X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=makegroupcommand.cpp;h=1c04fecb477d09e0e6de73b1307a3878fcc8e4b3;hp=12be82690fc7068e4d713353ee84d79aa6330ba7;hb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;hpb=c887ae6cd9f1c5b6e1b73a1384f154392be4efa3

diff --git a/makegroupcommand.cpp b/makegroupcommand.cpp
index 12be826..1c04fec 100644
--- a/makegroupcommand.cpp
+++ b/makegroupcommand.cpp
@@ -25,8 +25,7 @@ vector<string> MakeGroupCommand::getValidParameters(){
 //**********************************************************************************************************************
 MakeGroupCommand::MakeGroupCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["group"] = tempOutNames;
 	}
@@ -63,10 +62,10 @@ vector<string> MakeGroupCommand::getRequiredFiles(){
 MakeGroupCommand::MakeGroupCommand(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 {
 			
@@ -198,7 +197,7 @@ void MakeGroupCommand::help(){
 
 int MakeGroupCommand::execute(){
 	try {
-		if (abort == true) { return 0;	}
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[0]); }