Index

A

aa_reconstruction (augur.ancestral.Mode attribute) add() (augur.filter.subsample.PriorityQueue method) add_arguments() (augur.argparse_.HelpFormatter method) add_command_subparsers() (in module augur.argparse_) add_core_args() (in module augur.export_v1) add_default_command() (in module augur.argparse_) add_option_args() (in module augur.export_v1) add_subparser() (in module augur.argparse_) add_tsv_metadata_to_nodes() (in module augur.export_v1) add_validation_arguments() (in module augur.argparse_) add_version_alias() (in module augur) alignment_frequencies (class in augur.frequency_estimators) AlignmentError AlignmentKdeFrequencies (class in augur.frequency_estimators) AmbiguousDate (class in augur.dates.ambiguous_date) analyse_insertions() (in module augur.align) Ancestral_JSON (class in augur.ancestral) Ancestral_Reconstruction (class in augur.ancestral) annotate_parents_for_tree() (in module augur.utils) annotate_strains() (in module augur.sequence_traits) annotate_strains_by_gene() (in module augur.sequence_traits) annotate_tree() (augur.titer_model.SubstitutionModel method) annotations (augur.ancestral.Ancestral_JSON attribute) (augur.util_support.node_data_file.NodeDataFile property) Annotations_JSON (class in augur.ancestral) apply_filters() (in module augur.filter.include_exclude_rules) are_mutations_defined() (in module augur.export_v2) ArgparseEnum (class in augur.types) args (augur.subsample.Sample attribute) argtype() (augur.types.ArgparseEnum class method) as_file() (in module augur.data) as_json() (in module augur.io.json) assert_only_less_significant_uncertainty() (augur.dates.ambiguous_date.AmbiguousDate method) assign_aa_fasta() (in module augur.translate) assign_aa_vcf() (in module augur.translate) assign_clades() (in module augur.clades) assign_titers() (augur.titer_model.TiterModel method) attach_features() (in module augur.sequence_traits) attr_confidence() (in module augur.export_v2) AttrInfo (class in augur.validate_export) augur module augur() (in module augur.utils) augur.align module augur.ancestral module augur.argparse_ module augur.clades module augur.curate module augur.curate.abbreviate_authors module augur.curate.apply_geolocation_rules module augur.curate.apply_record_annotations module augur.curate.format_dates module augur.curate.format_dates_directives module augur.curate.normalize_strings module augur.curate.parse_genbank_location module augur.curate.passthru module augur.curate.rename module augur.curate.titlecase module augur.curate.transform_strain_name module augur.data module augur.dates module augur.dates.ambiguous_date module augur.dates.errors module augur.debug module augur.distance module augur.errors module augur.export module augur.export_v1 module augur.export_v2 module augur.filter module augur.filter.arguments module augur.filter.constants module augur.filter.include_exclude_rules module augur.filter.io module

augur.filter.subsample module augur.filter.validate_arguments module augur.filter.weights_file module augur.frequencies module augur.frequency_estimators module augur.import_ module augur.import_.beast module augur.index module augur.io module augur.io.file module augur.io.json module augur.io.metadata module augur.io.print module augur.io.sequences module augur.io.shell_command_runner module augur.io.strains module augur.lbi module augur.mask module augur.measurements module augur.measurements.concat module augur.measurements.export module augur.merge module augur.parse module augur.proximity module augur.read_file module augur.reconstruct_sequences module augur.refine module augur.sequence_traits module augur.subsample module augur.titer_model module augur.titers module augur.traits module augur.translate module augur.tree module augur.types module augur.util_support module augur.util_support.auspice_config module augur.util_support.color_parser module augur.util_support.color_parser_line module augur.util_support.node_data module augur.util_support.node_data_file module augur.util_support.node_data_reader module augur.util_support.warnings module augur.utils module augur.validate module augur.validate_export module augur.version module augur.write_file module AUGUR_DEBUG AUGUR_MINIFY_JSON, [1], [2], [3], [4] AugurArgs (in module augur.subsample) AugurError AugurJSONEncoder (class in augur.io.json) AugurOption (in module augur.subsample) auspice_config_v2() (in module augur.validate) available_cpu_cores() (in module augur.utils)

B

BooleanFlags (in module augur.subsample) branches (augur.util_support.node_data_file.NodeDataFile property) BranchLabeller (class in augur.traits) build_fasttree() (in module augur.tree)

build_iqtree() (in module augur.tree) build_node_data() (augur.util_support.node_data_reader.NodeDataReader method) build_raxml() (in module augur.tree) BytesWrittenCounterIO (class in augur.io.json)

