Combine aligned and split samples into final set of disambiguated reads.

def resolve(items, run_parallel):
    """Combine aligned and split samples into final set of disambiguated reads.
    """
    out = []
    to_process = collections.defaultdict(list)
    for data in [x[0] for x in items]:
        if "disambiguate" in data:
            split_part = tuple([int(x) for x in data["align_split"].split("-")]) if data.get("combine") else None
            to_process[(dd.get_sample_name(data), split_part)].append(data)
        else:
            out.append([data])
    if len(to_process) > 0:
        dis1 = run_parallel("run_disambiguate",
                            [(xs, xs[0]["config"]) for xs in to_process.values()])
        disambigs_by_name = collections.defaultdict(list)
        print(len(dis1))
        for xs in dis1:
            assert len(xs) == 1
            data = xs[0]
            disambigs_by_name[dd.get_sample_name(data)].append(data)
        dis2 = run_parallel("disambiguate_merge_extras",
                            [(xs, xs[0]["config"]) for xs in disambigs_by_name.values()])
    else:
        dis2 = []
    return out + dis2