X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=screenseqscommand.cpp;h=150a27e54273dfcf7c61d8c1582efe794e0362ba;hp=65b5956cce5c0a6418d5d9524218b35b0b335aa8;hb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;hpb=c887ae6cd9f1c5b6e1b73a1384f154392be4efa3

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 65b5956..150a27e 100644
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -26,8 +26,7 @@ vector<string> ScreenSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 ScreenSeqsCommand::ScreenSeqsCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["fasta"] = tempOutNames;
 		outputTypes["name"] = tempOutNames;
@@ -67,10 +66,10 @@ vector<string> ScreenSeqsCommand::getRequiredFiles(){
 
 ScreenSeqsCommand::ScreenSeqsCommand(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
@@ -247,7 +246,7 @@ ScreenSeqsCommand::~ScreenSeqsCommand(){	/*	do nothing	*/	}
 int ScreenSeqsCommand::execute(){
 	try{
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		//if the user want to optimize we need to no the 90% mark
 		vector<unsigned long int> positions;