gpf package

Subpackages

• gpf.common_reports package
  • Submodules
  • gpf.common_reports.common_report module
    • CommonReport
      • CommonReport.load()
      • CommonReport.save()
      • CommonReport.to_dict()
  • gpf.common_reports.denovo_report module
    • DenovoReport
      • DenovoReport.from_genotype_study()
      • DenovoReport.is_empty()
      • DenovoReport.to_dict()
    • DenovoReportTable
      • DenovoReportTable.from_variants()
      • DenovoReportTable.is_empty()
      • DenovoReportTable.to_dict()
    • EffectCell
      • EffectCell.column_name
      • EffectCell.count_variant()
      • EffectCell.is_empty()
      • EffectCell.number_of_children_with_event
      • EffectCell.number_of_observed_events
      • EffectCell.observed_rate_per_child
      • EffectCell.percent_of_children_with_events
      • EffectCell.to_dict()
    • EffectRow
      • EffectRow.count_variant()
      • EffectRow.get_empty()
      • EffectRow.is_row_empty()
      • EffectRow.remove_elements()
      • EffectRow.to_dict()
  • gpf.common_reports.family_counter module
    • FamiliesGroupCounters
      • FamiliesGroupCounters.from_families()
      • FamiliesGroupCounters.to_dict()
    • FamilyCounter
      • FamilyCounter.family
      • FamilyCounter.from_family()
      • FamilyCounter.to_dict()
    • get_family_pedigree()
    • get_family_type()
  • gpf.common_reports.family_report module
    • FamiliesReport
      • FamiliesReport.from_families_data()
      • FamiliesReport.from_study()
      • FamiliesReport.to_dict()
  • gpf.common_reports.people_counter module
    • PeopleCounter
      • PeopleCounter.from_person_set()
      • PeopleCounter.is_empty()
      • PeopleCounter.is_empty_field()
      • PeopleCounter.to_dict()
    • PeopleCounters
      • PeopleCounters.from_person_set_collection()
      • PeopleCounters.to_dict()
    • PeopleReport
      • PeopleReport.from_person_set_collections()
      • PeopleReport.to_dict()
  • Module contents
• gpf.configuration package
  • Subpackages
    • gpf.configuration.schemas package
      • Submodules
      • gpf.configuration.schemas.dae_conf module
      • gpf.configuration.schemas.gene_profile module
      • gpf.configuration.schemas.gene_weights_db module
      • gpf.configuration.schemas.person_sets module
      • gpf.configuration.schemas.phenotype_data module
      • gpf.configuration.schemas.study_config module
      • gpf.configuration.schemas.wdae_study_config module
      • Module contents
  • Submodules
  • gpf.configuration.gpf_config_parser module
    • DefaultBox
    • FrozenBox
    • GPFConfigParser
      • GPFConfigParser.collect_directory_configs()
      • GPFConfigParser.filetype_parsers
      • GPFConfigParser.load_config()
      • GPFConfigParser.load_config_dict()
      • GPFConfigParser.load_config_raw()
      • GPFConfigParser.load_directory_configs()
      • GPFConfigParser.merge_config()
      • GPFConfigParser.modify_tuple()
      • GPFConfigParser.parse_and_interpolate()
      • GPFConfigParser.parse_and_interpolate_file()
      • GPFConfigParser.process_config()
      • GPFConfigParser.process_config_raw()
      • GPFConfigParser.validate_config()
    • GPFConfigValidator
      • GPFConfigValidator.checkers
      • GPFConfigValidator.coercers
      • GPFConfigValidator.default_setters
      • GPFConfigValidator.normalization_rules
      • GPFConfigValidator.rules
      • GPFConfigValidator.validation_rules
  • gpf.configuration.study_config_builder module
    • ConfigDumper
      • ConfigDumper.increase_indent()
    • StudyConfigBuilder
      • StudyConfigBuilder.build_config()
    • TOMLDict
      • TOMLDict.from_dict()
    • TOMLList
      • TOMLList.from_list()
  • gpf.configuration.utils module
    • validate_existing_path()
    • validate_path()
  • Module contents
• gpf.duckdb_storage package
  • Submodules
  • gpf.duckdb_storage.duckdb2_variants module
    • DuckDb2Runner
      • DuckDb2Runner.run()
    • DuckDb2Variants
      • DuckDb2Variants.build_family_variants_query_runner()
      • DuckDb2Variants.build_summary_variants_query_runner()
      • DuckDb2Variants.fetch_annotation()
  • gpf.duckdb_storage.duckdb_connection_factory module
    • DuckDbConnectionFactory
