Searched refs:intronMotifs (Results 1 – 6 of 6) sorted by relevance
5 …if ( (align.intronMotifs[1]==0 && align.intronMotifs[2]==0) || (align.intronMotifs[1]>0 && align.i… in ChimericSegment()7 } else if ( (align.Str==0) == (align.intronMotifs[1]>0)) {//strand the same as RNA. in ChimericSegment()23 segGood = segGood && align.intronMotifs[0]==0; //no non-canonical unannotated juncions. in segmentCheck()
214 trA.intronMotifs[0]=0;trA.intronMotifs[1]=0;trA.intronMotifs[2]=0; in stitchWindowSeeds()219 trA.intronMotifs[trA.sjStr[iex]]++; in stitchWindowSeeds()223 if (trA.intronMotifs[1]>0 && trA.intronMotifs[2]==0) in stitchWindowSeeds()225 else if (trA.intronMotifs[1]==0 && trA.intronMotifs[2]>0) in stitchWindowSeeds()230 …if (trA.intronMotifs[1]>0 && trA.intronMotifs[2]>0 && P.outFilterIntronStrands=="RemoveInconsisten… in stitchWindowSeeds()
22 … && trBest->intronMotifs[0]==0 && (trBest->intronMotifs[1]==0 || trBest->intronMotifs[2]==0) ) ) { in chimericDetectionOld()37 if (trBest->intronMotifs[1]==0 && trBest->intronMotifs[2]==0) {//strand is undefined in chimericDetectionOld()39 } else if ( (trBest->Str==0) == (trBest->intronMotifs[1]>0)) {//strand the same as RNA in chimericDetectionOld()49 …if (trAll[iW][iWt]->intronMotifs[0]>0) continue; //do not stitch a window to itself, or to a windo… in chimericDetectionOld()51 …if (trAll[iW][iWt]->intronMotifs[1]==0 && trAll[iW][iWt]->intronMotifs[2]==0) {//strand is undefin… in chimericDetectionOld()53 …} else if ( (trAll[iW][iWt]->Str==0) == (trAll[iW][iWt]->intronMotifs[1]>0)) {//strand the same as… in chimericDetectionOld()
112 trA.intronMotifs[0]=0;trA.intronMotifs[1]=0;trA.intronMotifs[2]=0; in stitchWindowAligns()118 trA.intronMotifs[trA.sjStr[iex]]++; in stitchWindowAligns()123 if (trA.intronMotifs[1]>0 && trA.intronMotifs[2]==0) in stitchWindowAligns()125 else if (trA.intronMotifs[1]==0 && trA.intronMotifs[2]>0) in stitchWindowAligns()130 …if (trA.intronMotifs[1]>0 && trA.intronMotifs[2]>0 && P.outFilterIntronStrands=="RemoveInconsisten… in stitchWindowAligns()
19 uint intronMotifs[3]; variable
232 intronMotifs[ii]=t.intronMotifs[ii]; in peOverlapSEtoPE()