X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=chimeracheckcommand.cpp;h=c766b9a2dab6c2994df147423f61d14bf6f088a6;hb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;hp=3104fac58c9b6c4ff9bc1dc4870fcc77c0541853;hpb=c887ae6cd9f1c5b6e1b73a1384f154392be4efa3;p=mothur.git

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 3104fac..c766b9a 100644
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -47,6 +47,7 @@ vector<string> ChimeraCheckCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 ChimeraCheckCommand::ChimeraCheckCommand(){	
 	try {
+		abort = true; calledHelp = true;
 		vector<string> tempOutNames;
 		outputTypes["chimera"] = tempOutNames;
 	}
@@ -58,10 +59,10 @@ ChimeraCheckCommand::ChimeraCheckCommand(){
 //***************************************************************************************************************
 ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
 	try {
-		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
@@ -280,7 +281,7 @@ ChimeraCheckCommand::~ChimeraCheckCommand(){	/*	do nothing	*/	}
 int ChimeraCheckCommand::execute(){
 	try{
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		for (int i = 0; i < fastaFileNames.size(); i++) {