C

calc_confidence() (augur.frequency_estimators.alignment_frequencies method) (augur.frequency_estimators.tree_frequencies method) calc_freqs() (augur.frequency_estimators.nested_frequencies method) calc_tree_dates() (in module augur.import_.beast) calculate_LBI() (in module augur.lbi) calculate_sequences_per_group() (in module augur.filter.subsample) changes() (augur.traits.BranchLabeller method) check_against_tree_file() (augur.util_support.node_data_reader.NodeDataReader method) check_arg_combinations() (in module augur.translate) check_arguments() (in module augur.align) check_conflicting_args() (in module augur.tree) check_duplicates() (in module augur.align) cleanup_outputs() (in module augur.filter.io) collapse_colinear_mutations() (augur.titer_model.SubstitutionModel method) collect_mutations() (in module augur.ancestral) collect_node_data() (in module augur.import_.beast) (in module augur.refine) collect_sequences() (in module augur.ancestral) collectAAMutationGenesV1() (in module augur.validate_export) collectBranchLabels() (in module augur.validate_export) collectMutationGenes() (in module augur.validate_export) collectTreeAttrsV1() (in module augur.validate_export) collectTreeAttrsV2() (in module augur.validate_export) ColorParser (class in augur.util_support.color_parser) ColorParserLine (class in augur.util_support.color_parser_line) column_type_pair() (in module augur.filter.io) columns (augur.io.metadata.Metadata attribute) compile_potencies() (augur.titer_model.TiterModel method) compile_substitution_effects() (augur.titer_model.SubstitutionModel method) compile_titers() (augur.titer_model.TiterModel method) compile_virus_effects() (augur.titer_model.TiterModel method) compute_entropies_for_discrete_traits() (in module augur.import_.beast)

confidence (augur.export_v2.ConfidenceCategorical attribute) (augur.export_v2.ConfidenceNumeric attribute) ConfidenceCategorical (class in augur.export_v2) ConfidenceNumeric (class in augur.export_v2) configure_warnings() (in module augur.util_support.warnings) ConflictingArgumentsException connect_dependencies() (augur.subsample.FilterSample method) (augur.subsample.ProximalSample method) (augur.subsample.Sample method) construct_author_info_v1() (in module augur.export_v1) construct_cds_feature() (in module augur.ancestral) construct_filters() (in module augur.filter.include_exclude_rules) construct_mut() (in module augur.translate) CONTEXT_LENGTH (augur.io.json.JSONDecodeError attribute) contextualize_char() (in module augur.io.json) convert_tree_to_json_structure() (in module augur.export_v1) (in module augur.export_v2) copyfileobj() (in module augur.read_file) correct_alignment() (in module augur.ancestral) count (augur.validate_export.AttrInfo attribute) count_observations() (in module augur.frequency_estimators) count_strains() (augur.titer_model.TiterCollection static method) count_unique() (in module augur.merge) counter_to_disambiguation_suffix() (in module augur.export_v2) create_author_data() (in module augur.export_v2) create_branch_labels() (in module augur.export_v2) create_branch_mutations() (in module augur.export_v2) create_mask() (in module augur.ancestral) create_queues_by_group() (in module augur.filter.subsample) create_shared_parser() (in module augur.curate) cross_validate() (augur.titer_model.TreeModel method) CustomOrderedDict (class in augur.export_v2) CyclicGeolocationRulesError

D

DataErrorMethod (class in augur.types) date_to_numeric() (in module augur.dates) deep_add_or_update() (augur.util_support.node_data.NodeData method) default() (augur.io.json.AugurJSONEncoder method) (augur.io.json.JsonEncoder method) delimiter (augur.io.metadata.Metadata attribute) depends_on (augur.subsample.Sample attribute) deprecated() (in module augur.util_support.warnings)

deprecationWarningsEmitted() (in module augur.util_support.warnings) determine_autologous_titers() (augur.titer_model.TiterCollection method) determine_relevant_mutations() (augur.titer_model.SubstitutionModel method) directive_is_included() (in module augur.curate.format_dates) distance_fn() (in module augur.proximity) dtps (augur.frequency_estimators.freq_est_clipped attribute) dump_ndjson() (in module augur.io.json) DuplicatedNonDictAttributeError

E

elide_path() (in module augur.validate) EmptyDict (class in augur.export_v2) EmptyOutputReportingMethod (class in augur.types) end (augur.ancestral.Nuc_Annotation attribute) ensure_config_is_v1() (in module augur.export_v1) ensure_no_duplicate_names() (in module augur.validate_export) ensure_no_multiple_mutations() (in module augur.clades) ensure_reference_strain_present() (in module augur.align) entropy (augur.export_v2.ConfidenceCategorical attribute) environment variable AUGUR_DEBUG, [1] AUGUR_MINIFY_JSON, [1], [2], [3], [4], [5] AUGUR_PROFILE AUGUR_RECURSION_LIMIT AUGUR_SEARCH_PATHS