      • DuckDbConnectionFactory.connect()
  • gpf.duckdb_storage.duckdb_genotype_storage module
    • AbstractDuckDbStorage
      • AbstractDuckDbStorage.build_study_layout()
      • AbstractDuckDbStorage.connect()
      • AbstractDuckDbStorage.is_read_only()
      • AbstractDuckDbStorage.shutdown()
    • DuckDbParquetStorage
      • DuckDbParquetStorage.build_study_layout()
      • DuckDbParquetStorage.get_storage_types()
      • DuckDbParquetStorage.start()
    • DuckDbS3ParquetStorage
      • DuckDbS3ParquetStorage.build_study_layout()
      • DuckDbS3ParquetStorage.get_storage_types()
      • DuckDbS3ParquetStorage.start()
    • DuckDbS3Storage
      • DuckDbS3Storage.build_study_layout()
      • DuckDbS3Storage.get_db_filename()
      • DuckDbS3Storage.get_storage_types()
      • DuckDbS3Storage.start()
    • DuckDbStorage
      • DuckDbStorage.build_study_layout()
      • DuckDbStorage.get_db_filename()
      • DuckDbStorage.get_storage_types()
      • DuckDbStorage.start()
    • duckdb_parquet_storage_factory()
    • duckdb_s3_parquet_storage_factory()
    • duckdb_s3_storage_factory()
    • duckdb_storage_factory()
  • gpf.duckdb_storage.duckdb_import_storage module
    • AbstractDuckDbImportStorage
      • AbstractDuckDbImportStorage.do_study_config()
      • AbstractDuckDbImportStorage.generate_import_task_graph()
    • DuckDbImportStorage
    • DuckDbLegacyImportStorage
    • DuckDbParquetImportStorage
    • DuckDbS3ImportStorage
    • DuckDbS3ParquetImportStorage
  • gpf.duckdb_storage.duckdb_legacy_genotype_storage module
    • DuckDbLegacyStorage
      • DuckDbLegacyStorage.VALIDATION_SCHEMA
      • DuckDbLegacyStorage.close()
      • DuckDbLegacyStorage.connect()
      • DuckDbLegacyStorage.create_database_connection()
      • DuckDbLegacyStorage.create_parquet_scans_layout_from_layout()
      • DuckDbLegacyStorage.create_parquet_scans_layout_relative()
      • DuckDbLegacyStorage.create_table()
      • DuckDbLegacyStorage.create_table_layout()
      • DuckDbLegacyStorage.create_table_partitioned()
      • DuckDbLegacyStorage.get_base_dir()
      • DuckDbLegacyStorage.get_db()
      • DuckDbLegacyStorage.get_db_filename()
      • DuckDbLegacyStorage.get_memory_limit()
      • DuckDbLegacyStorage.get_storage_types()
      • DuckDbLegacyStorage.get_work_dir()
      • DuckDbLegacyStorage.import_dataset()
      • DuckDbLegacyStorage.shutdown()
      • DuckDbLegacyStorage.start()
      • DuckDbLegacyStorage.validate_and_normalize_config()
    • duckdb_connect()
  • gpf.duckdb_storage.duckdb_storage_config module
    • DuckDbBaseConf
      • DuckDbBaseConf.id
      • DuckDbBaseConf.memory_limit
      • DuckDbBaseConf.model_computed_fields
      • DuckDbBaseConf.model_config
      • DuckDbBaseConf.model_fields
    • DuckDbConf
      • DuckDbConf.base_dir
      • DuckDbConf.db
      • DuckDbConf.model_computed_fields
      • DuckDbConf.model_config
      • DuckDbConf.model_fields
      • DuckDbConf.read_only
      • DuckDbConf.storage_type
    • DuckDbParquetConf
      • DuckDbParquetConf.base_dir
      • DuckDbParquetConf.model_computed_fields
      • DuckDbParquetConf.model_config
      • DuckDbParquetConf.model_fields
      • DuckDbParquetConf.storage_type
    • DuckDbS3Conf
      • DuckDbS3Conf.bucket_url
      • DuckDbS3Conf.db
      • DuckDbS3Conf.endpoint_url
      • DuckDbS3Conf.model_computed_fields
      • DuckDbS3Conf.model_config
      • DuckDbS3Conf.model_fields
      • DuckDbS3Conf.storage_type
      • DuckDbS3Conf.use_ssl
    • DuckDbS3ParquetConf
      • DuckDbS3ParquetConf.bucket_url
      • DuckDbS3ParquetConf.endpoint_url
      • DuckDbS3ParquetConf.model_computed_fields
      • DuckDbS3ParquetConf.model_config
      • DuckDbS3ParquetConf.model_fields
      • DuckDbS3ParquetConf.storage_type
      • DuckDbS3ParquetConf.use_ssl
    • parse_duckdb_config()
  • gpf.duckdb_storage.duckdb_storage_helpers module
    • create_database_connection()
    • create_duckdb_tables()
    • create_memory_connection()
    • create_relative_parquet_scans_layout()
    • create_s3_attach_db_clause()
    • create_s3_filesystem()
    • create_s3_secret_clause()
    • create_study_parquet_tables_layout()
    • create_table_layout()
    • get_study_config_tables()
