source - OpenGrok cross reference for /dports/biology/star/STAR-2.7.9a/source/

Name		Date	Size	#Lines	LOC
..		07-May-2022	-
SimpleGoodTuring/	H	03-May-2022	-	301	151
opal/	H	03-May-2022	-	39,751	34,268
AlignVsTranscript.h	H A D	05-May-2021	170	9	7
BAMbinSortByCoordinate.cpp	H A D	05-May-2021	3.4 KiB	82	64
BAMbinSortByCoordinate.h	H A D	05-May-2021	336	12	9
BAMbinSortUnmapped.cpp	H A D	05-May-2021	3.9 KiB	92	71
BAMbinSortUnmapped.h	H A D	05-May-2021	303	13	9
BAMfunctions.cpp	H A D	03-May-2022	6.6 KiB	195	145
BAMfunctions.h	H A D	05-May-2021	3.2 KiB	79	72
BAMoutput.cpp	H A D	05-May-2021	6.8 KiB	187	146
BAMoutput.h	H A D	05-May-2021	1.2 KiB	38	31
Chain.cpp	H A D	05-May-2021	4.9 KiB	127	93
Chain.h	H A D	05-May-2021	716	30	23
ChimericAlign.cpp	H A D	05-May-2021	1.4 KiB	33	17
ChimericAlign.h	H A D	05-May-2021	1.3 KiB	42	30
ChimericAlign_chimericBAMoutput.cpp	H A D	05-May-2021	5.3 KiB	106	87
ChimericAlign_chimericJunctionOutput.cpp	H A D	05-May-2021	1.7 KiB	24	21
ChimericAlign_chimericStitching.cpp	H A D	05-May-2021	6.4 KiB	182	150
ChimericDetection.cpp	H A D	05-May-2021	390	7	5
ChimericDetection.h	H A D	05-May-2021	772	30	23
ChimericDetection_chimericDetectionMult.cpp	H A D	05-May-2021	6.2 KiB	139	93
ChimericSegment.cpp	H A D	05-May-2021	1.7 KiB	32	22
ChimericSegment.h	H A D	05-May-2021	546	23	18
ChimericTranscript.h	H A D	05-May-2021	488	19	15
ClipCR4.cpp	H A D	05-May-2021	2.8 KiB	110	88
ClipCR4.h	H A D	05-May-2021	806	42	26
ClipMate.h	H A D	05-May-2021	803	34	23
ClipMate_clip.cpp	H A D	05-May-2021	2.3 KiB	79	53
ClipMate_clipChunk.cpp	H A D	05-May-2021	1.9 KiB	62	43
ClipMate_initialize.cpp	H A D	05-May-2021	742	33	25
ErrorWarning.cpp	H A D	05-May-2021	1.3 KiB	38	31
ErrorWarning.h	H A D	05-May-2021	319	10	7
GTF.cpp	H A D	05-May-2021	8 KiB	172	139
GTF.h	H A D	05-May-2021	922	37	29
GTF_superTranscript.cpp	H A D	05-May-2021	11.7 KiB	258	202
GTF_transcriptGeneSJ.cpp	H A D	05-May-2021	8.5 KiB	184	152
Genome.cpp	H A D	05-May-2021	9.4 KiB	224	178
Genome.h	H A D	05-May-2021	4 KiB	108	79
Genome_genomeGenerate.cpp	H A D	05-May-2021	18 KiB	439	338
Genome_genomeLoad.cpp	H A D	05-May-2021	23 KiB	521	398
Genome_genomeOutLoad.cpp	H A D	05-May-2021	2.1 KiB	59	41
Genome_insertSequences.cpp	H A D	05-May-2021	1.3 KiB	34	20
Genome_transformGenome.cpp	H A D	05-May-2021	12.5 KiB	324	244
GlobalVariables.cpp	H A D	05-May-2021	105	5	3
GlobalVariables.h	H A D	05-May-2021	157	10	6
InOutStreams.cpp	H A D	05-May-2021	1,015	45	32
InOutStreams.h	H A D	05-May-2021	540	24	16
IncludeDefine.h	H A D	03-May-2022	5.7 KiB	253	193
Makefile	H A D	03-May-2022	8.7 KiB	193	142
OutSJ.cpp	H A D	05-May-2021	4.6 KiB	115	91
OutSJ.h	H A D	05-May-2021	1.5 KiB	57	41