ERROR (augur.types.EmptyOutputReportingMethod attribute) (augur.types.ValidationMode attribute) ERROR_ALL (augur.types.DataErrorMethod attribute) ERROR_FIRST (augur.types.DataErrorMethod attribute) estimate() (augur.frequency_estimators.AlignmentKdeFrequencies method) (augur.frequency_estimators.TreeKdeFrequencies method) estimate_clade_frequencies() (augur.frequency_estimators.tree_frequencies method) estimate_frequencies() (augur.frequency_estimators.KdeFrequencies class method) estimate_genotype_frequency() (augur.frequency_estimators.alignment_frequencies method) estimate_tip_frequencies_to_proportion() (augur.frequency_estimators.TreeKdeFrequencies method) export_v1() (in module augur.validate) export_v2() (in module augur.validate) ExtendOverwriteDefault (class in augur.argparse_) extract_variables() (in module augur.filter.include_exclude_rules)

F

fake_alignment() (in module augur.import_.beast) fatal() (in module augur.validate) fe (augur.frequency_estimators.freq_est_clipped attribute) fields (augur.util_support.color_parser_line.ColorParserLine property) filter sample filter_by_ambiguous_date() (in module augur.filter.include_exclude_rules) filter_by_exclude() (in module augur.filter.include_exclude_rules) filter_by_exclude_all() (in module augur.filter.include_exclude_rules) filter_by_exclude_where() (in module augur.filter.include_exclude_rules) filter_by_invalid_characters() (in module augur.filter.include_exclude_rules) filter_by_max_date() (in module augur.filter.include_exclude_rules) filter_by_max_length() (in module augur.filter.include_exclude_rules) filter_by_min_date() (in module augur.filter.include_exclude_rules) filter_by_min_length() (in module augur.filter.include_exclude_rules) filter_by_query() (in module augur.filter.include_exclude_rules) filter_by_sequence_ids() (in module augur.filter.include_exclude_rules) FILTER_FINAL_CLI_OPTIONS (in module augur.subsample) FILTER_GLOBAL_CLI_OPTIONS (in module augur.subsample) FILTER_SAMPLE_CONFIG (in module augur.subsample) filter_strains() (augur.titer_model.TiterCollection static method) FilterSample (class in augur.subsample) find_executable() (in module augur.tree) find_feature_errors() (in module augur.io.sequences)

find_most_recent_tip() (in module augur.import_.beast) find_titer_splits() (augur.titer_model.TreeModel method) first_line() (in module augur.utils) fit_func() (augur.titer_model.TiterModel method) fit_l1reg() (augur.titer_model.TiterModel method) fit_nnl1reg() (augur.titer_model.TiterModel method) fit_nnl2reg() (augur.titer_model.TiterModel method) fit_nnls() (augur.titer_model.TiterModel method) fix_dates() (in module augur.parse) fix_freq() (in module augur.frequency_estimators) flanking_masks() (in module augur.proximity) float_to_datestring() (in module augur.frequency_estimators) fmt_components (augur.dates.ambiguous_date.AmbiguousDate property) force_include_strains() (in module augur.filter.include_exclude_rules) force_include_where() (in module augur.filter.include_exclude_rules) format_date() (in module augur.curate.format_dates) format_frequencies() (in module augur.frequencies) format_number() (in module augur.export_v2) format_path() (in module augur.validate) format_to_iso_date() (in module augur.curate.format_dates) format_to_iso_interval() (in module augur.curate.format_dates) freq_est_clipped (class in augur.frequency_estimators) frequency_estimator (class in augur.frequency_estimators) from_json() (augur.frequency_estimators.KdeFrequencies class method)

G

GENE_PATTERN (in module augur.ancestral) generate_alignment_cmd() (in module augur.align) generated_by (augur.util_support.node_data_file.NodeDataFile property) genome_features_to_auspice_annotation() (in module augur.utils) get_additional_metadata_columns() (in module augur.export_v2) get_annotated_geolocation() (in module augur.curate.apply_geolocation_rules) get_augur_version() (in module augur.utils) get_biopython_format() (in module augur.io.sequences) get_bounds() (in module augur.dates.ambiguous_date) get_characters_by_sequence_type() (in module augur.index) get_chrom_name() (in module augur.mask) get_config_colorings_as_dict() (in module augur.export_v2) get_default_weight() (in module augur.filter.weights_file) get_densities_for_observations() (augur.frequency_estimators.KdeFrequencies class method) get_density_for_observation() (augur.frequency_estimators.KdeFrequencies class method) get_distance_between_nodes() (in module augur.distance) get_distances_to_all_pairs() (in module augur.distance) get_distances_to_last_ancestor() (in module augur.distance) get_distances_to_root() (in module augur.distance) get_groups_for_subsampling() (in module augur.filter.subsample) get_items() (augur.filter.subsample.PriorityQueue method) get_json_name() (in module augur.utils) get_mutations() (augur.titer_model.SubstitutionModel method)

