code: def piped_bamprep(data, region=None, out_file=None):
      
      data["region"] = region
      if not _need_prep(data):
          return [data]
      else:
          utils.safe_makedir(os.path.dirname(out_file))
          if region[0] == "nochrom":
              prep_bam = shared.write_nochr_reads(data["work_bam"], out_file, data["config"])
          elif region[0] == "noanalysis":
              prep_bam = shared.write_noanalysis_reads(data["work_bam"], region[1], out_file,
                                                       data["config"])
          else:
              if not utils.file_exists(out_file):
                  with tx_tmpdir(data) as tmp_dir:
                      _piped_bamprep_region(data, region, out_file, tmp_dir)
              prep_bam = out_file
          bam.index(prep_bam, data["config"])
          data["work_bam"] = prep_bam
          return [data]
docs: Perform full BAM preparation using pipes to avoid intermediate disk IO.
  
      Handles realignment of original BAMs.