feeb7ee7651d3a85ebc34c4fb32243a841eacdf2
braney
  Mon Apr 16 16:23:04 2012 -0700
on-going work on annoGrator (#6152).  Started using Sequence Ontology numbers from EBI, and added a generic variant structure as input to gpFx library
diff --git src/hg/inc/variant.h src/hg/inc/variant.h
index 204c9ce..d4805be 100644
--- src/hg/inc/variant.h
+++ src/hg/inc/variant.h
@@ -1,26 +1,29 @@
+/* variant.h -- a generic variant.  Meant to be capture information that's
+ *              in VCF or pgSNP  */
 
 #ifndef VARIANT_H
 #define VARIANT_H
 
 #include "pgSnp.h"
 
-struct allele
+struct allele   // a single allele in a variant. 
     {
     struct allele *next;
     int length;
     char *sequence;
     };
 
-struct variant
+struct variant   // a single variant
     {
     struct variant *next;  /* Next in singly linked list. */
     char *chrom;	/* Chromosome */
     unsigned chromStart;	/* Start position in chrom */
     unsigned chromEnd;	/* End position in chrom */
+    unsigned numAlleles;   /* the number of alleles */
     struct allele *alleles;	/* alleles */
     };
 
 struct variant *variantFromPgSnp(struct pgSnp *pgSnp);
 /* convert pgSnp record to variant record */
 
 #endif /* VARIANT_H*/