X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=clusterfragmentscommand.cpp;fp=clusterfragmentscommand.cpp;h=a8277ffb029fdd6e5f3e110614836e37292ce9a3;hp=24070d2bb0e8b8f781eece4e35e7dec4f42d6797;hb=c69e2e9749626cfbf1d6cb0125ae94f869e00b18;hpb=c887ae6cd9f1c5b6e1b73a1384f154392be4efa3

diff --git a/clusterfragmentscommand.cpp b/clusterfragmentscommand.cpp
index 24070d2..a8277ff 100644
--- a/clusterfragmentscommand.cpp
+++ b/clusterfragmentscommand.cpp
@@ -40,8 +40,7 @@ vector<string> ClusterFragmentsCommand::getValidParameters(){
 //**********************************************************************************************************************
 ClusterFragmentsCommand::ClusterFragmentsCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["fasta"] = tempOutNames;
 		outputTypes["name"] = tempOutNames;
@@ -77,10 +76,10 @@ vector<string> ClusterFragmentsCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 ClusterFragmentsCommand::ClusterFragmentsCommand(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
@@ -182,7 +181,7 @@ void ClusterFragmentsCommand::help(){
 int ClusterFragmentsCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		int start = time(NULL);