adding labels to list file.

[mothur.git] / removegroupscommand.cpp

diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index 64f9ab6822301310e975e6bbe58736e953eed4f2..9db35cb4bcb1fb78daa9545ecf4464b29c09d2e2 100644 (file)
--- 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();