38bc9e01ce6e7b22f0533c6624a64a17fd6c7bff
angie
  Fri Sep 27 17:20:54 2013 -0700
Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons.  Now, instead of iterating through
exons and building a new genePred along with a sequence that has
one exon's modification, we project the variant start and end onto
cDNA and CDS coords up front.  Then there is only one modification
to make per allele, and in fact we only care about the actual
modification when there's a CDS change.
A new SO term, exon_loss, has been incorporated into gpFx and
hgVai's/annoGratorGpVar's filtering.
fixes #11771

diff --git src/hg/inc/gpFx.h src/hg/inc/gpFx.h
index 9da9bc5..d7cd639 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, char *refAllele,
+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
 
 #endif /* GPFX_H */