3afb1ad18d251832c36c02910ba194a3996ab47a
braney
  Mon May 9 14:56:22 2016 -0700
some changes to bigPsl format

diff --git src/hg/hgTracks/bigBedTrack.c src/hg/hgTracks/bigBedTrack.c
index feeb189..cb2fffa 100644
--- src/hg/hgTracks/bigBedTrack.c
+++ src/hg/hgTracks/bigBedTrack.c
@@ -160,31 +160,31 @@
 char *scoreFilter = cartOrTdbString(cart, track->tdb, "scoreFilter", NULL);
 char *mouseOverField = cartOrTdbString(cart, track->tdb, "mouseOverField", NULL);
 int minScore = 0;
 if (scoreFilter)
     minScore = atoi(scoreFilter);
 
 int mouseOverIdx = bbExtraFieldIndex(tdb, mouseOverField);
 
 for (bb = bbList; bb != NULL; bb = bb->next)
     {
     bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow));
     struct linkedFeatures *lf;
     if (sameString(track->tdb->type, "bigPsl"))
 	{
 	char *seq, *cds;
-	struct psl *psl = pslFromBigPsl(chromName, bb, seqBaseCount, &seq, &cds); 
+	struct psl *psl = pslFromBigPsl(chromName, bb,  &seq, &cds); 
 	int sizeMul = 1;  // we're assuming not protein at the moment
 	boolean isXeno = 0;  // just affects grayIx
 	boolean nameGetsPos = FALSE; // we want the name to stay the name
 
 	lf = lfFromPslx(psl, sizeMul, isXeno, nameGetsPos, track);
 	lf->original = psl;
 	if (lf->orientation == -1)
 	    reverseComplement(seq, strlen(seq));
 	lf->extra = seq;
 	lf->cds = cds;
 	}
     else
 	{
 	struct bed *bed = bedLoadN(bedRow, fieldCount);
 	lf = bedMungToLinkedFeatures(&bed, tdb, fieldCount,