changes while testing

[mothur.git] / mgclustercommand.cpp

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index b9c9d1eb845543bc38893068081b9367b913980b..e76dd4860b03826db116323af7e42528a591c526 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -247,7 +247,7 @@ int MGClusterCommand::execute(){
         if(countfile != "") {
             //map<string, int> nameMapCounts = m->readNames(namefile);
             ct = new CountTable();
-            ct->readTable(countfile);
+            ct->readTable(countfile, false);
             rabund = new RAbundVector();
             createRabund(ct, list, rabund);
         }else {
@@ -271,10 +271,10 @@ int MGClusterCommand::execute(){
                
         map<string, string> variables; 
         variables["[filename]"] = fileroot;
-        if (countfile != "") { variables["[tag2]"] = "unique_list"; }
         variables["[clustertag]"] = tag;
         string sabundFileName = getOutputFileName("sabund", variables);
         string rabundFileName = getOutputFileName("rabund", variables);
+        if (countfile != "") { variables["[tag2]"] = "unique_list"; }
         string listFileName = getOutputFileName("list", variables);
         
         if (countfile == "") {
@@ -312,10 +312,13 @@ int MGClusterCommand::execute(){
                                outputTypes.clear();
                                return 0; 
                        }
-               
+            
+            
                        //cluster using cluster classes
                        while (distMatrix->getSmallDist() < cutoff && distMatrix->getNNodes() > 0){
                                
+                if (m->debug) {  cout << "numNodes=" << distMatrix->getNNodes() << " smallDist = " << distMatrix->getSmallDist() << endl; }
+                
                                cluster->update(cutoff);
                                
                                if (m->control_pressed) {