04c67a0e7bcb65c217598e5e44084bf4c5c0674d
angie
  Tue Mar 5 12:16:10 2013 -0800
Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along
with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output.

diff --git src/hg/lib/variant.c src/hg/lib/variant.c
index a9e8425..8cc7a52 100644
--- src/hg/lib/variant.c
+++ src/hg/lib/variant.c
@@ -31,31 +31,31 @@
     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);
+assert(newAllele->length >= 0);
 newAllele->sequence = cloneString(&allele->sequence[delFront]);
 newAllele->sequence[newAllele->length] = 0;   // cut off delRear part
 
 return newAllele;
 }
 
 static char *addDashes(char *input, int count)
 /* add dashes at the end of a sequence to pad it out so it's length is count */
 {
 char *ret = needMem(count + 1);
 int inLen = strlen(input);
 
 safecpy(ret, count + 1, input);
 count -= inLen;
 
@@ -91,31 +91,36 @@
 	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)
+    if (sameString(thisAlleleString, "-") && alleleLength == 0)
+	{
+	alleleStringLength = 0;
+	thisAlleleString[0] = '\0';
+	}
+    else if (alleleStringLength != alleleLength)
 	{
 	if ( alleleStringLength < alleleLength)
 	    {
 	    thisAlleleString = addDashes(thisAlleleString, alleleLength);
 	    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);