15d0836b4dba65919e83ce5ef0aaafe5a0edc72f
angie
  Wed Apr 17 12:49:53 2013 -0700
Making annoGratorGpVar able to handle VCF input too.  In order for a grator tosee what type of input is coming from the primary source, the streamer should
be passed in along with the primary row, as it is for formatters now.
refs #6152

diff --git src/hg/inc/variant.h src/hg/inc/variant.h
index 429d2f0..f31091c 100644
--- src/hg/inc/variant.h
+++ src/hg/inc/variant.h
@@ -12,24 +12,29 @@
     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);
+struct variant *variantNew(char *chrom, unsigned start, unsigned end, unsigned numAlleles,
+			   char *slashSepAlleles, struct lm *lm);
+/* Create a variant from basic information that is easy to extract from most other variant
+ * formats: coords, allele count, and string of slash-separated alleles. */
+
+struct variant *variantFromPgSnp(struct pgSnp *pgSnp, struct lm *lm);
 /* 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*/