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/inc/gpFx.h src/hg/inc/gpFx.h
index 03892b4..68972dd 100644
--- src/hg/inc/gpFx.h
+++ src/hg/inc/gpFx.h
@@ -52,16 +52,19 @@
 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
 
 boolean hasAltAllele(struct allele *alleles);
 /* Return TRUE if alleles include at least one non-reference allele. */
 
 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. */
 
+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. */
+
 #endif /* GPFX_H */