trim.seqs fix

[mothur.git] / collectcommand.cpp

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 3dd2436a8a88cf21b8cd7705a799ed9ab6450ebf..4b59296fd645fa2947a31959f299d5628b8951cf 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -72,7 +72,7 @@ vector<string> CollectCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 CollectCommand::CollectCommand(){      
        try {
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["sobs"] = tempOutNames;
                outputTypes["chao"] = tempOutNames;
@@ -109,7 +109,7 @@ CollectCommand::CollectCommand(){
 CollectCommand::CollectCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                allLines = 1;
                labels.clear();
                Estimators.clear();
@@ -236,7 +236,7 @@ CollectCommand::~CollectCommand(){}
 int CollectCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                string hadShared = "";
                if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName);  }