//**********************************************************************************************************************
ChimeraCcodeCommand::ChimeraCcodeCommand(){
try {
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["chimera"] = tempOutNames;
outputTypes["mapinfo"] = tempOutNames;
//***************************************************************************************************************
ChimeraCcodeCommand::ChimeraCcodeCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
int ChimeraCcodeCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
for (int s = 0; s < fastaFileNames.size(); s++) {