+int GetSeqsCommand::readQual(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(qualfile); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(qualfile)) + "pick" + m->getExtension(qualfile);
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+
+
+ ifstream in;
+ m->openInputFile(qualfile, in);
+ string name;
+
+ bool wroteSomething = false;
+
+
+ while(!in.eof()){
+ string saveName = "";
+ string name = "";
+ string scores = "";
+
+ in >> name;
+
+ if (name.length() != 0) {
+ saveName = name.substr(1);
+ while (!in.eof()) {
+ char c = in.get();
+ if (c == 10 || c == 13){ break; }
+ else { name += c; }
+ }
+ m->gobble(in);
+ }
+
+ while(in){
+ char letter= in.get();
+ if(letter == '>'){ in.putback(letter); break; }
+ else{ scores += letter; }
+ }
+
+ m->gobble(in);
+
+ if (names.count(saveName) != 0) {
+ wroteSomething = true;
+
+ out << name << endl << scores;
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+
+ if (wroteSomething == false) { m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine(); }
+ outputNames.push_back(outputFileName); outputTypes["qfile"].push_back(outputFileName);
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSeqsCommand", "readQual");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************