added modify names parameter to set.dir

[mothur.git] / getgroupscommand.cpp

diff --git a/getgroupscommand.cpp b/getgroupscommand.cpp
index e4f7450b4291e1ca281ebe806dd476fac86019b9..45e0a783e393ba828d8bd74c3884fa45779a92f2 100644 (file)
--- a/getgroupscommand.cpp
+++ b/getgroupscommand.cpp
@@ -370,7 +370,7 @@ int GetGroupsCommand::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);
+            ct.readTable(countfile, true);
             if (!ct.hasGroupInfo()) { m->mothurOut("[ERROR]: your count file does not contain group info, aborting.\n"); return 0; }
                 
             vector<string> gNamesOfGroups = ct.getNamesOfGroups();