get_numerical_date_from_value() (in module augur.dates) get_numerical_dates() (in module augur.dates) get_params() (augur.frequency_estimators.KdeFrequencies method) get_parent_name_by_child_name_for_tree() (in module augur.utils) get_path_no_terminals() (augur.titer_model.TreeModel method) get_pivots() (in module augur.frequency_estimators) get_probabilistic_group_sizes() (in module augur.filter.subsample) get_reference_sequence_from_root_node() (in module augur.clades) get_referenced_files() (in module augur.subsample) get_root_date_offset() (in module augur.import_.beast) get_root_sequence() (in module augur.export_v1) get_sequence() (in module augur.reconstruct_sequences) get_unique_keys() (in module augur.validate) get_useful_metadata_columns() (in module augur.filter.io) get_valid_range() (in module augur.proximity) get_values_across_nodes() (in module augur.export_v2) get_weighted_columns() (in module augur.filter.weights_file) get_weighted_group_sizes() (in module augur.filter.subsample) get_year_month_day() (in module augur.dates) get_year_week() (in module augur.dates) good_pivots (augur.frequency_estimators.freq_est_clipped attribute) good_tps (augur.frequency_estimators.freq_est_clipped attribute) Group (in module augur.filter.subsample) grouped() (in module augur.validate)

H

HelpFormatter (class in augur.argparse_)

hex_code (augur.util_support.color_parser_line.ColorParserLine property) HideAsFalseAction (class in augur.argparse_)

I

id_column (augur.io.metadata.Metadata attribute) incomplete (augur.subsample.Sample attribute) indented_list() (in module augur.io.print) index_sequence() (in module augur.index) index_sequences() (in module augur.index) index_vcf() (in module augur.index) infer_substitution_model (class in augur.titers) infer_tree_model (class in augur.titers) initial_guess() (augur.frequency_estimators.frequency_estimator method) InsufficientDataException InvalidDate InvalidDelimiter InvalidOption InvalidTreeError

InvalidUseOfRemoveOutgroup InvalidWeightsFile InvalidYearBounds invoke_command() (augur.io.shell_command_runner.ShellCommandRunner method) is_comment_or_blank() (augur.util_support.color_parser_line.ColorParserLine method) is_date_ambiguous() (in module augur.dates) is_generated_by_incompatible_augur (augur.util_support.node_data_file.NodeDataFile property) is_node_attr_defined() (in module augur.export_v2) is_node_in_clade() (in module augur.clades) is_numeric() (in module augur.export_v2) is_valid() (in module augur.export_v2) is_vcf (augur.ancestral.Mode attribute) is_vcf() (in module augur.io.sequences) items() (augur.util_support.node_data_file.NodeDataFile method)

J

json_size() (in module augur.io.json) json_to_tree() (in module augur.utils)

JSONDecodeError JsonEncoder (class in augur.io.json)

K

KdeFrequencies (class in augur.frequency_estimators)

L

learn() (augur.frequency_estimators.freq_est_clipped method) (augur.frequency_estimators.frequency_estimator method) load_alignments() (in module augur.reconstruct_sequences) load_context() (in module augur.proximity) load_features() (in module augur.io.sequences) (in module augur.utils) load_focal_sequences() (in module augur.proximity) load_from_file() (augur.titer_model.TiterCollection static method)

load_geolocation_rules() (in module augur.curate.apply_geolocation_rules) load_json() (in module augur.io.json) (in module augur.validate) load_json_schema() (in module augur.validate) load_mask_sites() (in module augur.utils) load_ndjson() (in module augur.io.json) logit_inv() (in module augur.frequency_estimators) logit_transform() (in module augur.frequency_estimators)