    • join_base_url_and_parquet_scan()
  • gpf.duckdb_storage.duckdb_variants module
    • DuckDbQueryDialect
      • DuckDbQueryDialect.add_unnest_in_join()
      • DuckDbQueryDialect.array_item_suffix()
      • DuckDbQueryDialect.build_array_join()
      • DuckDbQueryDialect.build_table_name()
      • DuckDbQueryDialect.escape_char()
      • DuckDbQueryDialect.escape_quote_char()
      • DuckDbQueryDialect.float_type()
      • DuckDbQueryDialect.int_type()
      • DuckDbQueryDialect.use_bit_and_function()
    • DuckDbRunner
      • DuckDbRunner.run()
    • DuckDbVariants
      • DuckDbVariants.RUNNER_CLASS
  • Module contents
• gpf.enrichment_tool package
  • Subpackages
    • gpf.enrichment_tool.resource_implementations package
      • Submodules
      • gpf.enrichment_tool.resource_implementations.enrichment_resource_impl module
      • Module contents
  • Submodules
  • gpf.enrichment_tool.base_enrichment_background module
    • BaseEnrichmentBackground
      • BaseEnrichmentBackground.background_id
      • BaseEnrichmentBackground.background_type
      • BaseEnrichmentBackground.calc_enrichment_test()
      • BaseEnrichmentBackground.is_loaded()
      • BaseEnrichmentBackground.load()
      • BaseEnrichmentBackground.name
      • BaseEnrichmentBackground.resource_id
    • BaseEnrichmentResourceBackground
      • BaseEnrichmentResourceBackground.filename
      • BaseEnrichmentResourceBackground.get_schema()
      • BaseEnrichmentResourceBackground.name
  • gpf.enrichment_tool.build_coding_length_enrichment_background module
    • build_coding_length_background()
    • cli()
  • gpf.enrichment_tool.build_ur_synonymous_enrichment_background module
    • cli()
  • gpf.enrichment_tool.enrichment_cache_builder module
    • build_enrichment_event_counts_cache()
    • cli()
  • gpf.enrichment_tool.enrichment_utils module
    • get_enrichment_cache_path()
    • get_enrichment_config()
  • gpf.enrichment_tool.event_counters module
    • CounterBase
      • CounterBase.event_counts()
      • CounterBase.events()
      • CounterBase.select_events_in_person_set()
      • CounterBase.split_events()
    • EnrichmentResult
      • EnrichmentResult.all
      • EnrichmentResult.female
      • EnrichmentResult.male
      • EnrichmentResult.rec
      • EnrichmentResult.rec_genes
      • EnrichmentResult.unspecified
    • EnrichmentSingleResult
    • EventCountersResult
      • EventCountersResult.all
      • EventCountersResult.female
      • EventCountersResult.from_events_result()
      • EventCountersResult.male
      • EventCountersResult.rec
      • EventCountersResult.rec_genes
      • EventCountersResult.unspecified
    • EventsCounter
      • EventsCounter.events()
    • EventsResult
      • EventsResult.all
      • EventsResult.female
      • EventsResult.male
      • EventsResult.rec
      • EventsResult.unspecified
    • GeneEventsCounter
      • GeneEventsCounter.events()
    • VariantEventsResult
      • VariantEventsResult.all
      • VariantEventsResult.female
      • VariantEventsResult.male
      • VariantEventsResult.rec
      • VariantEventsResult.unspecified
    • filter_denovo_one_event_per_family()
    • filter_denovo_one_gene_per_events()
    • filter_denovo_one_gene_per_recurrent_events()
    • filter_overlapping_events()
    • get_sym_2_fn()
    • overlap_enrichment_result_dict()
    • overlap_event_counts()
  • gpf.enrichment_tool.gene_weights_background module
    • GeneScoreEnrichmentBackground
      • GeneScoreEnrichmentBackground.background_id
      • GeneScoreEnrichmentBackground.background_type
      • GeneScoreEnrichmentBackground.calc_enrichment_test()
      • GeneScoreEnrichmentBackground.calc_expected_observed_pvalue()
      • GeneScoreEnrichmentBackground.filename
      • GeneScoreEnrichmentBackground.genes_prob()
      • GeneScoreEnrichmentBackground.genes_weight()
      • GeneScoreEnrichmentBackground.is_loaded()
      • GeneScoreEnrichmentBackground.load()
      • GeneScoreEnrichmentBackground.name
      • GeneScoreEnrichmentBackground.resource_id
      • GeneScoreEnrichmentBackground.score_id
    • GeneWeightsEnrichmentBackground
      • GeneWeightsEnrichmentBackground.calc_enrichment_test()
      • GeneWeightsEnrichmentBackground.calc_expected_observed_pvalue()
