26d6cd9597d40b55635b1fbacc8dd64978887474
angie
  Mon Jun 17 10:51:53 2013 -0700
As Jonathan pointed out in note 46, Ensembl VEP always shows a/the alternate allele,even when the allele isn't used to make the functional prediction -- follow suit.
refs #6152

diff --git src/hg/inc/gpFx.h src/hg/inc/gpFx.h
index d7cd639..9da9bc5 100644
--- src/hg/inc/gpFx.h
+++ src/hg/inc/gpFx.h
@@ -34,23 +34,23 @@
 	    char *codonOld;	// codons, before change by variant (starting at cdsPos)
 	    char *codonNew;	// codons, changed by variant
 	    } codingChange;
 	struct nonCodingExon	// variant in non-coding gene or UTR of coding gene
 	    {
 	    uint exonNumber;	// 0-based exon number (from genePred, beware false "introns")
 	    uint cDnaPosition;	// offset of variant in transcript cDNA
 	    } nonCodingExon;
 	struct intron 		// intron_variant
 	    {
 	    uint intronNumber;	// 0-based intron number (from genePred, beware false "introns")
 	    } intron;
 	} details;
     };
 
-struct gpFx *gpFxPredEffect(struct variant *variant, struct genePred *pred,
+struct gpFx *gpFxPredEffect(struct variant *variant, struct genePred *pred, char *refAllele,
 			    struct dnaSeq *transcriptSequence, struct lm *lm);
 // return the predicted effect(s) of a variation list on a genePred
 
 // number of bases up or downstream that we flag
 #define GPRANGE 5000
 
 #endif /* GPFX_H */