Combine shorter sequences which are fully contained in longer sequences.

    Parameters
    ----------
    variant_sequences : list
       List of VariantSequence objects

    Returns a (potentially shorter) list without any contained subsequences.

def collapse_substrings(variant_sequences):
    """
    Combine shorter sequences which are fully contained in longer sequences.

    Parameters
    ----------
    variant_sequences : list
       List of VariantSequence objects

    Returns a (potentially shorter) list without any contained subsequences.
    """
    if len(variant_sequences) <= 1:
        # if we don't have at least two VariantSequences then just
        # return your input
        return variant_sequences

    # dictionary mapping VariantSequence objects to lists of reads
    # they absorb from substring VariantSequences
    extra_reads_from_substrings = defaultdict(set)
    result_list = []
    # sort by longest to shortest total length
    for short_variant_sequence in sorted(
            variant_sequences,
            key=lambda seq: -len(seq)):
        found_superstring = False
        for long_variant_sequence in result_list:
            found_superstring = long_variant_sequence.contains(short_variant_sequence)
            if found_superstring:
                extra_reads_from_substrings[long_variant_sequence].update(
                    short_variant_sequence.reads)
        if not found_superstring:
            result_list.append(short_variant_sequence)
    # add to each VariantSequence the reads it absorbed from dropped substrings
    # and then return
    return [
        variant_sequence.add_reads(
            extra_reads_from_substrings[variant_sequence])
        for variant_sequence in result_list
    ]