      • GeneWeightsEnrichmentBackground.genes_prob()
      • GeneWeightsEnrichmentBackground.genes_weight()
      • GeneWeightsEnrichmentBackground.is_loaded()
      • GeneWeightsEnrichmentBackground.load()
  • gpf.enrichment_tool.genotype_helper module
    • AlleleEvent
      • AlleleEvent.effect_genes
      • AlleleEvent.persons
    • GeneEffect
      • GeneEffect.effect
      • GeneEffect.gene
    • GenotypeHelper
      • GenotypeHelper.collect_denovo_events()
      • GenotypeHelper.get_denovo_events()
    • VariantEvent
      • VariantEvent.allele_events
      • VariantEvent.family_id
      • VariantEvent.fvuid
  • gpf.enrichment_tool.samocha_background module
    • SamochaEnrichmentBackground
      • SamochaEnrichmentBackground.calc_enrichment_test()
      • SamochaEnrichmentBackground.get_schema()
      • SamochaEnrichmentBackground.is_loaded()
      • SamochaEnrichmentBackground.load()
      • SamochaEnrichmentBackground.name
    • poisson_test()
  • Module contents
• gpf.gene_profile package
  • Submodules
  • gpf.gene_profile.convert_gene_profile_to_duckdb module
    • main()
  • gpf.gene_profile.db module
    • GeneProfileDB
      • GeneProfileDB.PAGE_SIZE
      • GeneProfileDB.get_gp()
      • GeneProfileDB.gp_from_table_row()
      • GeneProfileDB.gp_from_table_row_single_view()
      • GeneProfileDB.list_symbols()
      • GeneProfileDB.query_gps()
    • GeneProfileDBWriter
      • GeneProfileDBWriter.build_configuration()
      • GeneProfileDBWriter.create_gp_table()
      • GeneProfileDBWriter.drop_gp_table()
      • GeneProfileDBWriter.insert_gp()
      • GeneProfileDBWriter.insert_gps()
      • GeneProfileDBWriter.update_gps_with_values()
  • gpf.gene_profile.exporter module
    • cli_export()
  • gpf.gene_profile.generate_gene_profile module
    • add_variant_count()
    • build_partitions()
    • build_rare_query()
    • collect_variant_counts()
    • count_variant()
    • generate_gp()
    • main()
    • process_region()
  • gpf.gene_profile.statistic module
    • GPStatistic
      • GPStatistic.to_json()
  • Module contents
• gpf.gene_sets package
  • Submodules
  • gpf.gene_sets.denovo_gene_set_collection module
    • DenovoGeneSetCollection
      • DenovoGeneSetCollection.add_gene()
      • DenovoGeneSetCollection.build_collection()
      • DenovoGeneSetCollection.create_empty_collection()
      • DenovoGeneSetCollection.get_all_gene_sets()
      • DenovoGeneSetCollection.get_gene_set()
      • DenovoGeneSetCollection.get_gene_set_from_collections()
      • DenovoGeneSetCollection.get_gene_sets_types_legend()
      • DenovoGeneSetCollection.get_person_set_collection_legend()
      • DenovoGeneSetCollection.is_cached()
      • DenovoGeneSetCollection.load()
      • DenovoGeneSetCollection.save()
  • gpf.gene_sets.denovo_gene_set_helpers module
    • DenovoGeneSetHelpers
      • DenovoGeneSetHelpers.build_collection()
      • DenovoGeneSetHelpers.load_collection()
      • DenovoGeneSetHelpers.load_collection_from_dict()
  • gpf.gene_sets.denovo_gene_sets_config module
    • DGSCQuery
      • DGSCQuery.effects
      • DGSCQuery.gene_set_id
      • DGSCQuery.model_computed_fields
      • DGSCQuery.model_config
      • DGSCQuery.model_fields
      • DGSCQuery.psc_id
      • DGSCQuery.recurrency
      • DGSCQuery.selected_person_sets
      • DGSCQuery.sex
    • DGSSpec
      • DGSSpec.criterias
      • DGSSpec.gene_set_id
      • DGSSpec.model_computed_fields
      • DGSSpec.model_config
      • DGSSpec.model_fields
    • DenovoGeneSetsConfig
      • DenovoGeneSetsConfig.effect_types
      • DenovoGeneSetsConfig.enabled
      • DenovoGeneSetsConfig.gene_sets_ids
      • DenovoGeneSetsConfig.model_computed_fields
      • DenovoGeneSetsConfig.model_config
      • DenovoGeneSetsConfig.model_fields
      • DenovoGeneSetsConfig.recurrency
      • DenovoGeneSetsConfig.selected_person_set_collections
      • DenovoGeneSetsConfig.sexes
    • EffectsCriteria
      • EffectsCriteria.effects
      • EffectsCriteria.model_computed_fields
      • EffectsCriteria.model_config
      • EffectsCriteria.model_fields
      • EffectsCriteria.name
    • RecurrentCriteria
      • RecurrentCriteria.end
      • RecurrentCriteria.model_computed_fields
