paralellized parsimony, unifrac.unweighted, phylo.diversity, indicator commands for...

[mothur.git] / clustersplitcommand.cpp

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 92f0e486898f80b2c6f85bb984a5b7662bc18340..74867ebdeb0ec271d07d727b7cf9c8d19aa13284 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -442,8 +442,7 @@ int ClusterSplitCommand::execute(){
         if (m->debug) { m->mothurOut("[DEBUG]: distName.size() = " + toString(distName.size()) + ".\n"); }
                 
                //output a merged distance file
-               if (splitmethod == "fasta")             { createMergedDistanceFile(distName); }
-                       
+               //if (splitmethod == "fasta")           { createMergedDistanceFile(distName); }
                                
                if (m->control_pressed) { return 0; }
                
@@ -1169,7 +1168,7 @@ string ClusterSplitCommand::clusterClassicFile(string thisDistFile, string thisN
             cluster->readPhylipFile(thisDistFile, nameMap);
                }else if (countfile != "") {
             ct = new CountTable();
-            ct->readTable(thisNamefile);
+            ct->readTable(thisNamefile, false);
             cluster->readPhylipFile(thisDistFile, ct);
         }
         tag = cluster->getTag();
@@ -1297,7 +1296,7 @@ string ClusterSplitCommand::clusterFile(string thisDistFile, string thisNamefile
             read->read(nameMap);
                }else if (countfile != "") {
             ct = new CountTable();
-            ct->readTable(thisNamefile);
+            ct->readTable(thisNamefile, false);
             read->read(ct);
         }else { read->read(nameMap); }