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#include "ReadAlign.h"
#include "BAMfunctions.h"
void ReadAlign::chimericDetectionPEmerged(ReadAlign &seRA) {
chimRecord=false;
if (P.pCh.segmentMin==0) {//no chimeric detection requested
return;
};
if (P.pCh.multimapNmax==0) {
// runs old chimeric detection routines.
seRA.multMapSelect(); //this needs to be done for ChimericDetectionOld, may not need it for the new algorithm
seRA.mappedFilter();
chimRecord=seRA.chimericDetectionOld();
if (!chimRecord) {
return;
};
peOverlapChimericSEtoPE(&seRA.trChim[0], &seRA.trChim[1], &trChim[0], &trChim[1]);
chimericDetectionOldOutput();
} else if (trBest->maxScore <= (int) (readLength[0]+readLength[1]) - (int) P.pCh.nonchimScoreDropMin) {//require big enough drop in the best score
// new chimeric detection routine
chimRecord=seRA.chimDet->chimericDetectionMult(seRA.nW, seRA.readLength, seRA.trBest->maxScore, this);
};
if ( chimRecord ) {
statsRA.chimericAll++;
};
return;
};
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