X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getrelabundcommand.cpp;fp=getrelabundcommand.cpp;h=5e48203f87e11fe14f54033b966b0bbd55bdde60;hb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;hp=08e9228b215819f5e19e4d697137384294392422;hpb=c887ae6cd9f1c5b6e1b73a1384f154392be4efa3;p=mothur.git

diff --git a/getrelabundcommand.cpp b/getrelabundcommand.cpp
index 08e9228..5e48203 100644
--- a/getrelabundcommand.cpp
+++ b/getrelabundcommand.cpp
@@ -24,8 +24,7 @@ vector<string> GetRelAbundCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetRelAbundCommand::GetRelAbundCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["relabund"] = tempOutNames;
 	}
@@ -61,12 +60,12 @@ vector<string> GetRelAbundCommand::getRequiredFiles(){
 GetRelAbundCommand::GetRelAbundCommand(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
@@ -167,7 +166,7 @@ GetRelAbundCommand::~GetRelAbundCommand(){
 int GetRelAbundCommand::execute(){
 	try {
 	
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "relabund";
 		ofstream out;