<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
 def _read_pyMatch(fn, precursors):
 """ read pyMatch file and perform realignment of hits """

    with open(fn) as handle:
        reads = defaultdict(realign)
        for line in handle:
            query_name, seq, chrom, reference_start, end, mism, add = line.split()
            reference_start = int(reference_start)
            # chrom = handle.getrname(cols[1])
            # print("%s %s %s %s" % (line.query_name, line.reference_start, line.query_sequence, chrom))
            if query_name not in reads:
                reads[query_name].sequence = seq
            iso = isomir()
            iso.align = line
            iso.start = reference_start
            iso.subs, iso.add = _realign(reads[query_name].sequence, precursors[chrom], reference_start)
            logger.debug("%s %s %s %s %s" % (query_name, reference_start, chrom, iso.subs, iso.add))
            if len(iso.subs) > 1:
                continue
            reads[query_name].set_precursor(chrom, iso)

        reads = _clean_hits(reads)
    return reads