04c67a0e7bcb65c217598e5e44084bf4c5c0674d
angie
  Tue Mar 5 12:16:10 2013 -0800
Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along
with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output.

diff --git src/hg/inc/gpFx.h src/hg/inc/gpFx.h
index 0f55a90..bc69c42 100644
--- src/hg/inc/gpFx.h
+++ src/hg/inc/gpFx.h
@@ -1,27 +1,29 @@
 #ifndef GPFX_H
 #define GPFX_H
 
 #include "variant.h"
-#include "soterm.h"
+#include "soTerm.h"
 
 // a single gpFx variant effect call
 struct gpFx
 {
 struct gpFx *next;
-
-struct soCall so;
+    char *allele;		// Allele sequence used to determine functional effect
+    struct soCall so;		// Sequence Ontology ID of effect and plus associated data
 };
 
 struct gpFx *gpFxPredEffect(struct variant *variant, struct genePred *pred,
     struct dnaSeq *transcriptSequence);
 // return the predicted effect(s) of a variation list on a genePred
 
 // number of bases up or downstream that we flag
-#define GPRANGE 500
+#define GPRANGE 5000
 
 #define gpFxIsCodingChange(gpfx) (gpfx->so.soNumber == inframe_deletion || \
+				  gpfx->so.soNumber == inframe_insertion || \
 				  gpfx->so.soNumber == frameshift_variant || \
 				  gpfx->so.soNumber == synonymous_variant || \
-				  gpfx->so.soNumber == non_synonymous_variant)
+				  gpfx->so.soNumber == missense_variant || \
+				  gpfx->so.soNumber == stop_gained)
 
 #endif /* GPFX_H */