added [ERROR] flag if command aborts

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index d2c0fcb64f92652a14dee26e40e89ae5dc9a19dd..00f78626b6270455f5a8f35464923fe72e9ff527 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -27,8 +27,7 @@ vector<string> SeqErrorCommand::getValidParameters(){
 //**********************************************************************************************************************
 SeqErrorCommand::SeqErrorCommand(){    
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["error.summary"] = tempOutNames;
                outputTypes["error.seq"] = tempOutNames;
@@ -73,10 +72,10 @@ vector<string> SeqErrorCommand::getRequiredFiles(){
 SeqErrorCommand::SeqErrorCommand(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 {
                        string temp;
@@ -231,7 +230,7 @@ SeqErrorCommand::~SeqErrorCommand(){
 
 int SeqErrorCommand::execute(){
        try{
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 
                string errorSummaryFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.summary";
                m->openOutputFile(errorSummaryFileName, errorSummaryFile);