      • RecurrentCriteria.model_config
      • RecurrentCriteria.model_fields
      • RecurrentCriteria.name
      • RecurrentCriteria.start
    • SexesCriteria
      • SexesCriteria.model_computed_fields
      • SexesCriteria.model_config
      • SexesCriteria.model_fields
      • SexesCriteria.name
      • SexesCriteria.sexes
    • SingleCriteria
      • SingleCriteria.end
      • SingleCriteria.model_computed_fields
      • SingleCriteria.model_config
      • SingleCriteria.model_fields
      • SingleCriteria.name
      • SingleCriteria.start
    • TripleCriteria
      • TripleCriteria.end
      • TripleCriteria.model_computed_fields
      • TripleCriteria.model_config
      • TripleCriteria.model_fields
      • TripleCriteria.name
      • TripleCriteria.start
    • create_denovo_gene_set_spec()
    • parse_denovo_gene_sets_config()
    • parse_denovo_gene_sets_study_config()
    • parse_dgsc_query()
    • parse_recurrency_criteria()
  • gpf.gene_sets.denovo_gene_sets_db module
    • DenovoGeneSetsDb
      • DenovoGeneSetsDb.build_cache()
      • DenovoGeneSetsDb.collections_descriptions
      • DenovoGeneSetsDb.denovo_gene_sets_types
      • DenovoGeneSetsDb.get_all_gene_sets()
      • DenovoGeneSetsDb.get_collection_types_legend()
      • DenovoGeneSetsDb.get_gene_set()
      • DenovoGeneSetsDb.get_gene_set_ids()
      • DenovoGeneSetsDb.get_genotype_data_ids()
      • DenovoGeneSetsDb.has_gene_sets()
      • DenovoGeneSetsDb.reload()
      • DenovoGeneSetsDb.update_cache()
  • gpf.gene_sets.gene_sets_db module
    • GeneSetsDb
      • GeneSetsDb.collections_descriptions
      • GeneSetsDb.get_all_gene_sets()
      • GeneSetsDb.get_gene_set()
      • GeneSetsDb.get_gene_set_collection_ids()
      • GeneSetsDb.get_gene_set_ids()
      • GeneSetsDb.has_gene_set_collection()
  • Module contents
• gpf.genomic_scores package
  • Submodules
  • gpf.genomic_scores.scores module
    • GenomicScoresRegistry
      • GenomicScoresRegistry.build_genomic_scores_registry()
      • GenomicScoresRegistry.get_scores()
    • ScoreDesc
      • ScoreDesc.description
      • ScoreDesc.from_json()
      • ScoreDesc.help
      • ScoreDesc.hist
      • ScoreDesc.large_values_desc
      • ScoreDesc.name
      • ScoreDesc.resource_id
      • ScoreDesc.small_values_desc
      • ScoreDesc.source
      • ScoreDesc.to_json()
  • Module contents
• gpf.genotype_storage package
  • Submodules
  • gpf.genotype_storage.genotype_storage module
    • GenotypeStorage
      • GenotypeStorage.build_backend()
      • GenotypeStorage.create_runner()
      • GenotypeStorage.create_summary_runner()
      • GenotypeStorage.get_storage_types()
      • GenotypeStorage.is_read_only()
      • GenotypeStorage.loaded_variants
      • GenotypeStorage.read_only
      • GenotypeStorage.shutdown()
      • GenotypeStorage.start()
      • GenotypeStorage.study_configs
      • GenotypeStorage.validate_and_normalize_config()
  • gpf.genotype_storage.genotype_storage_genomic_context_cli module
    • Key Constants
    • See Also
    • CLIGenotypeStorageContextProvider
      • CLIGenotypeStorageContextProvider.add_argparser_arguments()
      • CLIGenotypeStorageContextProvider.init()
    • get_context_genotype_storages()
  • gpf.genotype_storage.genotype_storage_registry module
    • GenotypeStorageRegistry
      • GenotypeStorageRegistry.find_storage()
      • GenotypeStorageRegistry.get_all_genotype_storage_ids()
      • GenotypeStorageRegistry.get_all_genotype_storages()
      • GenotypeStorageRegistry.get_default_genotype_storage()
      • GenotypeStorageRegistry.get_genotype_storage()
      • GenotypeStorageRegistry.query_summary_variants()
      • GenotypeStorageRegistry.query_variants()
      • GenotypeStorageRegistry.register_default_storage()
      • GenotypeStorageRegistry.register_genotype_storage()
      • GenotypeStorageRegistry.register_storage_config()
      • GenotypeStorageRegistry.register_storages_configs()
      • GenotypeStorageRegistry.shutdown()
    • get_genotype_storage_factory()
    • get_genotype_storage_types()
    • register_genotype_storage_factory()
  • Module contents
• gpf.gpf_instance package
  • Subpackages
    • gpf.gpf_instance.adjustments package
      • Submodules
