//**********************************************************************************************************************
LibShuffCommand::LibShuffCommand(){
try {
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["coverage"] = tempOutNames;
outputTypes["libshuffsummary"] = tempOutNames;
LibShuffCommand::LibShuffCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
Groups.clear();
//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 LibShuffCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
savedDXYValues = form->evaluateAll();
savedMinValues = form->getSavedMins();