mavis.main

mavis.main.check_overlay_args()

parse the overlay options and check the formatting

def check_overlay_args(args, parser):

Args

• args
• parser

mavis.main.overlay_main()

generates an overlay diagram

def overlay_main(
    gene_name,
    output,
    buffer_length,
    read_depth_plots,
    markers,
    annotations,
    drawing_width_iter_increase,
    max_drawing_retries,
    min_mapping_quality,
    ymax_color='#FF0000',
    **kwargs
):

Args

• gene_name
• output
• buffer_length
• read_depth_plots
• markers
• annotations
• drawing_width_iter_increase
• max_drawing_retries
• min_mapping_quality
• ymax_color

mavis.main.main()

sets up the parser and checks the validity of command line args loads reference files and redirects into subcommand main functions

def main(argv=None):

Args

• argv (list): List of arguments, defaults to command line arguments