X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removerarecommand.cpp;h=24b616560de3bed794d423f4cb7a3544f0d48f5f;hb=e0ce7cbc93d7d2fbb753ca694182db092a0ea0e7;hp=f82c4b03ead17a723b7d61e2643e5054907d9fd4;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/removerarecommand.cpp b/removerarecommand.cpp
index f82c4b0..24b6165 100644
--- a/removerarecommand.cpp
+++ b/removerarecommand.cpp
@@ -220,7 +220,7 @@ RemoveRareCommand::RemoveRareCommand(string option)  {
 			
 			string temp = validParameter.validFile(parameters, "nseqs", false);	 
 			if (temp == "not found") { m->mothurOut("nseqs is a required parameter."); m->mothurOutEndLine(); abort = true; }
-			else { convert(temp, nseqs); }
+			else { m->mothurConvert(temp, nseqs); }
 			
 			temp = validParameter.validFile(parameters, "bygroup", false);	 if (temp == "not found") { temp = "f"; }
 			byGroup = m->isTrue(temp);
@@ -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);  }