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#include "funPrimaryAlignMark.h"
void funPrimaryAlignMark(Transcript **trMult, uint64 nTr,
Parameters &P, int maxScore, std::uniform_real_distribution<double> rngUniformReal0to1, std::mt19937 rngMultOrder)
{
if (nTr==1){//unique mappers
trMult[0]->primaryFlag=true;
} else {//multimappers
int nbest=0;
if (P.outMultimapperOrder.random || P.outSAMmultNmax != (uint) -1 ) {//bring the best alignment to the top of the list. TODO sort alignments by the score?
for (uint itr=0; itr<nTr; itr++) {//move the best aligns to the top of the list
if ( trMult[itr]->maxScore == maxScore ) {
swap(trMult[itr],trMult[nbest]);
++nbest;
};
};
};
if (P.outMultimapperOrder.random) {//shuffle separately the best aligns, and the rest
for (int itr=nbest-1; itr>=1; itr--) {//Fisher-Yates-Durstenfeld-Knuth shuffle
int rand1=int (rngUniformReal0to1(rngMultOrder)*itr+0.5);
swap(trMult[itr],trMult[rand1]);
};
for (int itr=nTr-nbest-1; itr>=1; itr--) {//Fisher-Yates-Durstenfeld-Knuth shuffle
int rand1=int (rngUniformReal0to1(rngMultOrder)*itr+0.5);
swap(trMult[nbest+itr],trMult[nbest+rand1]);
};
};
if ( P.outSAMprimaryFlag=="AllBestScore" ) {
for (uint itr=0; itr<nTr; itr++)
{//mark all best score aligns as primary
if ( trMult[itr]->maxScore == maxScore ) trMult[itr]->primaryFlag=true;
};
} else if (P.outMultimapperOrder.random || P.outSAMmultNmax != (uint) -1) {
trMult[0]->primaryFlag=true;//mark as primary the first one in the random ordered list: best scoring aligns are already in front of the list
} else {//old way
//trBest->primaryFlag=true; //cannot do it, trBest may not be defined
trMult[0]->primaryFlag=true;
};
};
};
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