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/lib/gpFx.c src/hg/lib/gpFx.c
index 8356404..9d13251 100644
--- src/hg/lib/gpFx.c
+++ src/hg/lib/gpFx.c
@@ -601,31 +601,31 @@
 boolean safeFromNMD = isSafeFromNMD(exonIx, allele->variant, pred);
 setSpecificCodingSoTerm(effect, oldaa, newaa, cdsBasesAdded, safeFromNMD);
 
 return effect;
 }
 
 
 static boolean hasAltAllele(struct allele *alleles)
 /* Make sure there's something to work on here... */
 {
 while (alleles != NULL && alleles->isReference)
     alleles = alleles->next;
 return (alleles != NULL);
 }
 
-static char *firstAltAllele(struct allele *alleles)
+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. */
 {
 while (alleles != NULL && alleles->isReference)
     alleles = alleles->next;
 if (alleles == NULL)
     errAbort("firstAltAllele: no alt allele in list");
 return alleles->sequence;
 }
 
 static struct gpFx *gpFxInExon(struct variant *variant, struct txCoords *txc, int exonIx,
 			       struct genePred *pred, struct dnaSeq *transcriptSeq, struct lm *lm)
 /* Given a variant that overlaps an exon of pred, figure out what each allele does. */
 {