added sff.multiple command. fixed issue with windows paralellization in chimera...

[mothur.git] / mgclustercommand.cpp

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index a845e0bfe080782b2b12d2f1a634925781578d70..477450475d479eb4308d9c2503086b9d7c03b051 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -268,7 +268,9 @@ int MGClusterCommand::execute(){
                
         string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
         string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
-        string listFileName = fileroot+ tag + "." + getOutputFileNameTag("list");
+        string listFileName = fileroot+ tag + ".";
+        if (countfile != "") { listFileName += "unique_"; }
+        listFileName += getOutputFileNameTag("list");
         
         if (countfile == "") {
             m->openOutputFile(sabundFileName,  sabundFile);
@@ -287,7 +289,7 @@ int MGClusterCommand::execute(){
                
                if (!hclusterWanted) {
                        //get distmatrix and overlap
-                       SparseMatrix* distMatrix = read->getDistMatrix();
+                       SparseDistanceMatrix* distMatrix = read->getDistMatrix();
                        overlapMatrix = read->getOverlapMatrix(); //already sorted by read 
                        delete read;