M

make_gaps_ambiguous() (in module augur.align) make_parser() (in module augur) make_pivots() (in module augur.frequency_estimators) make_seqgraph() (augur.titer_model.SubstitutionModel method) make_training_set() (augur.titer_model.TiterModel method) make_treegraph() (augur.titer_model.TreeModel method) mapping (augur.util_support.color_parser.ColorParser property) mark_char() (in module augur.io.json) mask (augur.ancestral.Ancestral_JSON attribute) (augur.ancestral.Mutations attribute) mask_fasta() (in module augur.mask) mask_sequence() (in module augur.mask) mask_sites_in_multiple_sequence_alignment() (in module augur.tree) mask_vcf() (in module augur.mask) max_day_for_year_month() (in module augur.dates.ambiguous_date) measurements() (in module augur.validate) measurements_collection_config() (in module augur.validate) merge_configs() (in module augur.util_support.auspice_config) merge_metadata() (in module augur.merge) merge_sequences() (in module augur.merge) Metadata (class in augur.io.metadata) MismatchNodeError MissingNodeError Mode (class in augur.ancestral) modified_env (augur.io.shell_command_runner.ShellCommandRunner property) module augur augur.align augur.ancestral augur.argparse_ augur.clades augur.curate augur.curate.abbreviate_authors augur.curate.apply_geolocation_rules augur.curate.apply_record_annotations augur.curate.format_dates augur.curate.format_dates_directives augur.curate.normalize_strings augur.curate.parse_genbank_location augur.curate.passthru augur.curate.rename augur.curate.titlecase augur.curate.transform_strain_name augur.data augur.dates augur.dates.ambiguous_date augur.dates.errors augur.debug augur.distance augur.errors augur.export augur.export_v1 augur.export_v2 augur.filter augur.filter.arguments augur.filter.constants augur.filter.include_exclude_rules augur.filter.io augur.filter.subsample augur.filter.validate_arguments augur.filter.weights_file augur.frequencies augur.frequency_estimators augur.import_ augur.import_.beast augur.index augur.io augur.io.file augur.io.json augur.io.metadata augur.io.print augur.io.sequences augur.io.shell_command_runner augur.io.strains augur.lbi augur.mask augur.measurements augur.measurements.concat augur.measurements.export augur.merge augur.parse augur.proximity augur.read_file augur.reconstruct_sequences augur.refine augur.sequence_traits augur.subsample augur.titer_model augur.titers augur.traits augur.translate augur.tree augur.types augur.util_support augur.util_support.auspice_config augur.util_support.color_parser augur.util_support.color_parser_line augur.util_support.node_data augur.util_support.node_data_file augur.util_support.node_data_reader augur.util_support.warnings augur.utils augur.validate augur.validate_export augur.version augur.write_file

move_to_end_if_present() (augur.export_v2.CustomOrderedDict method) mugration_inference() (in module augur.traits) mutation_frequencies() (augur.frequency_estimators.alignment_frequencies method) mutations (augur.ancestral.Ancestral_Reconstruction attribute) Mutations (class in augur.ancestral)

N

name (augur.merge.NamedMetadata attribute) NamedMetadata (class in augur.merge) nested_frequencies (class in augur.frequency_estimators) node_data_files (augur.util_support.node_data_reader.NodeDataReader property) node_data_prop_is_normal_trait() (in module augur.export_v2) node_div() (in module augur.export_v2) node_names_from_tree_file (augur.util_support.node_data_reader.NodeDataReader property) NodeData (class in augur.util_support.node_data) NodeDataFile (class in augur.util_support.node_data_file) NodeDataObject (class in augur.util_support.node_data_file) NodeDataReader (class in augur.util_support.node_data_reader) nodes (augur.ancestral.Ancestral_JSON attribute) (augur.ancestral.Mutations attribute) (augur.util_support.node_data_file.NodeDataFile property)

NoGeolocationRulesProvidedError normalize() (augur.titer_model.TiterCollection method) normalize_strings() (in module augur.curate.normalize_strings) normalize_titers() (augur.titer_model.TiterCollection method) normalize_to_frequencies() (augur.frequency_estimators.KdeFrequencies class method) NoVariationError nthreads_value() (in module augur.utils) nuc (augur.ancestral.Annotations_JSON attribute) Nuc_Annotation (class in augur.ancestral) nuc_reconstruction (augur.ancestral.Mode attribute) numeric_date() (in module augur.dates) numeric_date_type() (in module augur.dates)

O

obs (augur.frequency_estimators.freq_est_clipped attribute) onAllNodes (augur.validate_export.AttrInfo attribute)

open() (augur.io.metadata.Metadata method) open_file() (in module augur.io.file) orderKeys() (in module augur.export_v2)

