649465acaa28e9816268e2e56dd1ea632e823adf
angie
  Fri Oct 18 10:30:32 2013 -0700
Another fix for ML #11775: use a real alternate allele for intergenicvariants, so users aren't misled by the VEP placeholder "-".

diff --git src/hg/inc/gpFx.h src/hg/inc/gpFx.h
index d7cd639..5e35f3f 100644
--- src/hg/inc/gpFx.h
+++ src/hg/inc/gpFx.h
@@ -41,16 +41,21 @@
 	    } 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 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
 
+char *firstAltAllele(struct allele *alleles);
+/* Ensembl always reports an alternate allele, even if that allele is not being used
+ * to calculate any consequence.  When allele doesn't really matter, just use the
+ * first alternate allele that is given. */
+
 #endif /* GPFX_H */