code: def merge_extras(items, config):
      
      final = {}
      for extra_name in items[0]["disambiguate"].keys():
          in_files = []
          for data in items:
              in_files.append(data["disambiguate"][extra_name])
          out_file = "%s-allmerged%s" % os.path.splitext(in_files[0])
          if in_files[0].endswith(".bam"):
              merged_file = merge.merge_bam_files(in_files, os.path.dirname(out_file), items[0],
                                                  out_file=out_file)
          else:
              assert extra_name == "summary", extra_name
              merged_file = _merge_summary(in_files, out_file, items[0])
          final[extra_name] = merged_file
      out = []
      for data in items:
          data["disambiguate"] = final
          out.append([data])
      return out
docs: Merge extra disambiguated reads into a final BAM file.