- out << ">" << header.name << " length=" << (header.clipQualRight-header.clipQualLeft+1) << endl;
- for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) { out << read.qualScores[i] << '\t'; }
+ if(header.clipQualRight < header.clipQualLeft){
+ out << "0\t0\t0\t0";
+ }
+ else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
+ out << ">" << header.name << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
+ for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) { out << read.qualScores[i] << '\t'; }
+ }
+ else{
+ out << ">" << header.name << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
+ for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) { out << read.qualScores[i] << '\t'; }
+ }