code: static boolean requireLeftAlignment(String reference, String alternate, VariantKeyFields keyFields) {
          return (keyFields.getReference().isEmpty() || keyFields.getAlternate().isEmpty())
                  && requireLeftAlignment(reference, alternate);
      }
docs: Only requires left alignment if after trimming reference or alternate are empty and before trimming either
  reference or alternate is empty or the bases from each of them are equal.
  This excludes from left alignment all non pure indels: non blocked substitutions, MNVs, etc.
  @param reference
  @param alternate
  @param keyFields
  @return