X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getotuscommand.cpp;fp=getotuscommand.cpp;h=d29773ca340cf1119f04c312f897a0e5f2d7d4e8;hb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;hp=681deb7646540d663560ed68d5da61deadea0f44;hpb=220dc345e493cddc569521111ce32ac4d965ab7f;p=mothur.git

diff --git a/getotuscommand.cpp b/getotuscommand.cpp
index 681deb7..d29773c 100644
--- a/getotuscommand.cpp
+++ b/getotuscommand.cpp
@@ -134,7 +134,8 @@ GetOtusCommand::GetOtusCommand(string option)  {
 			//check for required parameters
 			accnosfile = validParameter.validFile(parameters, "accnos", true);
 			if (accnosfile == "not open") { abort = true; }
-			else if (accnosfile == "not found") {  accnosfile = ""; }	
+			else if (accnosfile == "not found") {  accnosfile = ""; }
+			else { m->setAccnosFile(accnosfile); }
 			
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") { abort = true; }
@@ -142,7 +143,7 @@ GetOtusCommand::GetOtusCommand(string option)  {
 				groupfile = m->getGroupFile(); 
 				if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}	
+			}else { m->setGroupFile(groupfile); }	
 			
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not open") { abort = true; }
@@ -150,7 +151,7 @@ GetOtusCommand::GetOtusCommand(string option)  {
 				listfile = m->getListFile(); 
 				if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}	
+			}else { m->setListFile(listfile); }	
 			
 			groups = validParameter.validFile(parameters, "groups", false);			
 			if (groups == "not found") { groups = ""; }