X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getoturepcommand.cpp;h=84d3871c3d74026c8d92af7e5b66dfa03ebcba21;hb=32abf5d58aed8087cd0bcb32d7aa9053f103f2c1;hp=9cc99732e715d40f0ef06743bb85870a147f7036;hpb=64b2b8d59acac0332e61b6622e7d16a300bdce3e;p=mothur.git

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 9cc9973..84d3871 100644
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -38,8 +38,7 @@ inline bool compareGroup(repStruct left, repStruct right){
 //**********************************************************************************************************************
 GetOTURepCommand::GetOTURepCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["fasta"] = tempOutNames;
 		outputTypes["name"] = tempOutNames;
@@ -88,13 +87,13 @@ vector<string> GetOTURepCommand::getRequiredFiles(){
 GetOTURepCommand::GetOTURepCommand(string option)  {
 	try{
 		globaldata = GlobalData::getInstance();
-		abort = false;
+		abort = false; calledHelp = false;   
 		allLines = 1;
 		labels.clear();
 				
 		//allow user to run help
 		if (option == "help") { 
-			help(); abort = true;
+			help(); abort = true; calledHelp = true;
 		} else {
 			//valid paramters for this command
 			string Array[] =  {"fasta","list","label","name","weighted", "group", "sorted", "phylip","column","large","cutoff","precision","groups","outputdir","inputdir"};
@@ -299,7 +298,7 @@ GetOTURepCommand::~GetOTURepCommand(){}
 int GetOTURepCommand::execute(){
 	try {
 	
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		int error;
 		
 		if (!large) {