added [ERROR] flag if command aborts

[mothur.git] / clustersplitcommand.cpp

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index c36e280e2925e3d07e6ef33e0756bbc039f08299..cb3fc40aaa6e42a0e802d0f47ec3f8897cc4fa61 100644 (file)
--- 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;