 5,454 SoloFeature_cellFiltering.cpp
- - rw-r--r-- 7,027 SoloFeature_collapseUMI_Graph.cpp
- - rw-r--r-- 14,123 SoloFeature_collapseUMIall.cpp
- - rwxr-xr-x 3,315 SoloFeature_countCBgeneUMI.cpp
- - rw-r--r-- 5,971 SoloFeature_countSmartSeq.cpp
- - rw-r--r-- 7,075 SoloFeature_countVelocyto.cpp
- - rw-r--r-- 10,636 SoloFeature_emptyDrops_CR.cpp
- - rw-r--r-- 5,272 SoloFeature_loadRawMatrix.cpp
- - rw-r--r-- 4,538 SoloFeature_outputResults.cpp
- - rwxr-xr-x 2,462 SoloFeature_processRecords.cpp
- - rwxr-xr-x 14,784 SoloFeature_quantTranscript.cpp
- - rw-r--r-- 2,813 SoloFeature_redistributeReadsByCB.cpp
- - rw-r--r-- 4,108 SoloFeature_statsOutput.cpp
- - rw-r--r-- 3,290 SoloFeature_sumThreads.cpp
- - rw-r--r-- 926 SoloFilteredCells.h
- - rwxr-xr-x 456 SoloRead.cpp
- - rwxr-xr-x 455 SoloRead.h
- - rwxr-xr-x 1,290 SoloReadBarcode.cpp
- - rw-r--r-- 1,416 SoloReadBarcode.h
- - rw-r--r-- 885 SoloReadBarcodeStats.h
- - rwxr-xr-x 15,352 SoloReadBarcode_getCBandUMI.cpp
- - rwxr-xr-x 1,816 SoloReadFeature.cpp
- - rwxr-xr-x 1,177 SoloReadFeature.h
- - rw-r--r-- 999 SoloReadFeatureStats.h
- - rwxr-xr-x 3,445 SoloReadFeature_inputRecords.cpp
- - rwxr-xr-x 7,758 SoloReadFeature_record.cpp
- - rwxr-xr-x 387 SoloRead_record.cpp
- - rwxr-xr-x 1,087 SpliceGraph.cpp
- - rwxr-xr-x 1,662 SpliceGraph.h
- - rwxr-xr-x 7,909 SpliceGraph_findSuperTr.cpp
- - rwxr-xr-x 9,283 SpliceGraph_swScoreSpliced.cpp
- - rwxr-xr-x 565 SpliceGraph_swTraceBack.cpp
- - rw-r--r-- 8,945 Stats.cpp
- - rw-r--r-- 1,519 Stats.h
- - rw-r--r-- 12,020 SuffixArrayFuns.cpp
- - rw-r--r-- 936 SuffixArrayFuns.h
- - rwxr-xr-x 3,706 SuperTranscriptome.cpp
- - rwxr-xr-x 1,203 SuperTranscriptome.h
- - rw-r--r-- 147 Test.hpp
- - rw-r--r-- 159 ThreadControl.cpp
- - rw-r--r-- 676 ThreadControl.h
- - rw-r--r-- 581 TimeFunctions.cpp
- - rw-r--r-- 168 TimeFunctions.h
- - rw-r--r-- 1,533 Transcript.cpp
- - rwxr-xr-x 2,867 Transcript.h
- - rw-r--r-- 2,152 Transcript_alignScore.cpp
- - rwxr-xr-x 6,347 Transcript_convertGenomeCigar.cpp
- - rw-r--r-- 2,566 Transcript_generateCigarP.cpp
- - rw-r--r-- 6,516 Transcript_transformGenome.cpp
- - rw-r--r-- 2,291 Transcript_variationAdjust.cpp
- - rw-r--r-- 86 Transcript_variationOutput.cpp
- - rwxr-xr-x 6,725 Transcriptome.cpp
- - rwxr-xr-x 1,992 Transcriptome.h
- - rwxr-xr-x 12,170 Transcriptome_classifyAlign.cpp
- - rw-r--r-- 2,640 Transcriptome_geneCountsAddAlign.cpp
- - rw-r--r-- 1,195 Transcriptome_geneFullAlignOverlap.cpp
- - rwxr-xr-x 5,274 Transcriptome_quantAlign.cpp
- - rw-r--r-- 30 VERSION
- - rw-r--r-- 5,735 Variation.cpp