      • gpf.gpf_instance.adjustments.adjust_command module
      • gpf.gpf_instance.adjustments.adjust_duckdb_storage module
      • gpf.gpf_instance.adjustments.adjust_impala_storage module
      • gpf.gpf_instance.adjustments.gpf_instance_adjustments module
      • Module contents
  • Submodules
  • gpf.gpf_instance.gpf_instance module
    • GPFInstance
      • GPFInstance.build()
      • GPFInstance.denovo_gene_sets_db
      • GPFInstance.gene_models
      • GPFInstance.gene_scores_db
      • GPFInstance.gene_sets_db
      • GPFInstance.genomic_scores
      • GPFInstance.genotype_storages
      • GPFInstance.get_all_gene_score_descs()
      • GPFInstance.get_all_gene_scores()
      • GPFInstance.get_all_genotype_data()
      • GPFInstance.get_all_phenotype_data()
      • GPFInstance.get_annotation_pipeline()
      • GPFInstance.get_annotation_pipeline_config()
      • GPFInstance.get_cache_path()
      • GPFInstance.get_dataset()
      • GPFInstance.get_gene_score()
      • GPFInstance.get_gene_score_desc()
      • GPFInstance.get_genotype_data()
      • GPFInstance.get_genotype_data_config()
      • GPFInstance.get_genotype_data_ids()
      • GPFInstance.get_gp_configuration()
      • GPFInstance.get_gp_statistic()
      • GPFInstance.get_pheno_cache_path()
      • GPFInstance.get_phenotype_data()
      • GPFInstance.get_phenotype_data_config()
      • GPFInstance.get_phenotype_data_ids()
      • GPFInstance.get_transcript_models()
      • GPFInstance.grr
      • GPFInstance.has_gene_score()
      • GPFInstance.has_phenotype_data()
      • GPFInstance.list_gp_gene_symbols()
      • GPFInstance.load()
      • GPFInstance.phenotype_storages
      • GPFInstance.query_gp_statistics()
      • GPFInstance.reference_genome
      • GPFInstance.reload()
  • Module contents
    • GPFInstance
      • GPFInstance.build()
      • GPFInstance.denovo_gene_sets_db
      • GPFInstance.gene_models
      • GPFInstance.gene_scores_db
      • GPFInstance.gene_sets_db
      • GPFInstance.genomic_scores
      • GPFInstance.genotype_storages
      • GPFInstance.get_all_gene_score_descs()
      • GPFInstance.get_all_gene_scores()
      • GPFInstance.get_all_genotype_data()
      • GPFInstance.get_all_phenotype_data()
      • GPFInstance.get_annotation_pipeline()
      • GPFInstance.get_annotation_pipeline_config()
      • GPFInstance.get_cache_path()
      • GPFInstance.get_dataset()
      • GPFInstance.get_gene_score()
      • GPFInstance.get_gene_score_desc()
      • GPFInstance.get_genotype_data()
      • GPFInstance.get_genotype_data_config()
      • GPFInstance.get_genotype_data_ids()
      • GPFInstance.get_gp_configuration()
      • GPFInstance.get_gp_statistic()
      • GPFInstance.get_pheno_cache_path()
      • GPFInstance.get_phenotype_data()
      • GPFInstance.get_phenotype_data_config()
      • GPFInstance.get_phenotype_data_ids()
      • GPFInstance.get_transcript_models()
      • GPFInstance.grr
      • GPFInstance.has_gene_score()
      • GPFInstance.has_phenotype_data()
      • GPFInstance.list_gp_gene_symbols()
      • GPFInstance.load()
      • GPFInstance.phenotype_storages
      • GPFInstance.query_gp_statistics()
      • GPFInstance.reference_genome
      • GPFInstance.reload()
• gpf.gpf_instance_plugin package
  • Submodules
  • gpf.gpf_instance_plugin.gpf_instance_context_plugin module
    • GPFInstanceContextProvider
      • GPFInstanceContextProvider.add_argparser_arguments()
      • GPFInstanceContextProvider.init()
    • GPFInstanceGenomicContext
      • GPFInstanceGenomicContext.get_context_keys()
      • GPFInstanceGenomicContext.get_context_object()
      • GPFInstanceGenomicContext.get_source()
  • Module contents
• gpf.import_tools package
  • Submodules
  • gpf.import_tools.cli module
    • main()
    • run_with_project()
  • gpf.import_tools.import_config module
  • gpf.import_tools.import_tools module
    • Bucket
      • Bucket.index
      • Bucket.region_bin
      • Bucket.regions
      • Bucket.type
    • ImportConfigNormalizer
      • ImportConfigNormalizer.normalize()
    • ImportProject
      • ImportProject.build_annotation_pipeline()
      • ImportProject.build_from_config()
      • ImportProject.build_from_file()
      • ImportProject.del_loader_prefix()
