X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=removerarecommand.cpp;fp=removerarecommand.cpp;h=351ace6db7ea98c033514086004091e6352f663e;hp=f82c4b03ead17a723b7d61e2643e5054907d9fd4;hb=55386dddad84cc1140d736cabaf4dd0ae16f2e01;hpb=990ded2eb38078a417fa00b4fbb4d3c24f4b5046

diff --git a/removerarecommand.cpp b/removerarecommand.cpp
index f82c4b0..351ace6 100644
--- a/removerarecommand.cpp
+++ b/removerarecommand.cpp
@@ -353,7 +353,8 @@ int RemoveRareCommand::processList(){
 		if (groupfile != "") { 
 			groupMap = new GroupMap(groupfile); groupMap->readMap(); 
 			SharedUtil util;
-			util.setGroups(Groups, groupMap->namesOfGroups);
+			vector<string> namesGroups = groupMap->getNamesOfGroups();
+			util.setGroups(Groups, namesGroups);
 			m->openOutputFile(outputGroupFileName, outGroup);
 		}
 		
@@ -624,7 +625,7 @@ int RemoveRareCommand::processRabund(){
 //**********************************************************************************************************************
 int RemoveRareCommand::processShared(){
 	try {
-		m->Groups = Groups;
+		m->setGroups(Groups);
 		
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }