cabb4fa228289aadbaf6a1a16461646fcb7aa774
braney
  Tue Apr 10 18:55:38 2012 -0700
interim check-in for #6152.   Adding variant structure and setup that allows maintaing multiple variants in one gp.
diff --git src/hg/inc/gpFx.h src/hg/inc/gpFx.h
index 9e4f3dd..217ccfa 100644
--- src/hg/inc/gpFx.h
+++ src/hg/inc/gpFx.h
@@ -1,28 +1,36 @@
 #ifndef GPFX_H
 #define GPFX_H
 
+#include "variant.h"
+
 struct gpFx
 {
 struct gpFx *next;
 enum gpFxType { 
 	gpFxNone, 
 	gpFxUtr5, 
 	gpFxUtr3, 
 	gpFxSynon, 
 	gpFxNonsynon, 
 	gpFxSplice5, 
+	gpFxUpstream, 
+	gpFxDownstream, 
 	gpFxIntron 
 	} gpFxType; ;
 
 int    gpFxNumber;        // exon or intron number
 int    gpFxTransOffset;    //offset in transcript
 char   *gpFxBaseChange;     //base change in transcript
 int    gpFxCodonChange;    //codon triplet change in transcript
 int    gpFxProteinOffset;  //offset in protein
 int    gpFxProteinChange;  //peptide change in protein
 };
 
-struct gpFx *gpFxPredEffect(struct pgSnp *pgSnp, struct genePred *pred);
-// return the predicted effect(s) of a variation on a genePred
+struct gpFx *gpFxPredEffect(struct variant *variant, struct genePred *pred,
+    char **returnTranscript, char **returnCoding);
+// return the predicted effect(s) of a variation list on a genePred
+
+// number of bases up or downstream that we flag
+#define GPRANGE 500
 
 #endif /* GPFX_H */