X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getgroupcommand.cpp;h=ab3ccfa36f3f2d4e6a7e1f5af6a38434640f3105;hb=a4f05f09c250323132a4b9427f41a3ededaec634;hp=40bfb26c6a21cfd29368720ef91782e8cd638ac6;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/getgroupcommand.cpp b/getgroupcommand.cpp
index 40bfb26..ab3ccfa 100644
--- a/getgroupcommand.cpp
+++ b/getgroupcommand.cpp
@@ -24,7 +24,7 @@ vector<string> GetgroupCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetgroupCommand::GetgroupCommand(){	
 	try {
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["bootgroup"] = tempOutNames;
 	}
@@ -60,10 +60,10 @@ vector<string> GetgroupCommand::getRequiredFiles(){
 GetgroupCommand::GetgroupCommand(string option)  {
 	try {
 		globaldata = GlobalData::getInstance();
-		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
@@ -134,7 +134,7 @@ GetgroupCommand::~GetgroupCommand(){
 int GetgroupCommand::execute(){
 	try {
 	
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 	
 		int num, inputData, count;
 		count = 0;