P

pair() (augur.util_support.color_parser_line.ColorParserLine method) pairs() (in module augur.merge) parse_authors() (in module augur.curate.abbreviate_authors) parse_beast_tree() (in module augur.import_.beast) parse_field_map() (in module augur.curate.rename) parse_file() (augur.util_support.color_parser.ColorParser method) parse_filter_query() (in module augur.filter.include_exclude_rules) parse_genes_argument() (in module augur.utils) parse_location() (in module augur.curate.parse_genbank_location) parse_nexus() (in module augur.import_.beast) parse_node_data_and_metadata() (in module augur.export_v2) parse_nodes() (in module augur.clades) parse_sequence() (in module augur.parse) path (augur.io.metadata.Metadata attribute) pivot_freq (augur.frequency_estimators.freq_est_clipped attribute) pivot_lower_cutoff (augur.frequency_estimators.freq_est_clipped attribute) pivot_upper_cutoff (augur.frequency_estimators.freq_est_clipped attribute) pivots (augur.frequency_estimators.freq_est_clipped attribute) postprocess() (in module augur.align) pq() (in module augur.frequency_estimators) predict_titer() (augur.titer_model.SubstitutionModel method) (augur.titer_model.TreeModel method)

prepare() (augur.frequency_estimators.tree_frequencies method) (augur.titer_model.SubstitutionModel method) (augur.titer_model.TreeModel method) (in module augur.align) prepare_tree() (augur.titer_model.TreeModel method) prettify() (in module augur.parse) prettify_alignment() (in module augur.align) print_debug() (in module augur.io.print) print_err() (in module augur.io.print) print_error() (augur.io.shell_command_runner.ShellCommandRunner static method) print_error_message() (augur.io.shell_command_runner.ShellCommandRunner method) print_what_to_do_next() (in module augur.import_.beast) PriorityQueue (class in augur.filter.subsample) process() (augur.traits.BranchLabeller method) process_annotations() (in module augur.export_v1) process_colorings() (in module augur.export_v1) process_geographic_info() (in module augur.export_v1) process_panels() (in module augur.export_v1) proximal sample PROXIMAL_SAMPLE_CONFIG (in module augur.subsample) ProximalSample (class in augur.subsample) proximity_argument_descriptions (in module augur.proximity) prune_seqs_matching_alignment() (in module augur.align)

R

range() (augur.dates.ambiguous_date.AmbiguousDate method) RE_AUGUR_AMBIGUOUS_DATE (in module augur.dates) RE_AUGUR_MISSING_DATE (in module augur.dates) RE_DATE_RANGE (in module augur.dates) RE_NUMERIC_DATE (in module augur.dates) RE_YEAR_MONTH_DAY (in module augur.dates) RE_YEAR_MONTH_ONLY (in module augur.dates) RE_YEAR_ONLY (in module augur.dates) read() (augur.util_support.node_data_reader.NodeDataReader method) read_alignment() (in module augur.align) read_and_validate_sequences() (in module augur.align) read_auspice_configs() (in module augur.util_support.auspice_config) read_bed_file() (in module augur.utils) read_colors() (in module augur.utils) read_csv_with_index_col() (in module augur.io.metadata) read_distance_map() (in module augur.distance) read_entries() (in module augur.utils) read_in_clade_definitions() (in module augur.clades) read_in_features() (in module augur.sequence_traits) read_in_translate_vcf() (in module augur.sequence_traits) read_json() (in module augur.util_support.auspice_config) read_lat_longs() (in module augur.utils) read_mask_file() (in module augur.utils) read_metadata() (in module augur.io.metadata) read_metadata_with_sequences() (in module augur.io.metadata) read_node_data() (in module augur.utils) read_priority_scores() (in module augur.filter.io) read_reference() (in module augur.align) read_sequence_ids() (in module augur.io.sequences) read_sequences() (in module augur.io.sequences) read_single_auspice_config() (in module augur.util_support.auspice_config) read_single_sequence() (in module augur.io.sequences) read_strains() (in module augur.io.strains) read_table_to_dict() (in module augur.io.metadata) read_titers() (augur.titer_model.TiterCollection method) read_tree() (in module augur.utils) read_weights_file() (in module augur.filter.weights_file) reconstruct_translations() (in module augur.ancestral) recursively_decorate_tree_json_v1_schema() (in module augur.export_v1) reference (augur.ancestral.Ancestral_JSON attribute) reference_virus_statistic() (augur.titer_model.TiterModel method) refine() (in module augur.refine) regex (augur.dates.ambiguous_date.AmbiguousDate property) register_arguments() (in module augur.align) (in module augur.filter) (in module augur.mask) (in module augur.proximity) register_parser() (in module augur.align) (in module augur.ancestral) (in module augur.clades) (in module augur.curate) (in module augur.curate.abbreviate_authors) (in module augur.curate.apply_geolocation_rules) (in module augur.curate.apply_record_annotations) (in module augur.curate.format_dates) (in module augur.curate.normalize_strings) (in module augur.curate.parse_genbank_location) (in module augur.curate.passthru) (in module augur.curate.rename) (in module augur.curate.titlecase) (in module augur.curate.transform_strain_name) (in module augur.distance) (in module augur.export) (in module augur.export_v1) (in module augur.export_v2) (in module augur.filter) (in module augur.frequencies) (in module augur.import_) (in module augur.import_.beast) (in module augur.index) (in module augur.lbi) (in module augur.mask) (in module augur.measurements) (in module augur.measurements.concat) (in module augur.measurements.export) (in module augur.merge) (in module augur.parse) (in module augur.proximity) (in module augur.read_file) (in module augur.reconstruct_sequences) (in module augur.refine) (in module augur.sequence_traits) (in module augur.subsample) (in module augur.titers) (in module augur.traits) (in module augur.translate) (in module augur.tree) (in module augur.validate) (in module augur.version) (in module augur.write_file)

