def _get_variant_effect(cls, variants, ref_sequence):
        '''variants = list of variants in the same codon.
           returns type of variant (cannot handle more than one indel in the same codon).'''
        assert len(variants) != 0

        var_types = [x.var_type for x in variants]
        if len(set(var_types)) != 1:
            return 'MULTIPLE', '.', '.'

        var_type = var_types[0]

        assert set([x.ref_name for x in variants]) == set([ref_sequence.id])
        codon_starts = [AssemblyVariants._get_codon_start(0, x.ref_start) for x in variants]
        assert len(set(codon_starts)) == 1
        codon_start = codon_starts[0]
        aa_start = codon_start // 3
        ref_codon = pyfastaq.sequences.Fasta('codon', ref_sequence[codon_start:codon_start+3])
        ref_aa = ref_codon.translate()

        if var_type == pymummer.variant.SNP:
            new_codon = list(ref_codon.seq)
            for v in variants:
                new_codon[v.ref_start - codon_start] = v.qry_base
            new_codon = pyfastaq.sequences.Fasta('new', ''.join(new_codon))
            qry_aa = new_codon.translate()

            if ref_aa.seq == qry_aa.seq:
                return ('SYN', '.', aa_start)
            elif qry_aa.seq == '*':
                return ('TRUNC', ref_aa.seq + str(aa_start + 1) + 'trunc', aa_start)
            else:
                return ('NONSYN', ref_aa.seq + str(aa_start + 1) + qry_aa.seq, aa_start)
        elif var_type in [pymummer.variant.INS, pymummer.variant.DEL]:
            if len(variants) > 1:
                return 'INDELS', '.', aa_start

            var = variants[0]

            if var_type == pymummer.variant.INS:
                new_seq = pyfastaq.sequences.Fasta('seq', var.qry_base)
            else:
                new_seq = pyfastaq.sequences.Fasta('seq', var.ref_base)

            if len(new_seq) % 3 != 0:
                return ('FSHIFT', ref_aa.seq + str(aa_start + 1) + 'fs', aa_start)

            new_seq_aa = new_seq.translate()
            if '*' in new_seq_aa.seq:
                return ('TRUNC', ref_aa.seq + str(aa_start + 1) + 'trunc', aa_start)
            elif var_type == pymummer.variant.INS:
                ref_codon_after_ins = pyfastaq.sequences.Fasta('codon', ref_sequence[codon_start+3:codon_start+6])
                aa_after_ins = ref_codon_after_ins.translate()
                return ('INS', ref_aa.seq + str(aa_start + 1) + '_' + aa_after_ins.seq + str(aa_start + 2) + 'ins' + new_seq_aa.seq , aa_start)
            else:
                if len(new_seq) == 3:
                    return ('DEL', ref_aa.seq + str(aa_start + 1) + 'del', aa_start)
                else:
                    assert len(new_seq) % 3 == 0
                    ref_codon_after_ins = pyfastaq.sequences.Fasta('codon', ref_sequence[codon_start+3:codon_start+6])
                    aa_after_ins = ref_codon_after_ins.translate()
                    return ('DEL', ref_aa.seq + str(aa_start + 1)+ '_' + aa_after_ins.seq + str(aa_start + 2) + 'del', aa_start)

        else:
            return ('UNKNOWN', '.', aa_start)
variants = list of variants in the same codon.
           returns type of variant (cannot handle more than one indel in the same codon).