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

[mothur.git] / clustersplitcommand.cpp

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 0e6798f39039ad9245e7e12131ac5722cdc34804..74867ebdeb0ec271d07d727b7cf9c8d19aa13284 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -439,9 +439,10 @@ int ClusterSplitCommand::execute(){
                vector< map<string, string> > distName = split->getDistanceFiles();  //returns map of distance files -> namefile sorted by distance file size
                delete split;
                
+        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; }
                
@@ -945,7 +946,7 @@ vector<string>  ClusterSplitCommand::createProcesses(vector< map<string, string>
             if ((processToAssign-1) == 1) { m->mothurOut(distName[i].begin()->first + "\n"); }
         }
         
-        //not lets reverse the order of ever other process, so we balance big files running with little ones
+        //now lets reverse the order of ever other process, so we balance big files running with little ones
         for (int i = 0; i < processors; i++) {
             //cout << i << endl;
             int remainder = ((i+1) % processors);
@@ -1167,7 +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();
@@ -1295,7 +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); }