src/gfServer/gfServer.c 1.56
1.56 2009/10/08 18:09:38 kent
Moving repMatch calculations from blat to library so can be shared with gfServer.
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);