added [ERROR] flag if command aborts

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index f5c7bd6876a9d98ed7c9dffa1e4fcd80b76005b2..6fd4e04a0e562e5ee44fd0a05fc7df9b1bfae3d4 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -25,8 +25,7 @@ vector<string> FilterSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 FilterSeqsCommand::FilterSeqsCommand(){        
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
                outputTypes["filter"] = tempOutNames;
@@ -62,11 +61,11 @@ vector<string> FilterSeqsCommand::getRequiredFiles(){
 /**************************************************************************************/
 FilterSeqsCommand::FilterSeqsCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                filterFileName = "";
                
                //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
@@ -240,7 +239,7 @@ void FilterSeqsCommand::help(){
 int FilterSeqsCommand::execute() {     
        try {
        
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                ifstream inFASTA;
                m->openInputFile(fastafileNames[0], inFASTA);