73b5a8a246d364e7ba27c711ebe7f6eff042ab30
kent
  Thu May 21 11:56:59 2015 -0700
Fixing fastMap bogus double-sided gaps redmine #15317

diff --git src/jkOwnLib/gfBlatLib.c src/jkOwnLib/gfBlatLib.c
index 2faefd6..cb9acc6 100644
--- src/jkOwnLib/gfBlatLib.c
+++ src/jkOwnLib/gfBlatLib.c
@@ -719,32 +719,32 @@
  * rangeList. */
 {
 struct gfSeqSource *target = clump->target;
 aaSeq *tSeq = target->seq;
 BIOPOL *qs, *ts, *qe, *te;
 struct gfHit *hit;
 int qStart = 0, tStart = 0, qEnd = 0, tEnd = 0, newQ = 0, newT = 0;
 boolean outOfIt = TRUE;		/* Logically outside of a clump. */
 struct gfRange *range;
 BIOPOL *lastQs = NULL, *lastQe = NULL, *lastTs = NULL, *lastTe = NULL;
 int (*scoreMatch)(char a, char b) = (isProt ? aaScore2 : dnaScore2);
 int maxDown, minSpan;
 
 if (fastMap)
     {
-    maxDown = 1;
-    minSpan = 50;
+    maxDown = 2;
+    minSpan = 20;
     }
 else
     {
     maxDown = 10;
     minSpan = 0;
     }
 
 
 if (tSeq == NULL)
     internalErr();
 
 /* The termination condition of this loop is a little complicated.
  * We want to output something either when the next hit can't be
  * merged into the previous, or at the end of the list.  To avoid
  * duplicating the output code we're forced to complicate the loop