X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=degapseqscommand.cpp;fp=degapseqscommand.cpp;h=5df61889747833ef27f5929d227c849ea7245769;hb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;hp=2514ae1a21bd491ffb924700b226b103ea2ca839;hpb=c887ae6cd9f1c5b6e1b73a1384f154392be4efa3;p=mothur.git

diff --git a/degapseqscommand.cpp b/degapseqscommand.cpp
index 2514ae1..5df6188 100644
--- a/degapseqscommand.cpp
+++ b/degapseqscommand.cpp
@@ -25,8 +25,7 @@ vector<string> DegapSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 DegapSeqsCommand::DegapSeqsCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["fasta"] = tempOutNames;
 	}
@@ -61,10 +60,10 @@ vector<string> DegapSeqsCommand::getRequiredFiles(){
 //***************************************************************************************************************
 DegapSeqsCommand::DegapSeqsCommand(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
@@ -189,7 +188,7 @@ DegapSeqsCommand::~DegapSeqsCommand(){	/*	do nothing	*/	}
 int DegapSeqsCommand::execute(){
 	try{
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		for (int s = 0; s < fastaFileNames.size(); s++) {