510ec86d77710a8670b5276a8eea40f3d6ab74cc
braney
  Fri Apr 7 12:16:08 2023 -0700
tweak bigChain support to work with snakes.  Change UI option to use the
words "rearrangement graph" instead of snake

diff --git src/hg/hgTracks/chainTrack.c src/hg/hgTracks/chainTrack.c
index 900bbbb..7dae716 100644
--- src/hg/hgTracks/chainTrack.c
+++ src/hg/hgTracks/chainTrack.c
@@ -376,30 +376,32 @@
     bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow));
     if ((optionChrStr != NULL) && !startsWith(optionChrStr, bedRow[7]))
         continue;
 
     if (chainCart->scoreFilter >0)
         {
         unsigned score = sqlUnsigned(bedRow[4]);
         if  (score < chainCart->scoreFilter)
             continue;
         }
 
     struct bed *bed = bedLoadN(bedRow, 6);
     lf = bedMungToLinkedFeatures(&bed, tg->tdb, fieldCount,
         0, 1000, FALSE);
 
+    lf->qSize = sqlUnsigned(bedRow[8]);
+
     if (*bedRow[5] == '-')
 	{
 	lf->orientation = -1;
         qs = sqlUnsigned(bedRow[8]) - sqlUnsigned(bedRow[10]);
 	}
     else
         {
 	lf->orientation = 1;
 	qs = sqlUnsigned(bedRow[9]);
 	}
 
     int len = strlen(bedRow[7]) + 32;
     lf->name = needMem(len);
     if (!doSnake)
         safef(lf->name, len, "%s %c %dk", bedRow[7], *bedRow[5], qs/1000);