      • ImportProject.get_annotation_pipeline_config()
      • ImportProject.get_genotype_storage()
      • ImportProject.get_gpf_instance()
      • ImportProject.get_import_storage()
      • ImportProject.get_import_variants_buckets()
      • ImportProject.get_input_filenames()
      • ImportProject.get_parquet_dataset_dir()
      • ImportProject.get_partition_descriptor()
      • ImportProject.get_pedigree()
      • ImportProject.get_pedigree_filename()
      • ImportProject.get_pedigree_loader()
      • ImportProject.get_pedigree_params()
      • ImportProject.get_processing_annotation_batch_size()
      • ImportProject.get_processing_parquet_dataset_dir()
      • ImportProject.get_row_group_size()
      • ImportProject.get_variant_loader()
      • ImportProject.get_variant_loader_chrom_lens()
      • ImportProject.get_variant_loader_chromosomes()
      • ImportProject.get_variant_loader_types()
      • ImportProject.get_variant_params()
      • ImportProject.has_denovo_variants()
      • ImportProject.has_genotype_storage()
      • ImportProject.has_variants()
      • ImportProject.include_reference
      • ImportProject.input_dir
      • ImportProject.study_id
      • ImportProject.work_dir
    • ImportStorage
      • ImportStorage.generate_import_task_graph()
    • construct_import_annotation_pipeline()
    • construct_import_annotation_pipeline_config()
    • get_import_storage_factory()
    • get_import_storage_types()
    • register_import_storage_factory()
    • save_study_config()
  • Module contents
• gpf.inmemory_storage package
  • Submodules
  • gpf.inmemory_storage.annotation_serialization module
    • build_annotation_filename()
    • variants_loader_annotate_and_save()
    • variants_loader_load_annotation()
  • gpf.inmemory_storage.inmemory_genotype_storage module
    • InmemoryGenotypeStorage
      • InmemoryGenotypeStorage.VALIDATION_SCHEMA
      • InmemoryGenotypeStorage.get_data_dir()
      • InmemoryGenotypeStorage.get_storage_types()
      • InmemoryGenotypeStorage.shutdown()
      • InmemoryGenotypeStorage.start()
      • InmemoryGenotypeStorage.validate_and_normalize_config()
  • gpf.inmemory_storage.inmemory_import_storage module
    • InmemoryImportStorage
      • InmemoryImportStorage.generate_import_task_graph()
  • gpf.inmemory_storage.raw_variants module
    • RawFamilyVariants
      • RawFamilyVariants.build_family_variants_query_runner()
      • RawFamilyVariants.build_summary_variants_query_runner()
      • RawFamilyVariants.family_variant_filter_function()
      • RawFamilyVariants.family_variants_iterator()
      • RawFamilyVariants.filter_allele()
      • RawFamilyVariants.filter_family_variant()
      • RawFamilyVariants.filter_gene_effects()
      • RawFamilyVariants.filter_real_attr()
      • RawFamilyVariants.filter_regions()
      • RawFamilyVariants.filter_summary_allele()
      • RawFamilyVariants.filter_summary_variant()
      • RawFamilyVariants.full_variants_iterator()
      • RawFamilyVariants.summary_variant_filter_function()
      • RawFamilyVariants.summary_variants_iterator()
    • RawMemoryVariants
      • RawMemoryVariants.full_variants
      • RawMemoryVariants.full_variants_iterator()
      • RawMemoryVariants.has_affected_status_queries()
    • RawVariantsQueryRunner
      • RawVariantsQueryRunner.run()
  • Module contents
• gpf.parquet package
  • Subpackages
    • gpf.parquet.schema2 package
      • Submodules
      • gpf.parquet.schema2.annotate_schema2_parquet module
      • gpf.parquet.schema2.loader module
      • gpf.parquet.schema2.merge_parquet module
      • gpf.parquet.schema2.parquet_io module
      • gpf.parquet.schema2.processing_pipeline module
      • gpf.parquet.schema2.serializers module
      • gpf.parquet.schema2.variants_parquet_writer module
      • Module contents
  • Submodules
  • gpf.parquet.helpers module
    • merge_parquets()
    • url_to_pyarrow_fs()
  • gpf.parquet.parquet_writer module
    • add_missing_parquet_fields()
    • append_meta_to_parquet()
    • collect_pedigree_parquet_schema()
    • fill_family_bins()
    • merge_variants_parquets()
    • pedigree_parquet_schema()
    • save_ped_df_to_parquet()
    • serialize_summary_schema()
