def add_collapse_mapped_isoforms_io_arguments(arg_parser):
    """Add arguments for collapse isoforms."""
    helpstr = "Input uncollapsed isoforms in a FASTA, FASTQ or ContigSet file."
    arg_parser.add_argument("input_isoforms", type=str, help=helpstr)

    helpstr = "Input SORTED SAM file mapping uncollapsed isoforms to reference genome using GMAP."
    arg_parser.add_argument("sam_filename", type=str, help=helpstr)

    helpstr = "Output prefix, will write output files to " + \
              "<output_prefix>.fastq|.gff|.group.txt|.abundance.txt|.read_stat.txt"
    arg_parser.add_argument("output_prefix", type=str, help=helpstr)

    helpstr = "Output collapsed isoforms to a FASTA, FASTQ, or ContigSet file."
    arg_parser.add_argument("--collapsed_isoforms", type=str, default=None, help=helpstr)
    return arg_parser