remove_reference_sequence() (in module augur.align) remove_temporary_files() (augur.subsample.Sample method) remove_unused_metadata_columns() (in module augur.util_support.auspice_config) requires_aligned_sequences() (in module augur.subsample) resolve_uncertain_int() (in module augur.dates.ambiguous_date) root_outside_of_treetime() (in module augur.refine) root_seq (augur.ancestral.Ancestral_Reconstruction attribute) rows() (augur.io.metadata.Metadata method) run() (augur.io.shell_command_runner.ShellCommandRunner method) (augur.subsample.Sample method) (augur.titers.infer_substitution_model method) (augur.titers.infer_tree_model method) (in module augur) (in module augur.align) (in module augur.ancestral) (in module augur.clades) (in module augur.curate) (in module augur.curate.abbreviate_authors) (in module augur.curate.apply_geolocation_rules) (in module augur.curate.apply_record_annotations) (in module augur.curate.format_dates) (in module augur.curate.normalize_strings) (in module augur.curate.parse_genbank_location) (in module augur.curate.passthru) (in module augur.curate.rename) (in module augur.curate.titlecase) (in module augur.curate.transform_strain_name) (in module augur.distance) (in module augur.export_v1) (in module augur.export_v2) (in module augur.filter) (in module augur.frequencies) (in module augur.import_.beast) (in module augur.index) (in module augur.lbi) (in module augur.mask) (in module augur.measurements.concat) (in module augur.measurements.export) (in module augur.merge) (in module augur.parse) (in module augur.proximity) (in module augur.read_file) (in module augur.reconstruct_sequences) (in module augur.refine) (in module augur.sequence_traits) (in module augur.subsample) (in module augur.traits) (in module augur.translate) (in module augur.tree) (in module augur.validate) (in module augur.version) (in module augur.write_file) run_ancestral() (in module augur.ancestral) run_shell_command() (in module augur.io.shell_command_runner) running_average() (in module augur.frequency_estimators)

S

safe_translate() (in module augur.translate) sample Sample (class in augur.subsample) select_nodes_in_season() (in module augur.lbi) select_top_k() (in module augur.proximity) seqkit() (in module augur.io.sequences) sequences_json() (in module augur.translate) sequences_vcf() (in module augur.translate) set_annotations() (in module augur.export_v2) set_branch_attrs_on_tree() (in module augur.export_v2) set_build_avatar() (in module augur.export_v2) set_build_url() (in module augur.export_v2) set_colorings() (in module augur.export_v2) set_description() (in module augur.export_v2) set_filters() (in module augur.export_v2) set_geo_resolutions() (in module augur.export_v2) set_maintainers() (in module augur.export_v2) set_node_attrs_on_tree() (in module augur.export_v2) set_order() (augur.export_v2.CustomOrderedDict method) set_panels() (in module augur.export_v2) set_title() (in module augur.export_v2) set_warning() (in module augur.export_v2) shell_args (augur.io.shell_command_runner.ShellCommandRunner property) shell_executable (augur.io.shell_command_runner.ShellCommandRunner property)

