Add command to insert exact matches

[jeromekelleher]

We want to take the ARG and add back in the exact matches. This mostly does the job:

import pickle, bz2

mdb = sc2ts.MatchDb(...)

with mdb.conn:
    sql = f"SELECT * FROM samples WHERE hmm_cost == 0 AND match_date <= '{date}'"
    samples = []
    for row in mdb.conn.execute(sql):
        pkl = row.pop("pickle")
        sample = pickle.loads(bz2.decompress(pkl))
        samples.append(sample)

total_exact_matches = sum(ts_in.metadata["sc2ts"]["cumulative_stats"]["exact_matches"]["pango"].values())
assert total_exact_matches == len(samples)
tables = ts_in.dump_tables()

samples_strain = ts_in.metadata["sc2ts"]["samples_strain"]
L = tables.sequence_length
for sample in samples:
    sample.flags |= sc2ts.NODE_IS_EXACT_MATCH
    # FIXME - time is wrong here, will result in very long branches
    u = sc2ts.add_sample_to_tables(sample, tables)
    parent = sample.hmm_match.path[0].parent
    tables.edges.add_row(0, L, parent=parent, child=u)
    samples_strain.append(sample.strain)

md = tables.metadata
md["sc2ts"]["samples_strain"] = samples_strain
tables.metadata = md

tables.sort()
ts_out = tables.tree_sequence()
ts_out

The main thing that's wrong here is the node times for the newly inserted samples are wildly wrong.