//**********************************************************************************************************************
ChopSeqsCommand::ChopSeqsCommand(){
try {
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["accnos"] = tempOutNames;
//**********************************************************************************************************************
ChopSeqsCommand::ChopSeqsCommand(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 ChopSeqsCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "chop.fasta";
string outputFileNameAccnos = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "chop.accnos";