//**********************************************************************************************************************
SplitGroupCommand::SplitGroupCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["name"] = tempOutNames;
//**********************************************************************************************************************
SplitGroupCommand::SplitGroupCommand(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 SplitGroupCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
groupMap = new GroupMap(groupfile);
groupMap->readMap();
(*(filehandles[it3->first])).close();
delete it3->second;
}
+
+ vector<string> newOutputNames;
+ //remove blank files
+ for (int i = 0; i < outputNames.size(); i++) {
+ if (m->isBlank(outputNames[i])) {
+ remove(outputNames[i].c_str());
+ }else { newOutputNames.push_back(outputNames[i]); }
+ }
+ outputNames = newOutputNames;
return 0;