+//**********************************************************************************************************************
+int ListSeqsCommand::readFastq(){
+ try {
+
+ ifstream in;
+ m->openInputFile(fastqfile, in);
+ string name;
+
+ //ofstream out;
+ //string newFastaName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "numsAdded.fasta";
+ //m->openOutputFile(newFastaName, out);
+ int count = 1;
+ //string lastName = "";
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); return 0; }
+
+ //read sequence name
+ string name = m->getline(in); m->gobble(in);
+
+ if (name[0] == '@') {
+ vector<string> splits = m->splitWhiteSpace(name);
+ name = splits[0];
+ name = name.substr(1);
+ m->checkName(name);
+ names.push_back(name);
+ //get rest of lines
+ name = m->getline(in); m->gobble(in);
+ name = m->getline(in); m->gobble(in);
+ name = m->getline(in); m->gobble(in);
+ }
+
+ m->gobble(in);
+ if (m->debug) { count++; cout << "[DEBUG]: count = " + toString(count) + ", name = " + name + "\n"; }
+ }
+ in.close();
+ //out.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ListSeqsCommand", "readFastq");
+ exit(1);
+ }
+}