c72b4b4412c574336911c4eb7135a9677c2773ef
braney
  Wed Apr 25 14:07:45 2012 -0700
ongoing #6152.   Added support for variants longer than 1 in CDS.
diff --git src/hg/inc/variant.h src/hg/inc/variant.h
index ac1e1c0..429d2f0 100644
--- src/hg/inc/variant.h
+++ src/hg/inc/variant.h
@@ -1,30 +1,35 @@
 /* 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   // a single allele in a variant. 
     {
     struct allele *next;
     struct variant *variant;
     int length;
     char *sequence;
     };
 
 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 */
 
+struct allele  *alleleClip(struct allele *allele, int sx, int ex);
+/* clip allele to be inside region defined by sx..ex.  Returns 
+ * pointer to new allele which should be freed by alleleFree, or variantFree
+ */
+
 #endif /* VARIANT_H*/