qFile >> seqName;
m->getline(qFile);
-
+ //cout << seqName << endl;
if (seqName == "") {
m->mothurOut("Error reading quality file, name blank at position, " + toString(qFile.tellg()));
m->mothurOutEndLine();
else{
seqName = seqName.substr(1);
}
+
string qScoreString = m->getline(qFile);
+ //cout << qScoreString << endl;
while(qFile.peek() != '>' && qFile.peek() != EOF){
- qScoreString += ' ' + m->getline(qFile);
+ if (m->control_pressed) { break; }
+ string temp = m->getline(qFile);
+ //cout << temp << endl;
+ qScoreString += ' ' + temp;
}
-
+ //cout << "done reading " << endl;
istringstream qScoreStringStream(qScoreString);
int count = 0;
while(!qScoreStringStream.eof()){
if (m->control_pressed) { break; }
- qScoreStringStream >> score;
+ string temp;
+ qScoreStringStream >> temp; m->gobble(qScoreStringStream);
+
+ //check temp to make sure its a number
+ if (!m->isContainingOnlyDigits(temp)) { m->mothurOut("[ERROR]: In sequence " + seqName + "'s quality scores, expected a number and got " + temp + ", setting score to 0."); m->mothurOutEndLine(); temp = "0"; }
+ convert(temp, score);
+
+ //cout << count << '\t' << score << endl;
qScores.push_back(score);
count++;
}
- qScores.pop_back();
+ //qScores.pop_back();
// string scores = "";
//
// qScores.pop_back();
seqLength = qScores.size();
-
+ //cout << "seqlength = " << seqLength << '\t' << count << endl;
}
catch(exception& e) {
void QualityScores::trimQScores(int start, int end){
try {
vector<int> hold;
-
+
+
+ //cout << seqName << '\t' << start << '\t' << end << '\t' << qScores.size() << endl;
+ //for (int i = 0; i < qScores.size(); i++) { cout << qScores[i] << end; }
if(end == -1){
hold = vector<int>(qScores.begin()+start, qScores.end());
qScores = hold;
if(seqLength < windowSize) { return 0; }
- while(start < seqLength){
+ while((start+windowSize) < seqLength){
double windowSum = 0.0000;
for(int i=start;i<end;i++){
windowSum += qScores[i];
}
double windowAverage = windowSum / (double)(end-start);
-
+
if(windowAverage < qThreshold){
end = end - stepSize;
break;
}
+
start += stepSize;
end = start + windowSize;
- if(end >= seqLength){ end = seqLength - 1; }
+
+ if(end >= seqLength){ end = seqLength; }
+
}
-
+
if(end == -1){ end = seqLength; }
//failed first window
return 1;
}
catch(exception& e) {
- m->errorOut(e, "QualityScores", "flipQScores");
+ m->errorOut(e, "QualityScores", "stripQualWindowAverage");
exit(1);
}
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; }
}
}