added [ERROR] flag if command aborts

[mothur.git] / getotuscommand.cpp

diff --git a/getotuscommand.cpp b/getotuscommand.cpp
index fd7c8d1d4d7cc22901fc88d5b363176081fa5a14..b075cb4bb61521c15e77c1a2e6966a6966daee4c 100644 (file)
--- a/getotuscommand.cpp
+++ b/getotuscommand.cpp
@@ -27,8 +27,7 @@ vector<string> GetOtusCommand::getValidParameters(){
 //**********************************************************************************************************************
 GetOtusCommand::GetOtusCommand(){      
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["group"] = tempOutNames;
                outputTypes["list"] = tempOutNames;
@@ -64,10 +63,10 @@ vector<string> GetOtusCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 GetOtusCommand::GetOtusCommand(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 GetOtusCommand::help(){
 int GetOtusCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                groupMap = new GroupMap(groupfile);
                groupMap->readMap();