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rna-star 2.7.11b%2Bdfsg-2
  • links: PTS, VCS
  • area: main
  • in suites: forky, sid, trixie
  • size: 3,492 kB
  • sloc: cpp: 21,951; awk: 827; ansic: 457; makefile: 192; sh: 31

Folder: source

d .. (parent)
d d rwxr-xr-x 47 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-- 2,826 ClipCR4.cpp
- - rw-r--r-- 806 ClipCR4.h
- - rw-r--r-- 803 ClipMate.h
- - rw-r--r-- 2,395 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 9,999 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 12,807 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 5,959 IncludeDefine.h
- - rw-r--r-- 9,164 Makefile
- - rw-r--r-- 4,969 OutSJ.cpp
- - rw-r--r-- 1,582 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 72,463 Parameters.cpp
- - rwxr-xr-x 12,025 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-- 5,517 ParametersClip_initialize.cpp
- - rw-r--r-- 2,769 ParametersGenome.cpp
- - rwxr-xr-x 1,492 ParametersGenome.h
- - rwxr-xr-x 37,379 ParametersSolo.cpp
- - rwxr-xr-x 6,964 ParametersSolo.h
- - rw-r--r-- 400 Parameters_closeReadsFiles.cpp
- - rw-r--r-- 5,214 Parameters_openReadsFiles.cpp
- - rw-r--r-- 8,835 Parameters_readFilesInit.cpp
- - rw-r--r-- 1,816 Parameters_readSAMheader.cpp
- - rw-r--r-- 11,899 Parameters_samAttributes.cpp
- - rw-r--r-- 1,126 Quantifications.cpp
- - rw-r--r-- 662 Quantifications.h
- - rwxr-xr-x 4,711 ReadAlign.cpp
- - rwxr-xr-x 9,271 ReadAlign.h
- - rw-r--r-- 6,122 ReadAlignChunk.cpp
- - rw-r--r-- 1,525 ReadAlignChunk.h
- - rw-r--r-- 6,824 ReadAlignChunk_mapChunk.cpp
- - rwxr-xr-x 17,604 ReadAlignChunk_processChunks.cpp
- - rw-r--r-- 2,752 ReadAlign_CIGAR.cpp
- - rwxr-xr-x 27,750 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-- 4,889 ReadAlign_maxMappableLength2strands.cpp
- - rw-r--r-- 3,966 ReadAlign_multMapSelect.cpp
- - rwxr-xr-x 4,534 ReadAlign_oneRead.cpp
- - rwxr-xr-x 16,576 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-- 13,052 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 3,027 ReadAlign_transformGenome.cpp
- - rw-r--r-- 4,071 ReadAlign_waspMap.cpp
- - rw-r--r-- 1,655 ReadAnnotations.h
- - rwxr-xr-x 11,248 STAR.cpp
- - rw-r--r-- 14,323 SequenceFuns.cpp
- - rw-r--r-- 1,539 SequenceFuns.h
- - rw-r--r-- 6,458 SharedMemory.cpp
- - rw-r--r-- 3,504 SharedMemory.h
- - rw-r--r-- 264 SjdbClass.h
- - rwxr-xr-x 3,245 Solo.cpp
- - rw-r--r-- 556 Solo.h
- - rw-r--r-- 6,348 SoloBarcode.cpp
- - rw-r--r-- 1,303 SoloBarcode.h
- - rwxr-xr-x 1,131 SoloBarcode_extractBarcode.cpp
- - rw-r--r-- 2,183 SoloCommon.h
- - rwxr-xr-x 2,207 SoloFeature.cpp
- - rwxr-xr-x 4,028 SoloFeature.h
- - rw-r--r-- 651 SoloFeatureTypes.h
- - rw-r--r-- 791 SoloFeature_addBAMtags.cpp
- - rw-r--r-- 5,796 SoloFeature_cellFiltering.cpp
- - rw-r--r-- 7,027 SoloFeature_collapseUMI_Graph.cpp
- - rw-r--r-- 28,564 SoloFeature_collapseUMIall.cpp
- - rwxr-xr-x 4,751 SoloFeature_countCBgeneUMI.cpp
- - rw-r--r-- 6,184 SoloFeature_countSmartSeq.cpp
- - rw-r--r-- 7,395 SoloFeature_countVelocyto.cpp
- - rw-r--r-- 10,786 SoloFeature_emptyDrops_CR.cpp
- - rw-r--r-- 5,983 SoloFeature_loadRawMatrix.cpp
- - rw-r--r-- 11,196 SoloFeature_outputResults.cpp
- - rwxr-xr-x 3,226 SoloFeature_processRecords.cpp
- - rwxr-xr-x 14,784 SoloFeature_quantTranscript.cpp
- - rw-r--r-- 2,813 SoloFeature_redistributeReadsByCB.cpp
- - rw-r--r-- 5,695 SoloFeature_statsOutput.cpp
- - rw-r--r-- 3,853 SoloFeature_sumThreads.cpp
- - rw-r--r-- 996 SoloFilteredCells.h
- - rwxr-xr-x 581 SoloRead.cpp
- - rwxr-xr-x 481 SoloRead.h
- - rwxr-xr-x 1,290 SoloReadBarcode.cpp
- - rw-r--r-- 1,479 SoloReadBarcode.h
- - rw-r--r-- 933 SoloReadBarcodeStats.h
- - rwxr-xr-x 18,634 SoloReadBarcode_getCBandUMI.cpp
- - rwxr-xr-x 1,991 SoloReadFeature.cpp
- - rwxr-xr-x 1,350 SoloReadFeature.h
- - rw-r--r-- 1,558 SoloReadFeatureStats.h
- - rwxr-xr-x 7,009 SoloReadFeature_inputRecords.cpp
- - rwxr-xr-x 12,482 SoloReadFeature_record.cpp
- - rwxr-xr-x 445 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 7,008 Transcriptome.cpp
- - rwxr-xr-x 2,356 Transcriptome.h
- - rw-r--r-- 10,451 Transcriptome_alignExonOverlap.cpp
- - rwxr-xr-x 12,358 Transcriptome_classifyAlign.cpp
- - rw-r--r-- 2,640 Transcriptome_geneCountsAddAlign.cpp
- - rw-r--r-- 2,321 Transcriptome_geneFullAlignOverlap.cpp
- - rw-r--r-- 1,865 Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp
- - rwxr-xr-x 5,274 Transcriptome_quantAlign.cpp
- - rw-r--r-- 31 VERSION
- - rw-r--r-- 6,139 Variation.cpp
- - rw-r--r-- 1,410 Variation.h
- - rw-r--r-- 10,571 bamRemoveDuplicates.cpp
- - rw-r--r-- 235 bamRemoveDuplicates.h
- - rw-r--r-- 4,818 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-- 2,037 funPrimaryAlignMark.cpp
- - rw-r--r-- 249 funPrimaryAlignMark.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-- 12,040 insertSeqSA.cpp
- - rw-r--r-- 318 insertSeqSA.h
- - rw-r--r-- 1,718 mapThreadsSpawn.cpp
- - rw-r--r-- 181 mapThreadsSpawn.h
- - rw-r--r-- 7,396 outputSJ.cpp
- - rw-r--r-- 105 outputSJ.h
- - rwxr-xr-x 55,492 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-- 7,600 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-- 13,264 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-- 1,354 soloInputFeatureUMI.cpp
- - rw-r--r-- 439 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-- 621 systemFunctions.cpp
- - rw-r--r-- 87 systemFunctions.h
- - rw-r--r-- 3,108 twoPassRunPass1.cpp
- - rw-r--r-- 267 twoPassRunPass1.h