added [ERROR] flag if command aborts

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 7267b91da4d2ec193508579e8226c33d6758e9c7..45de8d62df230820f35352c71f96d13db4a6cb0a 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -31,8 +31,7 @@ vector<string> TrimSeqsCommand::getValidParameters(){
 
 TrimSeqsCommand::TrimSeqsCommand(){    
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["fasta"] = tempOutNames;
                outputTypes["qual"] = tempOutNames;
@@ -76,11 +75,11 @@ vector<string> TrimSeqsCommand::getRequiredFiles(){
 TrimSeqsCommand::TrimSeqsCommand(string option)  {
        try {
                
-               abort = false;
+               abort = false; calledHelp = false;   
                comboStarts = 0;
                
                //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
@@ -316,7 +315,7 @@ TrimSeqsCommand::~TrimSeqsCommand(){        /*      do nothing      */      }
 int TrimSeqsCommand::execute(){
        try{
        
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                numFPrimers = 0;  //this needs to be initialized
                numRPrimers = 0;