-
- /*seqName = "";
- int score;
-
- qFile >> seqName;
- m->getline(qFile);
-
- if (seqName == "") {
- m->mothurOut("Error reading quality file, name blank at position, " + toString(qFile.tellg()));
- m->mothurOutEndLine();
- }
- else{
- seqName = seqName.substr(1);
- }
- cout << seqName << endl;
- string qScoreString = m->getline(qFile);
- cout << qScoreString << endl;
- istringstream qScoreStringStream(qScoreString);
- int count = 0;
- while(!qScoreStringStream.eof()){
- if (m->control_pressed) { break; }
- qScoreStringStream >> score;
- qScores.push_back(score);
- cout << score << '\t' << count << endl;
- count++;
- }
- 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);
-