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#include "ReadAlign.h"
void ReadAlign::calcCIGAR(Transcript const &trOut, uint nMates, uint iExMate, uint leftMate) {
matesCIGAR.clear();
for (uint imate=0;imate<nMates;imate++) {
uint iEx1 = (imate==0 ? 0 : iExMate+1);
uint iEx2 = (imate==0 ? iExMate : trOut.nExons-1);
uint Mate=trOut.exons[iEx1][EX_iFrag];
uint Str= trOut.Str;
samStreamCIGAR.str(std::string());
uint trimL;
if (Str==0 && Mate==0) {
trimL=clipMates[Mate][0].clippedN;
} else if (Str==0 && Mate==1) {
trimL=clipMates[Mate][1].clippedN;
} else if (Str==1 && Mate==0) {
trimL=clipMates[Mate][1].clippedN;
} else {
trimL=clipMates[Mate][0].clippedN;
};
uint trimL1 = trimL + trOut.exons[iEx1][EX_R] - (trOut.exons[iEx1][EX_R]<readLength[leftMate] ? 0 : readLength[leftMate]+1);
if (trimL1>0) {
samStreamCIGAR << trimL1 << "S"; //initial trimming
};
for (uint ii=iEx1;ii<=iEx2;ii++) {
if (ii>iEx1) {//record gaps
uint gapG=trOut.exons[ii][EX_G]-(trOut.exons[ii-1][EX_G]+trOut.exons[ii-1][EX_L]);
uint gapR=trOut.exons[ii][EX_R]-trOut.exons[ii-1][EX_R]-trOut.exons[ii-1][EX_L];
//it's possible to have a D or N and I at the same time
if (gapR>0){
samStreamCIGAR << gapR;
samStreamCIGAR << "I";
};
if (trOut.canonSJ[ii-1]>=0 || trOut.sjAnnot[ii-1]==1) {//junction: N
samStreamCIGAR << gapG;
samStreamCIGAR << "N";
} else if (gapG>0) {//deletion: N
samStreamCIGAR << gapG;
samStreamCIGAR << "D";
};
};
samStreamCIGAR << trOut.exons[ii][EX_L] << "M";
};
uint trimR1=(trOut.exons[iEx1][EX_R]<readLength[leftMate] ? \
readLengthOriginal[leftMate] : readLength[leftMate]+1+readLengthOriginal[Mate]) \
- trOut.exons[iEx2][EX_R]-trOut.exons[iEx2][EX_L] - trimL;
if ( trimR1 > 0 ) {
samStreamCIGAR << trimR1 << "S"; //final trimming
};
matesCIGAR.push_back(samStreamCIGAR.str());
};
};
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