2f19b4081ef0f0d93daf8f7ff1c26cf8879a4d14
braney
  Thu Apr 26 17:26:10 2012 -0700
more work on #6152.   Now with in-frame deletions!
diff --git src/hg/lib/variant.c src/hg/lib/variant.c
index fcbefbf..47dbe50 100644
--- src/hg/lib/variant.c
+++ src/hg/lib/variant.c
@@ -1,107 +1,128 @@
 /* variant.c -- routines to convert other variant formats to a generic
  *              variant structure */
 
 #include "common.h"
 #include "variant.h"
 
 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
  */
 {
 struct variant *oldVariant = allele->variant;
 int start = oldVariant->chromStart;
 int end = oldVariant->chromEnd;
 int oldVariantWidth = end - start;
 int delFront = 0;
 int delRear = 0;
 
 if (start < sx)
     {
     if (oldVariantWidth != allele->length)	 /* FIXME */
 	errAbort("cannot clip alleles that are a different length than variant region");
     delFront = sx - start;
     start = sx;
     }
 
 if (end > ex)
     {
     if (oldVariantWidth != allele->length)	 /* FIXME */
 	errAbort("cannot clip alleles that are a different length than variant region");
     delRear = end - ex;
     end = ex;
     }
 
 struct variant *newVariant;
 AllocVar(newVariant);
 newVariant->chrom = cloneString(oldVariant->chrom);
 newVariant->chromStart = start;
 newVariant->chromEnd = end;
 newVariant->numAlleles = 1;
 struct allele *newAllele;
 AllocVar(newAllele);
 newVariant->alleles = newAllele;
 newAllele->variant = newVariant;
 newAllele->length = allele->length - delRear - delFront;
 assert(newAllele->length > 0);
 newAllele->sequence = cloneString(&allele->sequence[delFront]);
 newAllele->sequence[newAllele->length] = 0;   // cut off delRear part
 
 return newAllele;
 }
 
+static char *makeDashes(int count)
+{
+char *ret = needMem(count + 1);
+char *ptr = ret;
+
+while(count--)
+    *ptr++ = '-';
+
+return ret;
+}
+
 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)
+	{
+	// check for special case of single '-'
+	if (sameString("-", thisAlleleString))
+	    {
+	    thisAlleleString = makeDashes(alleleLength);
+	    alleleStringLength = alleleLength;
+	    }
+	else
 	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;
+    toLowerN(thisAlleleString, alleleStringLength);
     allele->sequence = cloneString(thisAlleleString);
     }
 
 slReverse(&variant->alleles);
 
 return variant;
 }