X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=reversecommand.cpp;fp=reversecommand.cpp;h=d20f4af0acd4861cea64688e6e05460e42cbaf75;hb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;hp=7b58162d20d8ac1910323c2946f7f8b4c05299af;hpb=c887ae6cd9f1c5b6e1b73a1384f154392be4efa3;p=mothur.git

diff --git a/reversecommand.cpp b/reversecommand.cpp
index 7b58162..d20f4af 100644
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -25,8 +25,7 @@ vector<string> ReverseSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 ReverseSeqsCommand::ReverseSeqsCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["fasta"] = tempOutNames;
 	}
@@ -62,10 +61,10 @@ vector<string> ReverseSeqsCommand::getRequiredFiles(){
 
 ReverseSeqsCommand::ReverseSeqsCommand(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
@@ -144,7 +143,7 @@ ReverseSeqsCommand::~ReverseSeqsCommand(){	/*	do nothing	*/	}
 int ReverseSeqsCommand::execute(){
 	try{
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		ifstream inFASTA;
 		m->openInputFile(fasta, inFASTA);