while(qFile.peek() != '>' && qFile.peek() != EOF){
if (m->control_pressed) { break; }
string temp = m->getline(qFile); m->gobble(qFile);
- if (m->debug) { m->mothurOut("[DEBUG]: scores = '" + temp + "'\n."); }
+ //if (m->debug) { m->mothurOut("[DEBUG]: scores = '" + temp + "'\n."); }
qScoreString += ' ' + temp;
}
//cout << "done reading " << endl;
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"; }
if(seqName != sequence.getName()){
m->mothurOut("sequence name mismatch btwn fasta: " + sequence.getName() + " and qual file: " + seqName);
- m->mothurOutEndLine();
+ m->mothurOutEndLine(); m->control_pressed = true;
}
int end;