def _clean_alignment(args):
logger.info("<STR_LIT>")<EOL>bam_file, seq_obj = clean_bam_file(args.afile, args.mask)<EOL>logger.info("<STR_LIT>" % bam_file)<EOL>detect_complexity(bam_file, args.ref, args.out)<EOL>return bam_file, seq_obj<EOL>
Prepare alignment for cluster detection.