added [ERROR] flag if command aborts

[mothur.git] / deuniqueseqscommand.cpp

diff --git a/deuniqueseqscommand.cpp b/deuniqueseqscommand.cpp
index f6b32e68ead4b262c0c5a5c00dc07349ab2c455f..214359e3353f5521aa337085ce46136187d326c0 100644 (file)
--- a/deuniqueseqscommand.cpp
+++ b/deuniqueseqscommand.cpp
@@ -25,8 +25,7 @@ vector<string> DeUniqueSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 DeUniqueSeqsCommand::DeUniqueSeqsCommand(){    
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
        }
@@ -61,10 +60,10 @@ vector<string> DeUniqueSeqsCommand::getRequiredFiles(){
 /**************************************************************************************/
 DeUniqueSeqsCommand::DeUniqueSeqsCommand(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
@@ -153,7 +152,7 @@ void DeUniqueSeqsCommand::help(){
 int DeUniqueSeqsCommand::execute() {   
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 
                //prepare filenames and open files
                ofstream out;