PackedArray.cpp	H A D	05-May-2021	1.1 KiB	44	35
PackedArray.h	H A D	05-May-2021	788	35	27
ParameterInfo.h	H A D	05-May-2021	3.2 KiB	113	95
Parameters.cpp	H A D	05-May-2021	70.2 KiB	1,261	989
Parameters.h	H A D	05-May-2021	11.4 KiB	366	262
ParametersChimeric.h	H A D	05-May-2021	948	41	31
ParametersChimeric_initialize.cpp	H A D	05-May-2021	5.2 KiB	119	101
ParametersClip.h	H A D	05-May-2021	621	38	27
ParametersClip_initialize.cpp	H A D	05-May-2021	4.8 KiB	100	77
ParametersGenome.cpp	H A D	05-May-2021	2.6 KiB	57	49
ParametersGenome.h	H A D	05-May-2021	1.3 KiB	57	41
ParametersSolo.cpp	H A D	05-May-2021	33.1 KiB	652	535
ParametersSolo.h	H A D	05-May-2021	6.2 KiB	199	139
Parameters_closeReadsFiles.cpp	H A D	05-May-2021	400	12	12
Parameters_openReadsFiles.cpp	H A D	05-May-2021	5 KiB	111	86
Parameters_readFilesInit.cpp	H A D	05-May-2021	8.6 KiB	168	139
Parameters_readSAMheader.cpp	H A D	05-May-2021	1.8 KiB	44	39
Parameters_samAttributes.cpp	H A D	05-May-2021	10.7 KiB	246	227
Quantifications.cpp	H A D	05-May-2021	1.1 KiB	37	32
Quantifications.h	H A D	05-May-2021	662	23	17
ReadAlign.cpp	H A D	05-May-2021	4.5 KiB	119	92
ReadAlign.h	H A D	05-May-2021	9 KiB	236	156
ReadAlignChunk.cpp	H A D	05-May-2021	6 KiB	171	141
ReadAlignChunk.h	H A D	05-May-2021	1.5 KiB	50	39
ReadAlignChunk_mapChunk.cpp	H A D	05-May-2021	6.3 KiB	121	93
ReadAlignChunk_processChunks.cpp	H A D	05-May-2021	16.9 KiB	299	236
ReadAlign_CIGAR.cpp	H A D	05-May-2021	2.7 KiB	62	51
ReadAlign_alignBAM.cpp	H A D	05-May-2021	25.6 KiB	568	460
ReadAlign_assignAlignToWindow.cpp	H A D	05-May-2021	5.2 KiB	131	103
ReadAlign_calcCIGAR.cpp	H A D	05-May-2021	2.2 KiB	58	50
ReadAlign_chimericDetection.cpp	H A D	05-May-2021	1.9 KiB	58	40
ReadAlign_chimericDetectionOld.cpp	H A D	05-May-2021	13.8 KiB	313	252
ReadAlign_chimericDetectionOldOutput.cpp	H A D	05-May-2021	3.6 KiB	75	61
ReadAlign_chimericDetectionPEmerged.cpp	H A D	05-May-2021	1.1 KiB	40	24
ReadAlign_createExtendWindowsWithAlign.cpp	H A D	05-May-2021	3.5 KiB	86	68
ReadAlign_mapOneRead.cpp	H A D	05-May-2021	5.1 KiB	119	80
ReadAlign_mapOneReadSpliceGraph.cpp	H A D	05-May-2021	1.1 KiB	41	32
ReadAlign_mappedFilter.cpp	H A D	05-May-2021	901	21	19
ReadAlign_maxMappableLength2strands.cpp	H A D	05-May-2021	4.4 KiB	108	84
ReadAlign_multMapSelect.cpp	H A D	05-May-2021	3.8 KiB	95	77
ReadAlign_oneRead.cpp	H A D	05-May-2021	4.3 KiB	118	81
ReadAlign_outputAlignments.cpp	H A D	05-May-2021	15 KiB	298	234
ReadAlign_outputSpliceGraphSAM.cpp	H A D	05-May-2021	5.6 KiB	165	115
ReadAlign_outputTranscriptCIGARp.cpp	H A D	05-May-2021	2.7 KiB	66	49
ReadAlign_outputTranscriptSAM.cpp	H A D	05-May-2021	14.3 KiB	360	299
