trim.seqs fix

[mothur.git] / getotuscommand.cpp

diff --git a/getotuscommand.cpp b/getotuscommand.cpp
index ba9a5e7c98093b889c5b2d08c746e3da837bf33f..f10142bb74a67a9fa98bded8b8a2e0d48fa85358 100644 (file)
--- a/getotuscommand.cpp
+++ b/getotuscommand.cpp
@@ -27,8 +27,7 @@ vector<string> GetOtusCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetOtusCommand::GetOtusCommand(){      
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["group"] = tempOutNames;
                outputTypes["list"] = tempOutNames;
@@ -64,10 +63,10 @@ vector<string> GetOtusCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 GetOtusCommand::GetOtusCommand(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
@@ -182,12 +181,12 @@ void GetOtusCommand::help(){
 int GetOtusCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                groupMap = new GroupMap(groupfile);
                groupMap->readMap();
                
-               //get groups you want to remove
+               //get groups you want to get
                if (accnosfile != "") { readAccnos(); }
                
                //make sure groups are valid
@@ -381,7 +380,7 @@ int GetOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstream
                
                m->mothurOut(newList.getLabel() + " - selected " + toString(numOtus) + " of the " + toString(list->getNumBins()) + " OTUs."); m->mothurOutEndLine();
        
-               
+               return 0;
        }
        catch(exception& e) {
                m->errorOut(e, "GetOtusCommand", "processList");