added [ERROR] flag if command aborts

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index e4d0165d136da966addcf3f235a162cad9f5baa1..5c5d28b0390470ae05833f177fba7f7d1012e051 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -65,8 +65,7 @@ vector<string> TrimFlowsCommand::getRequiredFiles(){
 
 TrimFlowsCommand::TrimFlowsCommand(){  
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["flow"] = tempOutNames;
                outputTypes["fasta"] = tempOutNames;
@@ -101,11 +100,11 @@ void TrimFlowsCommand::help(){
 TrimFlowsCommand::TrimFlowsCommand(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
@@ -250,7 +249,7 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
 int TrimFlowsCommand::execute(){
        try{
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 
                string trimFlowFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "trim.flow";
                outputNames.push_back(trimFlowFileName); outputTypes["flow"].push_back(trimFlowFileName);