X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsabundcommand.cpp;h=799d8dced192019f65a633e946262db92c1e615f;hb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;hp=820868416b7bfc9bebcc27c8f73c24c6ddb7bbb4;hpb=10c8178dc5e3f96ef8e92a986f1eddd13e622173;p=mothur.git

diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index 8208684..799d8dc 100644
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -67,6 +67,7 @@ GetSAbundCommand::GetSAbundCommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -113,12 +114,12 @@ GetSAbundCommand::GetSAbundCommand(string option)  {
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not open") { listfile = ""; abort = true; }
 			else if (listfile == "not found") { listfile = ""; }
-			else {  format = "list"; inputfile = listfile; }
+			else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 			
 			rabundfile = validParameter.validFile(parameters, "rabund", true);
 			if (rabundfile == "not open") { rabundfile = ""; abort = true; }	
 			else if (rabundfile == "not found") { rabundfile = ""; }
-			else {  format = "rabund"; inputfile = rabundfile; }
+			else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
 			
 		
 						//check for optional parameter and set defaults