code: private Variant getGenomicVariant(Variant variant) {
          if (variant.getAlternate().equals(".")) {  // reference positions are not variants
              return null;
          } else {
              String ref;
              // large deletion
              if (variant.getAlternate().equals("<DEL>")) {
                  // .get("_") because studyId and fileId are empty strings when VariantSource is initialized at readInputFile
                  int end = Integer.valueOf(variant.getSourceEntries().get("_").getAttributes().get("END"));
                  ref = StringUtils.repeat("N", end - variant.getStart());
                  return new Variant(variant.getChromosome(), variant.getStart(),
                          ref, variant.getAlternate().equals("") ? "-" : variant.getAlternate());
                  // TODO: structural variants are not yet properly handled. Implement and remove this patch asap
              } else if (variant.getAlternate().startsWith("<")
                      || (variant.getAlternate().length() > 1 && variant.getReference().length() > 1)) {
                  return null;
              } else {
                  ref = variant.getReference().equals("") ? "-" : variant.getReference();
                  return new Variant(variant.getChromosome(), variant.getStart(),
                          ref, variant.getAlternate().equals("") ? "-" : variant.getAlternate());
              }
          }
      }
docs: TODO: use a external class for this (this method could be added to GenomicVariant class)