X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.cpp;h=3d667227ae2219347f2523ee1ff8286988299423;hb=5334a314651228c55fd0f206dec0209bc3148b24;hp=4cb98419fd23f540e174b068dd9a832b79fb3036;hpb=8173238f9f94af9baab8471de58bed7c8830948d;p=mothur.git

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 4cb9841..3d66722 100644
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -30,8 +30,7 @@ vector<string> DistanceCommand::getValidParameters(){
 //**********************************************************************************************************************
 DistanceCommand::DistanceCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["phylip"] = tempOutNames;
 		outputTypes["column"] = tempOutNames;
@@ -67,11 +66,11 @@ vector<string> DistanceCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 DistanceCommand::DistanceCommand(string option) {
 	try {
-		abort = false;
+		abort = false; calledHelp = false;   
 		Estimators.clear();
 				
 		//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
@@ -242,7 +241,7 @@ void DistanceCommand::help(){
 int DistanceCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		int startTime = time(NULL);
 		
@@ -314,7 +313,7 @@ int DistanceCommand::execute(){
 			//delete filename;
 
 			if (pid == 0) { //you are the root process 
-			
+				
 				//do your part
 				string outputMyPart;
 				
@@ -1151,6 +1150,8 @@ bool DistanceCommand::sanityCheck() {
 			remove(outputFile.c_str()); //temp file is bad because file mismatch above
 		}
 		
+		return good;
+		
 	}
 	catch(exception& e) {
 		m->errorOut(e, "DistanceCommand", "sanityCheck");