constants module

mavis.cluster.constants.DEFAULTS = WeakMavisNamespace(_defns={'min_clusters_per_file': 'the minimum number of breakpoint pairs to output to a file', 'max_files': 'The maximum number of files to output from clustering/splitting', 'cluster_initial_size_limit': 'the maximum cumulative size of both breakpoints for breakpoint pairs to be used in the initial clustering phase (combining based on overlap)', 'cluster_radius': 'maximum distance allowed between paired breakpoint pairs', 'max_proximity': 'the maximum distance away from an annotation before the region in considered to be uninformative', 'uninformative_filter': 'flag that determines if breakpoint pairs which are not within max_proximity to any annotations are filtered out prior to clustering', 'limit_to_chr': "A semi-colon delimited list of chromosome names to use. BreakpointPairs on other chromosomes will be filteredout. For example '1;2;3;4' would filter out events/breakpoint pairs on any chromosomes but 1, 2, 3, and 4"}, _types={'min_clusters_per_file': <class 'int'>, 'max_files': <class 'int'>, 'cluster_initial_size_limit': <class 'int'>, 'cluster_radius': <class 'int'>, 'max_proximity': <class 'int'>, 'uninformative_filter': <function cast_boolean>, 'limit_to_chr': <class 'mavis.util.ChrListString'>}, cluster_initial_size_limit=25, cluster_radius=100, limit_to_chr=['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', 'X', 'Y'], max_files=200, max_proximity=5000, min_clusters_per_file=50, uninformative_filter=True)

• cluster_initial_size_limit
• cluster_radius
• limit_to_chr
• max_files
• max_proximity
• min_clusters_per_file
• uninformative_filter