X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustersplitcommand.cpp;h=cb3fc40aaa6e42a0e802d0f47ec3f8897cc4fa61;hb=9f4c08cab5a7a9a0e156bd4a5a3a478b476162dc;hp=0aceb8bc842eb0ee47704f31d8cdb0b6649f9e4a;hpb=5694c92fbf646fe01abc87bde2af59e14a9a56b6;p=mothur.git

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 0aceb8b..cb3fc40 100644
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -31,8 +31,7 @@ vector<string> ClusterSplitCommand::getValidParameters(){
 //**********************************************************************************************************************
 ClusterSplitCommand::ClusterSplitCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["list"] = tempOutNames;
 		outputTypes["rabund"] = tempOutNames;
@@ -72,11 +71,11 @@ vector<string> ClusterSplitCommand::getRequiredFiles(){
 ClusterSplitCommand::ClusterSplitCommand(string option)  {
 	try{
 		globaldata = GlobalData::getInstance();
-		abort = false;
+		abort = false; calledHelp = false;   
 		format = "";
 		
 		//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
@@ -290,7 +289,7 @@ ClusterSplitCommand::~ClusterSplitCommand(){}
 int ClusterSplitCommand::execute(){
 	try {
 	
-		if (abort == true) {	return 0;	}
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		time_t estart;
 		vector<string> listFileNames;
@@ -380,7 +379,6 @@ int ClusterSplitCommand::execute(){
 					
 			//for each file group figure out which process will complete it
 			//want to divide the load intelligently so the big files are spread between processes
-			int count = 1;
 			for (int i = 0; i < distName.size(); i++) { 
 				int processToAssign = (i+1) % processors; 
 				if (processToAssign == 0) { processToAssign = processors; }