584b7af6bcac17cc116ca2c4801e60a149d49c2c
hiram
  Wed Aug 7 15:23:41 2024 -0700
BIGNUM needs to be a bit larger for chain/net processing on sequences over 1 Gb refs #34248

diff --git src/hg/mouseStuff/axtBest/axtBest.c src/hg/mouseStuff/axtBest/axtBest.c
index 2d5e8fa..7e8bf23 100644
--- src/hg/mouseStuff/axtBest/axtBest.c
+++ src/hg/mouseStuff/axtBest/axtBest.c
@@ -1,26 +1,28 @@
 /* axtBest - Remove second best alignments. 
  * This file is copyright 2002 Jim Kent, but license is hereby
  * granted for all use - public, private or commercial. */
 #include "common.h"
 #include "linefile.h"
 #include "memalloc.h"
 #include "hash.h"
 #include "options.h"
 #include "dnautil.h"
 #include "axt.h"
 
+#undef BIGNUM
+#define BIGNUM 0x7fffffff	/* larger than the standard size BIGNUM */
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "axtBest - Remove second best alignments\n"
   "usage:\n"
   "   axtBest in.axt chrom out.axt\n"
   "options:\n"
   "   -winSize=N  - Size of window, default 10000\n"
   "   -minScore=N - Minimum score alignments to consider.  Default 1000\n"
   "   -minOutSize=N - Minimum score of piece to output. Default 10\n"
   "   -matrix=file.mat - override default scoring matrix\n"
   "   -verbose=N - Alter verbosity (default 1)\n"
   "   -reads - allow reads to be split across introns but not chromosomes\n"