ReadAlign_outputTranscriptSJ.cpp	H A D	05-May-2021	3.2 KiB	57	40
ReadAlign_outputVariation.cpp	H A D	05-May-2021	163	14	8
ReadAlign_peOverlapMergeMap.cpp	H A D	05-May-2021	12.2 KiB	362	231
ReadAlign_quantTranscriptome.cpp	H A D	05-May-2021	4.3 KiB	92	63
ReadAlign_stitchPieces.cpp	H A D	05-May-2021	13.6 KiB	351	232
ReadAlign_stitchWindowSeeds.cpp	H A D	05-May-2021	11.9 KiB	279	203
ReadAlign_storeAligns.cpp	H A D	05-May-2021	5.6 KiB	161	119
ReadAlign_transformGenome.cpp	H A D	05-May-2021	2.8 KiB	72	54
ReadAlign_waspMap.cpp	H A D	05-May-2021	3.4 KiB	105	85
ReadAnnotations.h	H A D	05-May-2021	748	25	14
STAR.cpp	H A D	03-May-2022	9.9 KiB	261	188
SequenceFuns.cpp	H A D	05-May-2021	14 KiB	446	345
SequenceFuns.h	H A D	05-May-2021	1.5 KiB	33	22
SharedMemory.cpp	H A D	03-May-2022	6.3 KiB	291	240
SharedMemory.h	H A D	05-May-2021	3.4 KiB	183	144
SjdbClass.h	H A D	05-May-2021	264	18	13
Solo.cpp	H A D	05-May-2021	2.7 KiB	81	59
Solo.h	H A D	05-May-2021	556	31	21
SoloBarcode.cpp	H A D	05-May-2021	936	29	28
SoloBarcode.h	H A D	05-May-2021	913	27	20
SoloBarcode_extractBarcode.cpp	H A D	05-May-2021	1.1 KiB	35	30
SoloCommon.h	H A D	05-May-2021	385	23	18
SoloFeature.cpp	H A D	05-May-2021	1,001	26	22
SoloFeature.h	H A D	05-May-2021	3.7 KiB	102	76
SoloFeatureTypes.h	H A D	05-May-2021	557	12	8
SoloFeature_addBAMtags.cpp	H A D	05-May-2021	791	26	20
SoloFeature_cellFiltering.cpp	H A D	05-May-2021	5.5 KiB	129	90
SoloFeature_collapseUMI_Graph.cpp	H A D	05-May-2021	6.9 KiB	173	130
SoloFeature_collapseUMIall.cpp	H A D	05-May-2021	13.7 KiB	334	262
SoloFeature_collapseUMIall_multiMappers.cpp	H A D	05-May-2021	26.8 KiB	640	509
SoloFeature_countCBgeneUMI.cpp	H A D	05-May-2021	4 KiB	101	70
SoloFeature_countSmartSeq.cpp	H A D	05-May-2021	6 KiB	160	112
SoloFeature_countVelocyto.cpp	H A D	05-May-2021	7 KiB	162	123
SoloFeature_emptyDrops_CR.cpp	H A D	05-May-2021	10.4 KiB	230	183
SoloFeature_loadRawMatrix.cpp	H A D	05-May-2021	5.8 KiB	142	84
SoloFeature_outputResults.cpp	H A D	05-May-2021	9.1 KiB	207	139
SoloFeature_processRecords.cpp	H A D	05-May-2021	2.9 KiB	81	59
SoloFeature_quantTranscript.cpp	H A D	05-May-2021	14.4 KiB	328	248
SoloFeature_redistributeReadsByCB.cpp	H A D	05-May-2021	2.7 KiB	81	48
SoloFeature_statsOutput.cpp	H A D	05-May-2021	4 KiB	80	61
SoloFeature_sumThreads.cpp	H A D	05-May-2021	3.2 KiB	90	73
SoloFilteredCells.h	H A D	05-May-2021	996	34	28
SoloRead.cpp	H A D	05-May-2021	456	17	12
SoloRead.h	H A D	05-May-2021	455	23	17
SoloReadBarcode.cpp	H A D	05-May-2021	1.3 KiB	52	41
SoloReadBarcode.h	H A D	05-May-2021	1.4 KiB	46	34
SoloReadBarcodeStats.h	H A D	05-May-2021	885	27	23
SoloReadBarcode_getCBandUMI.cpp	H A D	05-May-2021	15 KiB	361	302
SoloReadFeature.cpp	H A D	05-May-2021	1.8 KiB	61	47
