code: def run(data):
      
      bwakit_dir = os.path.dirname(os.path.realpath(utils.which("run-bwamem")))
      hla_fqs = tz.get_in(["hla", "fastq"], data, [])
      if len(hla_fqs) > 0:
          hla_base = os.path.commonprefix(hla_fqs)
          while hla_base.endswith("."):
              hla_base = hla_base[:-1]
          out_file = hla_base + ".top"
          if not utils.file_exists(out_file):
              cmd = "{bwakit_dir}/run-HLA {hla_base}"
              do.run(cmd.format(**locals()), "HLA typing with bwakit")
              out_file = _organize_calls(out_file, hla_base, data)
          data["hla"].update({"call_file": out_file,
                              "hlacaller": "bwakit"})
      return data
docs: HLA typing with bwakit, parsing output from called genotype files.