X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sensspeccommand.cpp;h=6a22fd686096e83308faf7a68e98e9391d722fe0;hb=a4f05f09c250323132a4b9427f41a3ededaec634;hp=78dce1794003457a077fe993958c75909c1020a7;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index 78dce17..6a22fd6 100644
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -24,7 +24,7 @@ vector<string> SensSpecCommand::getValidParameters(){
 //**********************************************************************************************************************
 SensSpecCommand::SensSpecCommand(){	
 	try {
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["sensspec"] = tempOutNames;
 	}
@@ -61,10 +61,10 @@ vector<string> SensSpecCommand::getRequiredFiles(){
 SensSpecCommand::SensSpecCommand(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;
@@ -207,7 +207,7 @@ SensSpecCommand::~SensSpecCommand(){	/*	do nothing	*/	}
 
 int SensSpecCommand::execute(){
 	try{
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 
 		setUpOutput();
 		outputNames.push_back(sensSpecFileName); outputTypes["sensspec"].push_back(sensSpecFileName);