X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlistcountcommand.cpp;fp=getlistcountcommand.cpp;h=78f26047e0debdf3e620b2e0179bfab12fe93354;hb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;hp=1ecef653e11fe15d206b41fd958834be194455ff;hpb=c887ae6cd9f1c5b6e1b73a1384f154392be4efa3;p=mothur.git

diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp
index 1ecef65..78f2604 100644
--- a/getlistcountcommand.cpp
+++ b/getlistcountcommand.cpp
@@ -24,8 +24,7 @@ vector<string> GetListCountCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetListCountCommand::GetListCountCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["otu"] = tempOutNames;
 	}
@@ -61,12 +60,12 @@ vector<string> GetListCountCommand::getRequiredFiles(){
 GetListCountCommand::GetListCountCommand(string option)  {
 	try {
 		globaldata = GlobalData::getInstance();
-		abort = false;
+		abort = false; calledHelp = false;   
 		allLines = 1;
 		labels.clear();
 				
 		//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
@@ -168,7 +167,7 @@ GetListCountCommand::~GetListCountCommand(){}
 
 int GetListCountCommand::execute(){
 	try {
-		if (abort == true) {	return 0;	}
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 
 		globaldata->setFormat("list");