- - rw-r--r-- 1,397 Variation.h
- - rw-r--r-- 9,361 bamRemoveDuplicates.cpp
- - rw-r--r-- 235 bamRemoveDuplicates.h
- - rw-r--r-- 4,590 bamSortByCoordinate.cpp
- - rw-r--r-- 256 bamSortByCoordinate.h
- - rw-r--r-- 4,686 bam_cat.c
- - rw-r--r-- 156 bam_cat.h
- - rw-r--r-- 928 binarySearch2.cpp
- - rw-r--r-- 150 binarySearch2.h
- - rw-r--r-- 1,330 blocksOverlap.cpp
- - rw-r--r-- 168 blocksOverlap.h
- - rw-r--r-- 2,484 extendAlign.cpp
- - rw-r--r-- 254 extendAlign.h
- - rw-r--r-- 1,338 funCompareUintAndSuffixes.cpp
- - rw-r--r-- 263 funCompareUintAndSuffixes.h
- - rw-r--r-- 1,205 funCompareUintAndSuffixesMemcmp.cpp
- - rw-r--r-- 291 funCompareUintAndSuffixesMemcmp.h
- - rw-r--r-- 62 genomeGenerate.h
- - rwxr-xr-x 2,098 genomeParametersWrite.cpp
- - rw-r--r-- 216 genomeParametersWrite.h
- - rw-r--r-- 8,191 genomeSAindex.cpp
- - rw-r--r-- 479 genomeSAindex.h
- - rw-r--r-- 4,171 genomeScanFastaFiles.cpp
- - rw-r--r-- 231 genomeScanFastaFiles.h
- - rw-r--r-- 12,041 insertSeqSA.cpp
- - rw-r--r-- 318 insertSeqSA.h
- - rw-r--r-- 1,718 mapThreadsSpawn.cpp
- - rw-r--r-- 181 mapThreadsSpawn.h
- - rw-r--r-- 7,239 outputSJ.cpp
- - rw-r--r-- 105 outputSJ.h
- - rwxr-xr-x 52,514 parametersDefault
- - rw-r--r-- 203 readBarcodeLoad.h
- - rw-r--r-- 4,658 readLoad.cpp
- - rw-r--r-- 391 readLoad.h
- - rw-r--r-- 4,145 samHeaders.cpp
- - rw-r--r-- 208 samHeaders.h
- - rw-r--r-- 7,542 serviceFuns.cpp
- - rw-r--r-- 8,583 signalFromBAM.cpp
- - rw-r--r-- 276 signalFromBAM.h
- - rwxr-xr-x 575 sjAlignSplit.cpp
- - rwxr-xr-x 240 sjAlignSplit.h
- - rw-r--r-- 13,262 sjdbBuildIndex.cpp
- - rw-r--r-- 278 sjdbBuildIndex.h
- - rw-r--r-- 6,174 sjdbInsertJunctions.cpp
- - rw-r--r-- 242 sjdbInsertJunctions.h
- - rw-r--r-- 1,167 sjdbLoadFromFiles.cpp
- - rw-r--r-- 198 sjdbLoadFromFiles.h
- - rw-r--r-- 896 sjdbLoadFromStream.cpp
- - rw-r--r-- 185 sjdbLoadFromStream.h
- - rwxr-xr-x 10,315 sjdbPrepare.cpp
- - rw-r--r-- 241 sjdbPrepare.h
- - rw-r--r-- 1,151 soloInputFeatureUMI.cpp
- - rw-r--r-- 351 soloInputFeatureUMI.h
- - rw-r--r-- 88 sortSuffixesBucket.h
- - rw-r--r-- 20,675 stitchAlignToTranscript.cpp
- - rw-r--r-- 306 stitchAlignToTranscript.h
- - rw-r--r-- 1,975 stitchGapIndel.cpp
- - rwxr-xr-x 16,327 stitchWindowAligns.cpp
- - rwxr-xr-x 533 stitchWindowAligns.h
- - rw-r--r-- 7,028 streamFuns.cpp
- - rw-r--r-- 847 streamFuns.h
- - rw-r--r-- 413 stringSubstituteAll.cpp
- - rw-r--r-- 178 stringSubstituteAll.h
- - rw-r--r-- 677 sysRemoveDir.cpp
- - rw-r--r-- 117 sysRemoveDir.h
- - rw-r--r-- 2,528 twoPassRunPass1.cpp
- - rw-r--r-- 267 twoPassRunPass1.h