X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=splitgroupscommand.cpp;fp=splitgroupscommand.cpp;h=d389d8907bfaffde16b8ca9eac4dad0061341831;hb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;hp=3fa7d047b372a1c4335b9446c1b34d2aac9b702a;hpb=c887ae6cd9f1c5b6e1b73a1384f154392be4efa3;p=mothur.git

diff --git a/splitgroupscommand.cpp b/splitgroupscommand.cpp
index 3fa7d04..d389d89 100644
--- a/splitgroupscommand.cpp
+++ b/splitgroupscommand.cpp
@@ -48,8 +48,7 @@ vector<string> SplitGroupCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 SplitGroupCommand::SplitGroupCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["fasta"] = tempOutNames;
 		outputTypes["name"] = tempOutNames;
@@ -62,10 +61,10 @@ SplitGroupCommand::SplitGroupCommand(){
 //**********************************************************************************************************************
 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
@@ -171,7 +170,7 @@ SplitGroupCommand::~SplitGroupCommand(){ }
 int SplitGroupCommand::execute(){
 	try {
 	
-		if (abort == true) {	return 0;	}
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		groupMap = new GroupMap(groupfile);
 		groupMap->readMap();