}
string qScoreString = m->getline(qFile);
+ while(qFile.peek() != '>' && qFile.peek() != EOF){
+ qScoreString += ' ' + m->getline(qFile);
+ }
istringstream qScoreStringStream(qScoreString);
+ int count = 0;
while(!qScoreStringStream.eof()){
- qScoreStringStream >> score;
+ if (m->control_pressed) { break; }
+ qScoreStringStream >> score; m->gobble(qScoreStringStream);
+
qScores.push_back(score);
+ count++;
}
- qScores.pop_back();
+ //qScores.pop_back();
+
+// string scores = "";
+//
+// while(!qFile.eof()){
+//
+// qFile >> seqName;
+//
+// //get name
+// if (seqName.length() != 0) {
+// seqName = seqName.substr(1);
+// while (!qFile.eof()) {
+// char c = qFile.get();
+// //gobble junk on line
+// if (c == 10 || c == 13){ break; }
+// }
+// m->gobble(qFile);
+// }
+//
+// //get scores
+// while(qFile){
+// char letter=qFile.get();
+// if((letter == '>')){ qFile.putback(letter); break; }
+// else if (isprint(letter)) { scores += letter; }
+// }
+// m->gobble(qFile);
+//
+// break;
+// }
+//
+// //convert scores string to qScores
+// istringstream qScoreStringStream(scores);
+//
+// int score;
+// while(!qScoreStringStream.eof()){
+//
+// if (m->control_pressed) { break; }
+//
+// qScoreStringStream >> score;
+// qScores.push_back(score);
+// }
+//
+// qScores.pop_back();
+
seqLength = qScores.size();
+ //cout << "seqlenght = " << seqLength << '\t' << count << endl;
+
}
catch(exception& e) {
m->errorOut(e, "QualityScores", "QualityScores");
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;
int end = windowSize;
int start = 0;
-
+
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
+ if (end < windowSize) { return 0; }
+
sequence.setUnaligned(rawSequence.substr(0,end));
trimQScores(-1, end);