X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=normalizesharedcommand.cpp;fp=normalizesharedcommand.cpp;h=c0e7c1f7f037cf1f0d87ab169408825a547c5982;hb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;hp=85265015a7e6ea4de35552bd7d27d7efdc688348;hpb=c887ae6cd9f1c5b6e1b73a1384f154392be4efa3;p=mothur.git

diff --git a/normalizesharedcommand.cpp b/normalizesharedcommand.cpp
index 8526501..c0e7c1f 100644
--- a/normalizesharedcommand.cpp
+++ b/normalizesharedcommand.cpp
@@ -24,8 +24,7 @@ vector<string> NormalizeSharedCommand::getValidParameters(){
 //**********************************************************************************************************************
 NormalizeSharedCommand::NormalizeSharedCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["shared"] = tempOutNames;
 	}
@@ -62,12 +61,12 @@ vector<string> NormalizeSharedCommand::getRequiredFiles(){
 NormalizeSharedCommand::NormalizeSharedCommand(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
@@ -185,7 +184,7 @@ NormalizeSharedCommand::~NormalizeSharedCommand(){}
 int NormalizeSharedCommand::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)) + "norm.shared";
 		ofstream out;