code: def _clean_alignment(args):
      
      logger.info("Clean bam file with highly repetitive reads with low counts. sum(counts)/n_hits > 1%")
      bam_file, seq_obj = clean_bam_file(args.afile, args.mask)
      logger.info("Using %s file" % bam_file)
      detect_complexity(bam_file, args.ref, args.out)
      return bam_file, seq_obj
docs: Prepare alignment for cluster detection.