added namefile to align.check and added seqs from namefile to optimizing piece of...

[mothur.git] / mergefilecommand.cpp

diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
index d431dd32ff17dcef5e267b1e93a47c8fc93b324b..2b34a00b8c3961d581032dcf6b6929404428a3b4 100644 (file)
--- a/mergefilecommand.cpp
+++ b/mergefilecommand.cpp
@@ -24,7 +24,7 @@ vector<string> MergeFileCommand::getValidParameters(){
 //**********************************************************************************************************************
 MergeFileCommand::MergeFileCommand(){  
        try {
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["merge"] = tempOutNames;
        }
@@ -60,11 +60,11 @@ vector<string> MergeFileCommand::getRequiredFiles(){
 
 MergeFileCommand::MergeFileCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                
                if(option == "help") {
                        help();
-                       abort = true; 
+                       abort = true; calledHelp = true;
                }
                else {
                        //valid paramters for this command
@@ -136,7 +136,7 @@ MergeFileCommand::~MergeFileCommand()       {       /*      do nothing      */      }
 
 int MergeFileCommand::execute(){
        try {
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                ofstream outputFile;
                m->openOutputFile(outputFileName, outputFile);