added [ERROR] flag if command aborts

[mothur.git] / readotucommand.cpp

diff --git a/readotucommand.cpp b/readotucommand.cpp
index 8683fc3fa80154729ea5228fcaa38fb03726603a..67575561721451bfe172c7235bb172ed24606155 100644 (file)
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -24,8 +24,7 @@ vector<string> ReadOtuCommand::getValidParameters(){
 //**********************************************************************************************************************
 ReadOtuCommand::ReadOtuCommand(){      
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["rabund"] = tempOutNames;
                outputTypes["shared"] = tempOutNames;
@@ -62,11 +61,11 @@ vector<string> ReadOtuCommand::getRequiredFiles(){
 ReadOtuCommand::ReadOtuCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                allLines = 1;
                
                //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 @@ ReadOtuCommand::~ReadOtuCommand(){}
 int ReadOtuCommand::execute(){
        try {
        
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
        
                if (globaldata->getFormat() == "shared") {