//**********************************************************************************************************************
ChimeraCheckCommand::ChimeraCheckCommand(){
try {
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["chimera"] = tempOutNames;
}
//***************************************************************************************************************
ChimeraCheckCommand::ChimeraCheckCommand(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 ChimeraCheckCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
for (int i = 0; i < fastaFileNames.size(); i++) {
#ifdef USE_MPI
- int pid, end, numSeqsPerProcessor;
+ int pid, numSeqsPerProcessor;
int tag = 2001;
vector<unsigned long int> MPIPos;