m = MothurOut::getInstance();
int score;
- seqName = getSequenceName(qFile);
+ seqName = getSequenceName(qFile); m->gobble(qFile);
if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "'\n."); }
if (!m->control_pressed) {
- string qScoreString = m->getline(qFile);
+ string qScoreString = m->getline(qFile); m->gobble(qFile);
if (m->debug) { m->mothurOut("[DEBUG]: scores = '" + qScoreString + "'\n."); }
while(qFile.peek() != '>' && qFile.peek() != EOF){
if (m->control_pressed) { break; }
- string temp = m->getline(qFile);
- if (m->debug) { m->mothurOut("[DEBUG]: scores = '" + temp + "'\n."); }
+ string temp = m->getline(qFile); m->gobble(qFile);
+ //if (m->debug) { m->mothurOut("[DEBUG]: scores = '" + temp + "'\n."); }
qScoreString += ' ' + temp;
}
- //cout << "done reading " << endl;
+ //cout << "done reading " << endl;
istringstream qScoreStringStream(qScoreString);
int count = 0;
while(!qScoreStringStream.eof()){
string temp;
qScoreStringStream >> temp; m->gobble(qScoreStringStream);
- if (m->debug) { m->mothurOut("[DEBUG]: score " + toString(qScores.size()) + " = '" + temp + "'\n."); }
+ //if (m->debug) { m->mothurOut("[DEBUG]: score " + toString(qScores.size()) + " = '" + temp + "'\n."); }
//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"; }
}
seqLength = qScores.size();
- //cout << "seqlength = " << seqLength << '\t' << count << endl;
+ //cout << "seqlength = " << seqLength << endl;
}
catch(exception& e) {