X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=splitmatrix.cpp;fp=splitmatrix.cpp;h=8ccb867e250aed20816be57d779d6105316109f9;hb=4160a27002f4a3ca436fcd62eca0366b09f8e901;hp=80f311dc61cbd8d52342ee55d39c2284b161761d;hpb=d945488119ad368b180537f36ed40298ff170f39;p=mothur.git

diff --git a/splitmatrix.cpp b/splitmatrix.cpp
index 80f311d..8ccb867 100644
--- a/splitmatrix.cpp
+++ b/splitmatrix.cpp
@@ -186,6 +186,7 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
 		for (int i = 0; i < numGroups; i++) { 
 			
 			string options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors) + ", cutoff=" + toString(distCutoff);
+			if (outputDir != "") { options += ", outputdir=" + outputDir; }
 			
 			Command* command = new DistanceCommand(options);