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#include "ReadAlign.h"
#include "SequenceFuns.h"
#include "Stats.h"
#include "serviceFuns.cpp"
void ReadAlign::mapOneReadSpliceGraph()
{
#ifdef OFF_BEFORE_SEEDING
#warning OFF_BEFORE_SEEDING
nW=0;
return;
#endif
if (Lread<P.outFilterMatchNmin) {//read is too short (trimmed too much?)
mapMarker=MARKER_READ_TOO_SHORT;
trBest->rLength=0; //min good piece length
nW=0;
return;
};
resetN(); //reset aligns counters to 0
//reset/initialize a transcript
trInit->reset();
trInit->Chr=0; trInit->Str=0; trInit->roStr=0; trInit->cStart=0; trInit->gLength=0; //to generate nice output of 0 for non-mapped reads
trInit->iRead=iRead;
trInit->Lread=Lread;
trInit->nExons=0;
trInit->readLengthOriginal=readLengthOriginal;
trInit->readLengthPairOriginal=readLengthPairOriginal;
trInit->readLength=readLength;
trInit->readNmates=readNmates; //not readNends: this is alignment
trInit->readName=readName;
trBest=trInit;
splGraph->findSuperTr(Read1[0], Read1[2], Lread, readName, mapGen);
return;
};
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