main module

mavis.main.build_annotate_command(config, libconf, inputfile, outputdir)

returns the mavis command for running the annotate step

mavis.main.build_validate_command(config, libconf, inputfile, outputdir)

returns the mavis command for running the validate step

mavis.main.convert_main(inputs, outputfile, file_type, strand_specific=False, assume_no_untemplated=True)

mavis.main.main()

mavis.main.main_pipeline(config)

runs the pipeline subcommand. Runs clustering (or just splitting if clustering is skipped) and sets up submission scripts for the other pipeline stages/steps

mavis.main.overlay_main(gene_name, output, buffer_length, read_depth_plots, markers, annotations, annotations_filename, drawing_width_iter_increase, max_drawing_retries, **kwargs)

generates an overlay diagram

mavis.main.parse_overlay_args(parser, required, optional)

parse the overlay options and check the formatting

mavis.main.run_conversion(config, libconf, conversion_dir, assume_no_untemplated=True)

Converts files if not already converted. Returns a list of filenames