40665f857785f2b82af4f5de26642d2be9986d1e
angie
  Thu Dec 15 14:14:31 2016 -0800
If null variants (no_sequence_alteration) are not filtered out, then show them without bothering to intersect with genes.  This avoids wasted time and redundant output.

diff --git src/hg/lib/gpFx.c src/hg/lib/gpFx.c
index 7632f6c..5d6888c 100644
--- src/hg/lib/gpFx.c
+++ src/hg/lib/gpFx.c
@@ -977,31 +977,31 @@
 }
 
 static void checkVariantList(struct variant *variant)
 // check to see that we either have one variant (possibly with multiple
 // alleles) or that if we have a list of variants, they only have
 // one allele a piece.
 {
 if (variant->next == NULL)	 // just one variant
     return;
 
 for(; variant; variant = variant->next)
     if (variant->numAlleles != 1)
 	errAbort("gpFxPredEffect needs either 1 variant, or only 1 allele in all variants");
 }
 
-static struct gpFx *gpFxNoVariation(struct variant *variant, struct lm *lm)
+struct gpFx *gpFxNoVariation(struct variant *variant, struct lm *lm)
 /* Return a gpFx with SO term no_sequence_alteration, for VCF rows that aren't really variants. */
 {
 char *seq = NULL;
 struct allele *allele;
 for (allele = variant->alleles;  allele != NULL;  allele = allele->next)
     if (allele->isReference)
         {
         seq = allele->sequence;
         // Don't break out of the loop -- pick the last one we see because the first is likely
         // the "real" reference allele, while the other(s) is something like "<X>" or "<*>".
         }
 return gpFxNew(seq, "", no_sequence_alteration, none, lm);
 }
 
 struct gpFx *gpFxPredEffect(struct variant *variant, struct genePred *pred,