code: def add_rna_args(
          parser,
          min_mapping_quality_default=MIN_READ_MAPPING_QUALITY):
      
      rna_group = parser.add_argument_group("RNA")
      rna_group.add_argument(
          "--bam",
          required=True,
          help="BAM file containing RNAseq reads")
  
      rna_group.add_argument(
          "--min-mapping-quality",
          type=int,
          default=min_mapping_quality_default,
          help="Minimum MAPQ value to allow for a read (default %(default)s)")
  
      rna_group.add_argument(
          "--use-duplicate-reads",
          default=False,
          action="store_true")
  
      rna_group.add_argument(
          "--drop-secondary-alignments",
          default=False,
          action="store_true")
      return rna_group
docs: Extends an ArgumentParser instance with the following commandline arguments:
          --bam
          --min-reads
          --min-mapping-quality
          --use-duplicate-reads
          --drop-secondary-alignments