SoloReadFeature.h	H A D	05-May-2021	1.2 KiB	48	34
SoloReadFeatureStats.h	H A D	05-May-2021	1.3 KiB	49	32
SoloReadFeature_inputRecords.cpp	H A D	05-May-2021	3.4 KiB	94	80
SoloReadFeature_record.cpp	H A D	05-May-2021	8.9 KiB	199	157
SoloRead_record.cpp	H A D	05-May-2021	387	13	10
SpliceGraph.cpp	H A D	03-May-2022	1 KiB	33	19
SpliceGraph.h	H A D	05-May-2021	1.6 KiB	59	33
SpliceGraph_findSuperTr.cpp	H A D	05-May-2021	7.7 KiB	187	108
SpliceGraph_swScoreSpliced.cpp	H A D	05-May-2021	9.1 KiB	250	142
SpliceGraph_swTraceBack.cpp	H A D	05-May-2021	565	20	0
Stats.cpp	H A D	05-May-2021	8.7 KiB	157	133
Stats.h	H A D	05-May-2021	1.5 KiB	42	29
SuffixArrayFuns.cpp	H A D	03-May-2022	11.7 KiB	411	316
SuffixArrayFuns.h	H A D	05-May-2021	936	19	16
SuperTranscriptome.cpp	H A D	05-May-2021	3.6 KiB	93	72
SuperTranscriptome.h	H A D	05-May-2021	1.2 KiB	43	34
Test.hpp	H A D	05-May-2021	147	14	4
ThreadControl.cpp	H A D	05-May-2021	159	7	5
ThreadControl.h	H A D	05-May-2021	676	30	20
TimeFunctions.cpp	H A D	05-May-2021	581	21	18
TimeFunctions.h	H A D	05-May-2021	168	10	7
Transcript.cpp	H A D	05-May-2021	1.5 KiB	60	44
Transcript.h	H A D	05-May-2021	2.8 KiB	84	60
Transcript_alignScore.cpp	H A D	05-May-2021	2.1 KiB	61	57
Transcript_convertGenomeCigar.cpp	H A D	05-May-2021	6.2 KiB	162	112
Transcript_generateCigarP.cpp	H A D	05-May-2021	2.5 KiB	64	50
Transcript_transformGenome.cpp	H A D	05-May-2021	6.4 KiB	168	128
Transcript_variationAdjust.cpp	H A D	05-May-2021	2.2 KiB	75	55
Transcript_variationOutput.cpp	H A D	05-May-2021	86	7	4
Transcriptome.cpp	H A D	05-May-2021	6.6 KiB	187	157
Transcriptome.h	H A D	05-May-2021	1.9 KiB	61	46
Transcriptome_classifyAlign.cpp	H A D	05-May-2021	11.9 KiB	261	184
Transcriptome_geneCountsAddAlign.cpp	H A D	05-May-2021	2.6 KiB	64	41
Transcriptome_geneFullAlignOverlap.cpp	H A D	05-May-2021	1.2 KiB	34	25
Transcriptome_quantAlign.cpp	H A D	05-May-2021	5.2 KiB	115	99
VERSION	H A D	05-May-2021	30	2	1
Variation.cpp	H A D	05-May-2021	5.6 KiB	152	116
Variation.h	H A D	05-May-2021	1.4 KiB	54	29
bamRemoveDuplicates.cpp	H A D	03-May-2022	9.5 KiB	257	209
bamRemoveDuplicates.h	H A D	05-May-2021	235	11	7
bamSortByCoordinate.cpp	H A D	03-May-2022	4.5 KiB	93	83
bamSortByCoordinate.h	H A D	05-May-2021	256	12	8
bam_cat.c	H A D	03-May-2022	4.6 KiB	144	77
bam_cat.h	H A D	03-May-2022	156	9	5
binarySearch2.cpp	H A D	05-May-2021	928	44	35
binarySearch2.h	H A D	05-May-2021	150	8	5
blocksOverlap.cpp	H A D	05-May-2021	1.3 KiB	42	25
blocksOverlap.h	H A D	05-May-2021	168	11	6
extendAlign.cpp	H A D	05-May-2021	2.4 KiB	94	69
extendAlign.h	H A D	05-May-2021	254	7	4
funCompareUintAndSuffixes.cpp	H A D	05-May-2021	1.3 KiB	41	37
