X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustercommand.cpp;h=5d9225b0f9ca4c6f39de259454dfc1fb92e6c919;hb=662c0b60d65f79f672ab199300b7ee4975233465;hp=8a1d120934717524c2670699c8c487c8b6c8c6bc;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 8a1d120..5d9225b 100644
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -24,7 +24,7 @@ vector<string> ClusterCommand::getValidParameters(){
 //**********************************************************************************************************************
 ClusterCommand::ClusterCommand(){	
 	try {
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["list"] = tempOutNames;
 		outputTypes["rabund"] = tempOutNames;
@@ -64,10 +64,10 @@ ClusterCommand::ClusterCommand(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
@@ -198,7 +198,7 @@ ClusterCommand::~ClusterCommand(){
 int ClusterCommand::execute(){
 	try {
 	
-		if (abort == true) {	return 0;	}
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		time_t estart = time(NULL);
 		//int ndist = matrix->getNNodes();