code: def _prepare_bam(bam_file, bed_file, config):
      
      if not bam_file or not bed_file:
          return bam_file
      out_file = utils.append_stem(bam_file, '_filter')
      bedtools = config_utils.get_program("bedtools", config)
      if not utils.file_exists(out_file):
          with file_transaction(out_file) as tx_out:
              cmd = "{bedtools} subtract -nonamecheck -A -a {bam_file} -b {bed_file} > {tx_out}"
              do.run(cmd.format(**locals()), "Remove blacklist regions from %s" % bam_file)
      return out_file
docs: Remove regions from bed files