code: def _read_miraligner(fn):
      
      reads = defaultdict(realign)
      with open(fn) as in_handle:
          in_handle.next()
          for line in in_handle:
              cols = line.strip().split("\t")
              iso = isomir()
              query_name, seq = cols[1], cols[0]
              chrom, reference_start = cols[-2], cols[3]
              iso.mirna = cols[3]
              subs, add, iso.t5, iso.t3 = cols[6:10]
              if query_name not in reads:
                  reads[query_name].sequence = seq
              iso.align = line
              iso.start = reference_start
              iso.subs, iso.add = _parse_mut(subs), add
              logger.debug("%s %s %s %s %s" % (query_name, reference_start, chrom, iso.subs, iso.add))
              reads[query_name].set_precursor(chrom, iso)
      return reads
docs: Read ouput of miraligner and create compatible output.