Index: src/gfServer/gfServer.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/gfServer/gfServer.c,v
retrieving revision 1.55
retrieving revision 1.56
diff -b -B -U 4 -r1.55 -r1.56
--- src/gfServer/gfServer.c	23 Sep 2009 18:42:16 -0000	1.55
+++ src/gfServer/gfServer.c	8 Oct 2009 18:09:38 -0000	1.56
@@ -906,11 +906,13 @@
 tileSize = optionInt("tileSize", tileSize);
 stepSize = optionInt("stepSize", stepSize);
 if (stepSize == 0)
     stepSize = tileSize;
-repMatch = round( (double)tileSize/(double)stepSize * repMatch);
+if (optionExists("repMatch"))
+    repMatch = optionInt("repMatch", 0);
+else
+    repMatch = gfDefaultRepMatch(tileSize, stepSize, doTrans);
 minMatch = optionInt("minMatch", minMatch);
-repMatch = optionInt("repMatch", repMatch);
 maxDnaHits = optionInt("maxDnaHits", maxDnaHits);
 maxTransHits = optionInt("maxTransHits", maxTransHits);
 maxNtSize = optionInt("maxNtSize", maxNtSize);
 maxAaSize = optionInt("maxAaSize", maxAaSize);

