def set_align_options(p):
    """ Used in align() and batch()
    """
    p.add_option("--bwa", default="bwa", help="Run bwa at this path")
    p.add_option("--rg", help="Read group")
    p.add_option("--readtype",
                 choices=("pacbio", "pbread", "ont2d", "intractg"),
                 help="Read type in bwa-mem")
    p.set_cutoff(cutoff=800)