//**********************************************************************************************************************
RemoveGroupsCommand::RemoveGroupsCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["taxonomy"] = tempOutNames;
//**********************************************************************************************************************
RemoveGroupsCommand::RemoveGroupsCommand(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 RemoveGroupsCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
groupMap = new GroupMap(groupfile);
groupMap->readMap();
}
}
+
//if the name in the first column is in the set then print it and any other names in second column also in set
if (names.count(firstCol) == 0) {
names.insert(seqs[i]);
}
}
+
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveGroupsCommand", "fillNames");