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#include "IncludeDefine.h"
#include "Parameters.h"
#include "Transcript.h"
#include "ReadAlign.h"
#include "BAMfunctions.h"
#include "blocksOverlap.h"
//#include "SequenceFuns.h"
//#include "stitchWindowAligns.h"
//#include "sjSplitAlign.cpp"
//#include "PackedArray.h"
//#include "alignSpliceGraph.h"
//#include "GlobalVariables.h"
//#include <time.h>
void ReadAlign::chimericDetection() {
chimRecord=false;
if (P.pCh.segmentMin==0) {//no chimeric detection requested
return;
};
if (P.outFilterBySJoutStage>1) {//no chimeric output for stage=2. REVISIT: NOT SURE why
return;
};
//output chains for out-of-STAR chimeric detection
#ifdef OUTPUT_localChains
{
P.inOut->outLocalChains << readName <<"\t"<< Read0[0] <<"\t"<< Read0[1] << "\n";
for (uint iw=0; iw<nW; iw++) {
for (uint itr=0;itr<nWinTr[iw];itr++) {
P.inOut->outLocalChains << trAll[iw][itr]->maxScore<<"\t"<< trAll[iw][itr]->Chr<<"\t"<<trAll[iw][itr]->Str<<"\t"<<trAll[iw][itr]->nExons;
for (uint ib=0;ib<trAll[iw][itr]->nExons;ib++) {
P.inOut->outLocalChains <<"\t"<< trAll[iw][itr]->exons[ib][EX_G]-mapGen.chrStart[trAll[iw][itr]->Chr] \
<<"\t"<< trAll[iw][itr]->exons[ib][EX_R] <<"\t"<< trAll[iw][itr]->exons[ib][EX_L];
};
P.inOut->outLocalChains <<"\n";
};
};
};
#endif
if (P.pCh.multimapNmax==0) {
chimRecord=chimericDetectionOld();
chimericDetectionOldOutput();
} else if (trBest->maxScore <= (int) (readLength[0]+readLength[1]) - (int) P.pCh.nonchimScoreDropMin) {//require big enough drop in the best score
chimRecord=chimDet->chimericDetectionMult(nW, readLength, trBest->maxScore, NULL);
};
if ( chimRecord ) {
statsRA.chimericAll++;
};
return;
};//END
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