//outputTypes - makes something like outputTypes=fasta-name-qfile
map<string, vector<string> > thisOutputTypes = thisCommand->getOutputFiles();
map<string, vector<string> >::iterator itTypes;
//outputTypes - makes something like outputTypes=fasta-name-qfile
map<string, vector<string> > thisOutputTypes = thisCommand->getOutputFiles();
map<string, vector<string> >::iterator itTypes;