5a3cd681e0bebecf7acff2888b4aee6f2b5a0904
braney
  Fri Nov 8 11:08:32 2013 -0800
fix bug when the sequence is null from HAL snakes
diff --git src/hg/hgTracks/snakeTrack.c src/hg/hgTracks/snakeTrack.c
index ed7ac8d..452790e 100644
--- src/hg/hgTracks/snakeTrack.c
+++ src/hg/hgTracks/snakeTrack.c
@@ -1071,31 +1071,33 @@
 	    {
 	    lf = hel->val;
 	    }
 
 	struct snakeFeature  *sf;
 	AllocVar(sf);
 	slAddHead(&lf->components, sf);
 	
 	sf->start = cur->tStart;
 	sf->end = cur->tStart + cur->size;
 	sf->qStart = cur->qStart;
 	sf->qEnd = cur->qStart + cur->size;
 	sf->orientation = (cur->strand == '+') ? 1 : -1;
 	sf->tSequence = cloneString(cur->tSequence);
 	sf->qSequence = cloneString(cur->qSequence);
+	if (sf->tSequence != NULL)
 	    toUpperN(sf->tSequence, strlen(sf->tSequence));
+	if (sf->qSequence != NULL)
 	    toUpperN(sf->qSequence, strlen(sf->qSequence));
 	sf->qName = cur->qChrom;
 
 	cur = cur->next;
     }
     if (tg->visibility == tvFull)
 	{
 	for(lf=lfList; lf ; lf = lf->next)
 	    {
 	    slSort(&lf->components, snakeFeatureCmpQStart);
 	    }
 	}
     else if ((tg->visibility == tvPack) && (lfList != NULL))
 	{
 	assert(lfList->next == NULL);