+// string rawSequence = seq.getUnaligned();
+// int seqLength; // = rawSequence.length();
+// string name, temp, temp2;
+//
+// qFile >> name;
+//
+// //get rest of line
+// temp = "";
+// while (!qFile.eof()) {
+// char c = qFile.get();
+// if (c == 10 || c == 13){ break; }
+// else { temp += c; }
+// }
+//
+// int pos = temp.find("length");
+// if (pos == temp.npos) { m->mothurOut("Cannot find length in qfile for " + seq.getName()); m->mothurOutEndLine(); seqLength = 0; }
+// else {
+// string tempLength = temp.substr(pos);
+// istringstream iss (tempLength,istringstream::in);
+// iss >> temp;
+// }
+//
+// splitAtEquals(temp2, temp); //separates length=242, temp=length, temp2=242
+// convert(temp, seqLength); //converts string to int
+//
+// if (name.length() != 0) { if(name.substr(1) != seq.getName()) { m->mothurOut("sequence name mismatch btwn fasta and qual file"); m->mothurOutEndLine(); } }
+