+string ShhherCommand::createNamesFile(){
+ try{
+
+ vector<string> duplicateNames(numUniques, "");
+ for(int i=0;i<numSeqs;i++){
+ duplicateNames[mapSeqToUnique[i]] += seqNameVector[i] + ',';
+ }
+
+ string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names";
+
+ ofstream nameFile;
+ m->openOutputFile(nameFileName, nameFile);
+
+ for(int i=0;i<numUniques;i++){
+
+ if (m->control_pressed) { break; }
+
+ // nameFile << seqNameVector[mapUniqueToSeq[i]] << '\t' << duplicateNames[i].substr(0, duplicateNames[i].find_last_of(',')) << endl;
+ nameFile << mapUniqueToSeq[i] << '\t' << duplicateNames[i].substr(0, duplicateNames[i].find_last_of(',')) << endl;
+ }
+
+ nameFile.close();
+ return nameFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ShhherCommand", "createNamesFile");
+ exit(1);
+ }
+}
+/**************************************************************************************************/