X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerabellerophoncommand.cpp;h=22e4fe2956e18100b1e6a4920c25b9237a8d5504;hb=c3396974063d6efc5e5850ddf4ed8ab65cc94bb9;hp=5d7d6d452b2c741ad764623557f0a0d31895ba0e;hpb=4b6e3f7b5543822a2cca4fb076ab6af2ce8ca62d;p=mothur.git

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index 5d7d6d4..22e4fe2 100644
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -48,8 +48,7 @@ vector<string> ChimeraBellerophonCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 ChimeraBellerophonCommand::ChimeraBellerophonCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["chimera"] = tempOutNames;
 		outputTypes["accnos"] = tempOutNames;
@@ -63,10 +62,10 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(){
 //***************************************************************************************************************
 ChimeraBellerophonCommand::ChimeraBellerophonCommand(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
@@ -210,7 +209,7 @@ ChimeraBellerophonCommand::~ChimeraBellerophonCommand(){	/*	do nothing	*/	}
 int ChimeraBellerophonCommand::execute(){
 	try{
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		for (int i = 0; i < fastaFileNames.size(); i++) {