X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=removegroupscommand.cpp;h=9db35cb4bcb1fb78daa9545ecf4464b29c09d2e2;hp=64f9ab6822301310e975e6bbe58736e953eed4f2;hb=499f4ac6e321f9f03d4c3aa25c3b6880892c8b83;hpb=58e640f9968ed426ac8cc0ebe3c01564ce68b4d7

diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index 64f9ab6..9db35cb 100644
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -377,7 +377,7 @@ int RemoveGroupsCommand::execute(){
                 m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
             }
             CountTable ct;
-            ct.readTable(countfile, true);
+            ct.readTable(countfile, true, false);
             if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, aborting.\n"); return 0; }
             
             vector<string> gNamesOfGroups = ct.getNamesOfGroups();
@@ -560,9 +560,9 @@ int RemoveGroupsCommand::readShared(){
 		m->setGroups(groupsToKeep);
 		m->clearAllGroups();
 		m->saveNextLabel = "";
-		m->printedHeaders = false;
-		m->currentBinLabels.clear();
-		m->binLabelsInFile.clear();
+		m->printedSharedHeaders = false;
+		m->currentSharedBinLabels.clear();
+		m->sharedBinLabelsInFile.clear();
 		
 		InputData input(sharedfile, "sharedfile");
 		lookup = input.getSharedRAbundVectors();