funCompareUintAndSuffixes.h	H A D	05-May-2021	263	12	7
funCompareUintAndSuffixesMemcmp.cpp	H A D	05-May-2021	1.2 KiB	34	24
funCompareUintAndSuffixesMemcmp.h	H A D	05-May-2021	291	10	7
genomeGenerate.h	H A D	05-May-2021	62	5	2
genomeParametersWrite.cpp	H A D	05-May-2021	2 KiB	46	35
genomeParametersWrite.h	H A D	05-May-2021	216	9	6
genomeSAindex.cpp	H A D	05-May-2021	8 KiB	218	111
genomeSAindex.h	H A D	05-May-2021	479	12	9
genomeScanFastaFiles.cpp	H A D	05-May-2021	4.1 KiB	93	79
genomeScanFastaFiles.h	H A D	05-May-2021	231	11	7
insertSeqSA.cpp	H A D	05-May-2021	11.8 KiB	320	131
insertSeqSA.h	H A D	05-May-2021	318	12	8
mapThreadsSpawn.cpp	H A D	05-May-2021	1.7 KiB	34	29
mapThreadsSpawn.h	H A D	05-May-2021	181	7	6
outputSJ.cpp	H A D	05-May-2021	7.1 KiB	160	137
outputSJ.h	H A D	05-May-2021	105	5	4
parametersDefault	H A D	05-May-2021	52.4 KiB	901	685
parametersDefault.xxd	H A D	05-May-2021	323.1 KiB	4,474	4,473
readBarcodeLoad.h	H A D	05-May-2021	203	10	6
readLoad.cpp	H A D	05-May-2021	4.5 KiB	101	81
readLoad.h	H A D	05-May-2021	391	13	9
samHeaders.cpp	H A D	05-May-2021	4 KiB	108	86
samHeaders.h	H A D	05-May-2021	208	10	7
serviceFuns.cpp	H A D	05-May-2021	7.4 KiB	350	239
signalFromBAM.cpp	H A D	05-May-2021	8.4 KiB	210	178
signalFromBAM.h	H A D	03-May-2022	276	14	10
sjAlignSplit.cpp	H A D	05-May-2021	575	16	14
sjAlignSplit.h	H A D	05-May-2021	240	10	6
sjdbBuildIndex.cpp	H A D	05-May-2021	13 KiB	334	223
sjdbBuildIndex.h	H A D	05-May-2021	278	11	7
sjdbInsertJunctions.cpp	H A D	05-May-2021	6 KiB	103	78
sjdbInsertJunctions.h	H A D	05-May-2021	242	11	7
sjdbLoadFromFiles.cpp	H A D	05-May-2021	1.1 KiB	27	21
sjdbLoadFromFiles.h	H A D	05-May-2021	198	11	7
sjdbLoadFromStream.cpp	H A D	05-May-2021	896	29	29
sjdbLoadFromStream.h	H A D	05-May-2021	185	9	6
sjdbPrepare.cpp	H A D	05-May-2021	10.1 KiB	226	185
sjdbPrepare.h	H A D	05-May-2021	241	10	7
soloInputFeatureUMI.cpp	H A D	05-May-2021	1.1 KiB	40	33
soloInputFeatureUMI.h	H A D	05-May-2021	351	12	8
sortSuffixesBucket.h	H A D	05-May-2021	88	3	2
stitchAlignToTranscript.cpp	H A D	05-May-2021	20.2 KiB	416	317
stitchAlignToTranscript.h	H A D	05-May-2021	306	8	5
stitchGapIndel.cpp	H A D	05-May-2021	1.9 KiB	60	48
stitchWindowAligns.cpp	H A D	05-May-2021	15.9 KiB	356	258
stitchWindowAligns.h	H A D	05-May-2021	533	13	9
streamFuns.cpp	H A D	05-May-2021	6.9 KiB	150	124
streamFuns.h	H A D	05-May-2021	847	18	13
stringSubstituteAll.cpp	H A D	05-May-2021	413	11	9
stringSubstituteAll.h	H A D	05-May-2021	178	9	5
sysRemoveDir.cpp	H A D	05-May-2021	677	29	22
sysRemoveDir.h	H A D	05-May-2021	117	8	5
twoPassRunPass1.cpp	H A D	05-May-2021	2.5 KiB	77	52
twoPassRunPass1.h	H A D	05-May-2021	267	11	8