3ec9dec14cfbbe94f51eb94dd0cc861cad375f97
braney
  Tue Apr 17 18:58:18 2012 -0700
ongoing work on #6152.   Now with non-synonymous changes!  (well, at least with respect to the genomic DNA)
diff --git src/hg/lib/variant.c src/hg/lib/variant.c
index 5e7ebb9..90555b0 100644
--- src/hg/lib/variant.c
+++ src/hg/lib/variant.c
@@ -1,60 +1,61 @@
 /* variant.c -- routines to convert other variant formats to a generic
  *              variant structure */
 
 #include "common.h"
 #include "variant.h"
 
 struct variant *variantFromPgSnp(struct pgSnp *pgSnp)
 /* convert pgSnp record to variant record */
 {
 struct variant *variant;
 
 // this is probably the wrong way to do this.  Alleles in
 // variant should be their size in query bases
 int alleleLength = pgSnp->chromEnd - pgSnp->chromStart;
 
 // We have a new variant!
 AllocVar(variant);
 variant->chrom = cloneString(pgSnp->chrom);
 variant->chromStart = pgSnp->chromStart;
 variant->chromEnd = pgSnp->chromEnd;
 variant->numAlleles = pgSnp->alleleCount;
 
 // get the alleles.
 char *nextAlleleString = pgSnp->name;
 int alleleNumber = 0;
 for( ; alleleNumber < pgSnp->alleleCount; alleleNumber++)
     {
     if (nextAlleleString == NULL)
 	errAbort("number of alleles in pgSnp doesn't match number in name");
     
     char *thisAlleleString = nextAlleleString;
 
     // advance pointer to next variant string
     // probably there's some kent routine to do this behind the curtain
     nextAlleleString = strchr(thisAlleleString, '/');
     if (nextAlleleString)	 // null out '/' and move to next char
 	{
 	*nextAlleleString = 0;
 	nextAlleleString++;
 	}
 
     // this check probably not right, could be different per allele
     int alleleStringLength = strlen(thisAlleleString);
     if (alleleStringLength != alleleLength)
 	errAbort("length of allele number %d is %d, should be %d", 
 	    alleleNumber, alleleStringLength, alleleLength);
 
     // we have a new allele!
     struct allele *allele;
     AllocVar(allele);
     slAddHead(&variant->alleles, allele);
+    allele->variant = variant;
     allele->length = alleleStringLength;
     allele->sequence = cloneString(thisAlleleString);
     }
 
 slReverse(&variant->alleles);
 
 return variant;
 }