added [ERROR] flag if command aborts

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index a7ed94f67bb42a3805e08eb487923889c3a55af6..67b70f27cc0aa0592cd87d5b97c1471fc0edb5ff 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -27,6 +27,7 @@ vector<string> ChimeraSlayerCommand::getValidParameters(){
 //**********************************************************************************************************************
 ChimeraSlayerCommand::ChimeraSlayerCommand(){  
        try {
+               abort = true; calledHelp = true;
                vector<string> tempOutNames;
                outputTypes["chimera"] = tempOutNames;
                outputTypes["accnos"] = tempOutNames;
@@ -63,10 +64,10 @@ vector<string> ChimeraSlayerCommand::getRequiredFiles(){
 //***************************************************************************************************************
 ChimeraSlayerCommand::ChimeraSlayerCommand(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
@@ -343,7 +344,7 @@ ChimeraSlayerCommand::~ChimeraSlayerCommand(){      /*      do nothing      */      }
 int ChimeraSlayerCommand::execute(){
        try{
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                for (int s = 0; s < fastaFileNames.size(); s++) {