Correct rendered range of symbolic VCF alleles (#1580)

* Adjust the start position of non-ref symbolic alleles to include a padding base as described in the vcf spec.

Co-authored-by: Louis Bergelson <[email protected]>

src/main/java/org/broad/igv/variant/vcf/VCFVariant.java

@@ -385,6 +385,15 @@ private void calcStart() {
         if (variantContext.getType() == VariantContext.Type.INDEL || variantContext.getType() == VariantContext.Type.MIXED) {
             prefixLength = findCommonPrefixLength();
         }
+
+        /**
+         * The VCF spec defines POS as the base preceding the polymorphism for non-ref symbolic alleles.
+         *
+         */
+        if (variantContext.getType(true) == VariantContext.Type.SYMBOLIC) {
+            prefixLength = 1;
+        }
+
         this.start = (variantContext.getStart() - 1) + prefixLength;
     }