X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removegroupscommand.cpp;h=4462b52863f235cb8436d0db77fe5a3698823534;hb=0486bc2eed084ac387d2f59b6d23d13b2382daf7;hp=93646bcf8ad225a3db162dc2cb582cf2f164e481;hpb=e3e0858c684c4608d679840024e5095ddc8e2719;p=mothur.git

diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index 93646bc..4462b52 100644
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -27,8 +27,7 @@ vector<string> RemoveGroupsCommand::getValidParameters(){
 //**********************************************************************************************************************
 RemoveGroupsCommand::RemoveGroupsCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["fasta"] = tempOutNames;
 		outputTypes["taxonomy"] = tempOutNames;
@@ -67,10 +66,10 @@ vector<string> RemoveGroupsCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 RemoveGroupsCommand::RemoveGroupsCommand(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 {
 			//valid paramters for this command
@@ -222,7 +221,7 @@ void RemoveGroupsCommand::help(){
 int RemoveGroupsCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		groupMap = new GroupMap(groupfile);
 		groupMap->readMap();
@@ -420,6 +419,7 @@ int RemoveGroupsCommand::readName(){
 				}
 			}
 			
+			
 			//if the name in the first column is in the set then print it and any other names in second column also in set
 			if (names.count(firstCol) == 0) {
 				
@@ -587,6 +587,8 @@ int RemoveGroupsCommand::fillNames(){
 				names.insert(seqs[i]);
 			}
 		}
+		
+		return 0;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "RemoveGroupsCommand", "fillNames");