added modify names parameter to set.dir

[mothur.git] / countgroupscommand.cpp

diff --git a/countgroupscommand.cpp b/countgroupscommand.cpp
index 6da077485c5fcd7641d759ceb6820dc9652033a7..83c2d315d0b8f781caa02c04c4fed5e1cb6b6a0d 100644 (file)
--- a/countgroupscommand.cpp
+++ b/countgroupscommand.cpp
@@ -261,7 +261,7 @@ int CountGroupsCommand::execute(){
             m->openOutputFile(outputFileName, out);
             
                        CountTable ct;
-                       ct.readTable(countfile);
+                       ct.readTable(countfile, true);
             
                        //make sure groups are valid
                        //takes care of user setting groupNames that are invalid or setting groups=all