added [ERROR] flag if command aborts

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index ffddb8cfc9de4dd92feb4966dd8d31477e1363fa..e2f2636e491294a7e260e34340cef1e4e8273d40 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -48,7 +48,7 @@ vector<string> ShhherCommand::getValidParameters(){
 
 ShhherCommand::ShhherCommand(){        
        try {
-               abort = true;
+               abort = true; calledHelp = true;
                
                //initialize outputTypes
                vector<string> tempOutNames;
@@ -101,11 +101,11 @@ ShhherCommand::ShhherCommand(string option) {
 #endif
                
                
-               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 {
                        
@@ -237,6 +237,8 @@ void ShhherCommand::help(){
 #ifdef USE_MPI
 int ShhherCommand::execute(){
        try {
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
+               
                int tag = 1976;
                MPI_Status status;