ShellCommandRunner (class in augur.io.shell_command_runner) shorten_as_json() (in module augur.io.json) shorten_left() (in module augur.io.json) shquote_humanized() (in module augur.merge) signal_from_error() (augur.io.shell_command_runner.ShellCommandRunner static method) SILENT (augur.types.DataErrorMethod attribute) (augur.types.EmptyOutputReportingMethod attribute) SKIP (augur.types.ValidationMode attribute) skip_group_by_with_ambiguous_day() (in module augur.filter.include_exclude_rules) skip_group_by_with_ambiguous_month() (in module augur.filter.include_exclude_rules) skip_group_by_with_ambiguous_year() (in module augur.filter.include_exclude_rules) sqlite3() (in module augur.merge) sqlite3_table_columns() (in module augur.merge) sqlite_quote_dot() (in module augur.merge) sqlite_quote_id() (in module augur.merge) sqlite_quote_string() (in module augur.merge) SQLiteError start (augur.ancestral.Nuc_Annotation attribute) stiffLH() (augur.frequency_estimators.frequency_estimator method) strain_census() (augur.titer_model.TiterCollection method) strand (augur.ancestral.Nuc_Annotation attribute) strip_non_reference() (in module augur.align) subset_fasta() (in module augur.io.sequences) SubstitutionModel (class in augur.titer_model) summarise_parsed_traits() (in module augur.import_.beast)

T

table_name (augur.merge.NamedMetadata attribute) test_nested_estimator() (in module augur.frequency_estimators) test_simple_estimator() (in module augur.frequency_estimators) timestamp_to_float() (in module augur.frequency_estimators) tip_passes_filters() (augur.frequency_estimators.TreeKdeFrequencies method) titer_stats() (augur.titer_model.TiterModel method) TiterCollection (class in augur.titer_model) TiterModel (class in augur.titer_model) titlecase() (in module augur.curate.titlecase) to_json() (augur.frequency_estimators.KdeFrequencies method) to_numpy_array() (in module augur.proximity) TooManyGroupsError tps (augur.frequency_estimators.freq_est_clipped attribute) train() (augur.titer_model.SubstitutionModel method) (augur.titer_model.TreeModel method) trait (augur.util_support.color_parser_line.ColorParserLine property)

trait_value (augur.util_support.color_parser_line.ColorParserLine property) transfer_directly_from_config() (in module augur.export_v2) transform_columns() (in module augur.curate.rename) transform_geolocations() (in module augur.curate.apply_geolocation_rules) transform_name() (in module augur.curate.transform_strain_name) translate_feature() (in module augur.translate) translate_vcf_feature() (in module augur.translate) tree_frequencies (class in augur.frequency_estimators) tree_layout() (in module augur.export_v1) TreeAttrs (in module augur.validate_export) TreeKdeFrequencies (class in augur.frequency_estimators) TreeKdeFrequenciesError TreeModel (class in augur.titer_model) tt (augur.ancestral.Ancestral_Reconstruction attribute) tuple_to_date() (in module augur.dates.ambiguous_date) type (augur.ancestral.Nuc_Annotation attribute)

U

uncertain_date_components (augur.dates.ambiguous_date.AmbiguousDate property) update() (augur.util_support.node_data.NodeData method)

update_deprecated_names() (in module augur.util_support.auspice_config) url_name() (in module augur.export_v2)

V

valid (augur.frequency_estimators.freq_est_clipped attribute) valid_url() (in module augur.export_v2) validate() (augur.titer_model.TiterModel method) (augur.util_support.node_data_file.NodeDataFile method) (in module augur.validate) validate_arguments() (in module augur.ancestral) (in module augur.filter.validate_arguments) (in module augur.merge) validate_collection_config_fields() (in module augur.validate) validate_collection_display_defaults() (in module augur.validate)

validate_data_json() (in module augur.export_v2) validate_dates() (in module augur.dates) validate_json() (in module augur.validate) validate_measurements_config() (in module augur.validate) validate_records() (in module augur.curate) ValidateError validation_failure() (in module augur.validate) ValidationMode (class in augur.types) verifyMainJSONIsInternallyConsistent() (in module augur.validate_export) verifyMetaAndOrTreeJSONsAreInternallyConsistent() (in module augur.validate_export)

W

walk_commands() (in module augur.argparse_) WARN (augur.types.DataErrorMethod attribute) (augur.types.EmptyOutputReportingMethod attribute) (augur.types.ValidationMode attribute) warn() (in module augur.util_support.warnings) warn_if_clades_not_found() (in module augur.clades) write() (augur.io.json.BytesWrittenCounterIO method) write_augur_json() (in module augur.utils) write_json() (in module augur.io.json) (in module augur.utils)

write_out_informative_fasta() (in module augur.tree) write_output_metadata() (in module augur.filter.io) write_records_to_fasta() (in module augur.io.sequences) write_records_to_tsv() (in module augur.io.metadata) write_seqs() (in module augur.align) write_sequences() (in module augur.io.sequences) write_vcf() (in module augur.io.sequences) write_VCF_translation() (in module augur.io.sequences) written (augur.io.json.BytesWrittenCounterIO attribute)