added fasta method to cluster.split

[mothur.git] / clustersplitcommand.cpp

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index f6bf105cf915710947493d06b8d6461f309e9212..8d21d1a83e1eff3d518861273dff976650d8c56c 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -113,7 +113,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }  
                        else if (fastafile == "not found") { fastafile = ""; }
-                       else { splitmethod = "fasta";  }
+                       else { distfile = fastafile;  splitmethod = "fasta";  }
                        
                        taxFile = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxFile == "not open") { abort = true; }    
@@ -271,10 +271,10 @@ int ClusterSplitCommand::execute(){
                
                //split matrix into non-overlapping groups
                SplitMatrix* split;
-               if (splitmethod == "distance")                  {       split = new SplitMatrix(distfile, namefile, taxFile, cutoff, splitmethod, large);                                       }
-               else if (splitmethod == "classify")             {       split = new SplitMatrix(distfile, namefile, taxFile, taxLevelCutoff, splitmethod, large);                       }
-               else if (splitmethod == "fasta")                {       split = new SplitMatrix(fastafile, namefile, taxFile, taxLevelCutoff, splitmethod, processors);         }
-               else { m->mothurOut("Not a valid splitting method.  Valid splitting algorithms are distance, classify or fasta."); m->mothurOutEndLine(); return 0; }
+               if (splitmethod == "distance")                  {       split = new SplitMatrix(distfile, namefile, taxFile, cutoff, splitmethod, large);                                                       }
+               else if (splitmethod == "classify")             {       split = new SplitMatrix(distfile, namefile, taxFile, taxLevelCutoff, splitmethod, large);                                       }
+               else if (splitmethod == "fasta")                {       split = new SplitMatrix(fastafile, namefile, taxFile, taxLevelCutoff, splitmethod, processors, outputDir);      }
+               else { m->mothurOut("Not a valid splitting method.  Valid splitting algorithms are distance, classify or fasta."); m->mothurOutEndLine(); return 0;             }
                
                split->split();