Extends an ArgumentParser instance with the following commandline arguments:
        --bam
        --min-reads
        --min-mapping-quality
        --use-duplicate-reads
        --drop-secondary-alignments

def add_rna_args(
        parser,
        min_mapping_quality_default=MIN_READ_MAPPING_QUALITY):
    """
    Extends an ArgumentParser instance with the following commandline arguments:
        --bam
        --min-reads
        --min-mapping-quality
        --use-duplicate-reads
        --drop-secondary-alignments
    """
    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