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