augur.filter

Filter and subsample a sequence set.

augur.filter.register_arguments(parser)

Add arguments to parser. Kept as a separate function than register_parser to continue to support unit tests that use this function to create argparser.

augur.filter.register_parser(parent_subparsers)

augur.filter.run(args)

filter and subsample a set of sequences into an analysis set

• augur.filter._run
  • run()
• augur.filter.include_exclude_rules
  • apply_filters()
  • construct_filters()
  • extract_variables()
  • filter_by_ambiguous_date()
  • filter_by_exclude()
  • filter_by_exclude_all()
  • filter_by_exclude_where()
  • filter_by_max_date()
  • filter_by_max_length()
  • filter_by_min_date()
  • filter_by_min_length()
  • filter_by_non_nucleotide()
  • filter_by_query()
  • filter_by_sequence_index()
  • force_include_strains()
  • force_include_where()
  • parse_filter_query()
  • skip_group_by_with_ambiguous_day()
  • skip_group_by_with_ambiguous_month()
  • skip_group_by_with_ambiguous_year()
• augur.filter.io
  • cleanup_outputs()
  • column_type_pair()
  • get_useful_metadata_columns()
  • read_priority_scores()
  • write_metadata_based_outputs()
• augur.filter.subsample
  • PriorityQueue
    • PriorityQueue.add()
    • PriorityQueue.get_items()
  • TooManyGroupsError
  • calculate_sequences_per_group()
  • create_queues_by_group()
  • get_groups_for_subsampling()
• augur.filter.validate_arguments
  • validate_arguments()