X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mgclustercommand.cpp;h=24c4f27777d21ed88b6f3b41411394502802404e;hp=b9c9d1eb845543bc38893068081b9367b913980b;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=deba0af0ccdcb6005ed5b2b82649b137c63fbdf7

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index b9c9d1e..24c4f27 100644
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -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) {