mods in testing 1.16.0

[mothur.git] / splitmatrix.cpp

diff --git a/splitmatrix.cpp b/splitmatrix.cpp
index ec71e5bfd0090b1172d50403a6b54903a030c3f4..80f311dc61cbd8d52342ee55d39c2284b161761d 100644 (file)
--- a/splitmatrix.cpp
+++ b/splitmatrix.cpp
@@ -10,6 +10,7 @@
 #include "splitmatrix.h"
 #include "phylotree.h"
 #include "distancecommand.h"
+#include "seqsummarycommand.h"
 
 /***********************************************************************/
 
@@ -65,6 +66,8 @@ int SplitMatrix::splitDistance(){
         
                if (large)      { splitDistanceLarge(); }
                else            { splitDistanceRAM();   }
+               
+               return 0;
                        
        }
        catch(exception& e) {
@@ -182,9 +185,10 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
                //process each distance file
                for (int i = 0; i < numGroups; i++) { 
                        
-                       string options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(1) + ", cutoff=" + toString(distCutoff);
+                       string options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors) + ", cutoff=" + toString(distCutoff);
                        
                        Command* command = new DistanceCommand(options);
+                       
                        command->execute();
                        delete command;
                        
@@ -193,7 +197,7 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
                        //remove old names files just in case
                        remove((namefile + "." + toString(i) + ".temp").c_str());
                }
-               
+                       
                singleton = namefile + ".extra.temp";
                ofstream remainingNames;
                m->openOutputFile(singleton, remainingNames);