//**********************************************************************************************************************
ParseFastaQCommand::ParseFastaQCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["qual"] = tempOutNames;
//**********************************************************************************************************************
ParseFastaQCommand::ParseFastaQCommand(string option){
try {
- abort = false;
+ abort = false; calledHelp = false;
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
int ParseFastaQCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//open Output Files
string fastaFile = outputDir + m->getRootName(m->getSimpleName(fastaQFile)) + "fasta";