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/axtBestNear/axtBestNear.c src/hg/mouseStuff/axtBestNear/axtBestNear.c
index c75246f..c8d2db8 100644
--- src/hg/mouseStuff/axtBestNear/axtBestNear.c
+++ src/hg/mouseStuff/axtBestNear/axtBestNear.c
@@ -1,28 +1,31 @@
 /* axtBestNear - Remove near 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"
 
 #define NEARSIZE 2  /* keep this many best hits */
 
+#undef BIGNUM
+#define BIGNUM 0x7fffffff	/* larger than the standard size BIGNUM */
+
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "axtBestNear - Remove near best alignments\n"
   "usage:\n"
   "   axtBestNear 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"
   "   -near=N - allow alignments that are within N of the best Default 0.8 \n"
   "   -matrix=file.mat - override default scoring matrix\n"
   "Alignments scoring over minScore (where each matching base counts\n"
   "about +100 in the default scoring scheme) are projected onto the\n"