added modify names parameter to set.dir

[mothur.git] / classifyotucommand.cpp

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index d0ddc691236e59cdd0fcb6a2578249375fd8ad0e..170c234ac245e6c32e3174ad80145fbcc359f2f2 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -293,7 +293,7 @@ int ClassifyOtuCommand::execute(){
                if (namefile != "")     {       m->readNames(namefile, nameMap, true);  }
         if (groupfile != "")    {   groupMap = new GroupMap(groupfile);  groupMap->readMap();  groups = groupMap->getNamesOfGroups(); }
         else { groupMap = NULL;  }
-        if (countfile != "") {  ct = new CountTable(); ct->readTable(countfile);  if (ct->hasGroupInfo()) { groups = ct->getNamesOfGroups(); } }
+        if (countfile != "") {  ct = new CountTable(); ct->readTable(countfile, true);  if (ct->hasGroupInfo()) { groups = ct->getNamesOfGroups(); } }
         else {  ct = NULL;    }
         
                //read taxonomy file and save in map for easy access in building bin trees