if(errorSeq[i] == 'm') { qualErrorMap['m'][qScores[qIndex]] += weight; }
else if(errorSeq[i] == 's') { qualErrorMap['s'][qScores[qIndex]] += weight; }
else if(errorSeq[i] == 'i') { qualErrorMap['i'][qScores[qIndex]] += weight; }
- else if(errorSeq[i] == 'a') { qualErrorMap['a'][qScores[qIndex]] += weight; }
+ else if(errorSeq[i] == 'a') { qualErrorMap['a'][qScores[qIndex]] += weight; /*if(qScores[qIndex] != 0){ cout << qIndex << '\t'; }*/ }
else if(errorSeq[i] == 'd') { /* there are no qScores for deletions */ }
if(errorSeq[i] != 'd') { qIndex++; }
+
if(qIndex > stop){ break; }
}
}