code: private boolean isValid(Variant variant) {
          return (variant.getReference().matches(VARIANT_STRING_PATTERN)
                  && (variant.getAlternate().matches(VARIANT_STRING_PATTERN)
                    || variant.getAlternate().contains("[") || variant.getAlternate().contains("]")  // mated breakend
                    || variant.getAlternate().startsWith(".") || variant.getAlternate().endsWith(".")) // single breakend
                  && !variant.getAlternate().equals(variant.getReference()));
      }
docs: Checks whether a variant is valid.
  
  @param variant Variant object to be checked.
  @return   true/false depending on whether 'variant' does contain valid values. Currently just a simple check of
  reference/alternate attributes being strings of [A,C,G,T] of length >= 0 is performed to detect cases such as
  19:13318673:(CAG)4:(CAG)5 which are not currently supported by CellBase. Ref and alt alleles must be different
  as well for the variant to be valid. Functionality of the method may be improved in the future.