bdaa14f5971a9aca2e9793c7202eb3bca855d5be
kent
  Thu Jul 17 15:16:25 2014 -0700
Expanding limit on alignment size since machines are bigger now.
diff --git src/lib/axtAffine.c src/lib/axtAffine.c
index 27e184f..1c7e383 100644
--- src/lib/axtAffine.c
+++ src/lib/axtAffine.c
@@ -1,31 +1,31 @@
 /* axtAffine - do alignment of two (shortish) sequences with
  * affine gap scoring, and return the result as an axt. 
  * This file is copyright 2000-2004 Jim Kent, but license is hereby
  * granted for all use - public, private or commercial. */
 
 #include "common.h"
 #include "pairHmm.h"
 #include "axt.h"
 
 
 
 boolean axtAffineSmallEnough(double querySize, double targetSize)
 /* Return TRUE if it is reasonable to align sequences of given sizes
  * with axtAffine. */
 {
-return targetSize * querySize <= 1.0E8;
+return targetSize * querySize <= 1.0E9;
 }
 
 static void affineAlign(char *query, int querySize, 
 	char *target, int targetSize, struct axtScoreScheme *ss,
 	struct phmmMatrix **retMatrix, struct phmmAliPair **retPairList,
 	int *retScore)
 /* Use dynamic programming to do alignment including affine gap
  * scores. */
 {
 struct phmmMatrix *a;
 struct phmmState *hf, *iq, *it;
 int qIx, tIx, sIx;  /* Query, target, and state indices */
 int rowOffset, newCellOffset;
 int bestScore = -0x4fffffff;
 struct phmmMommy *bestCell = NULL;