  • gpf.parquet.partition_descriptor module
    • Partition
      • Partition.coding_bin
      • Partition.family_bin
      • Partition.frequency_bin
      • Partition.from_pylist()
      • Partition.is_empty()
      • Partition.region_bin
      • Partition.to_pylist()
    • PartitionDescriptor
      • PartitionDescriptor.build_family_partitions()
      • PartitionDescriptor.build_summary_partitions()
      • PartitionDescriptor.family_partition()
      • PartitionDescriptor.family_partition_schema()
      • PartitionDescriptor.get_variant_partitions()
      • PartitionDescriptor.has_coding_bins()
      • PartitionDescriptor.has_family_bins()
      • PartitionDescriptor.has_family_partitions()
      • PartitionDescriptor.has_frequency_bins()
      • PartitionDescriptor.has_partitions()
      • PartitionDescriptor.has_region_bins()
      • PartitionDescriptor.has_summary_partitions()
      • PartitionDescriptor.make_all_region_bins()
      • PartitionDescriptor.make_coding_bin()
      • PartitionDescriptor.make_family_bin()
      • PartitionDescriptor.make_frequency_bin()
      • PartitionDescriptor.make_region_bin()
      • PartitionDescriptor.make_region_bins_regions()
      • PartitionDescriptor.parse()
      • PartitionDescriptor.parse_dict()
      • PartitionDescriptor.parse_string()
      • PartitionDescriptor.partition_directory()
      • PartitionDescriptor.partition_filename()
      • PartitionDescriptor.path_to_partitions()
      • PartitionDescriptor.region_bins_count()
      • PartitionDescriptor.region_to_region_bins()
      • PartitionDescriptor.schema1_partition()
      • PartitionDescriptor.serialize()
      • PartitionDescriptor.summary_partition()
      • PartitionDescriptor.summary_partition_schema()
      • PartitionDescriptor.to_dict()
  • Module contents
• gpf.parquet_storage package
  • Submodules
  • gpf.parquet_storage.storage module
    • ParquetGenotypeStorage
      • ParquetGenotypeStorage.VALIDATION_SCHEMA
      • ParquetGenotypeStorage.get_storage_types()
      • ParquetGenotypeStorage.import_dataset()
      • ParquetGenotypeStorage.shutdown()
      • ParquetGenotypeStorage.start()
      • ParquetGenotypeStorage.validate_and_normalize_config()
    • ParquetImportStorage
      • ParquetImportStorage.generate_import_task_graph()
    • ParquetLoaderVariants
      • ParquetLoaderVariants.build_family_variants_query_runner()
      • ParquetLoaderVariants.build_summary_variants_query_runner()
      • ParquetLoaderVariants.has_affected_status_queries()
      • ParquetLoaderVariants.query_summary_variants()
      • ParquetLoaderVariants.query_variants()
  • Module contents
• gpf.pedigrees package
  • Submodules
  • gpf.pedigrees.drawing module
    • OffsetLayoutDrawer
      • OffsetLayoutDrawer.GAP
      • OffsetLayoutDrawer.draw()
    • PDFLayoutDrawer
      • PDFLayoutDrawer.add_page()
  • gpf.pedigrees.families_data module
    • FamiliesData
      • FamiliesData.broken_families
      • FamiliesData.close()
      • FamiliesData.combine()
      • FamiliesData.copy()
      • FamiliesData.families_of_persons()
      • FamiliesData.from_families()
      • FamiliesData.from_family_persons()
      • FamiliesData.from_pedigree_df()
      • FamiliesData.get()
      • FamiliesData.items()
      • FamiliesData.keys()
      • FamiliesData.ped_df
      • FamiliesData.pedigree_samples()
      • FamiliesData.persons_with_parent()
      • FamiliesData.persons_with_parents()
      • FamiliesData.persons_without_parents()
      • FamiliesData.real_persons
      • FamiliesData.redefine()
      • FamiliesData.values()
    • merge_families()
    • tag_families_data()
  • gpf.pedigrees.family module
    • Family
      • Family.add_members()
      • Family.from_persons()
      • Family.from_records()
      • Family.full_members
      • Family.get_columns()
      • Family.get_member()
      • Family.get_members_with_roles()
      • Family.get_members_with_statuses()
      • Family.has_members()
      • Family.member_has_both_parents()
      • Family.member_has_dad()
      • Family.member_has_mom()
      • Family.member_has_parent()
      • Family.member_ids
      • Family.member_is_child()
      • Family.member_is_parent()
      • Family.members_in_order
      • Family.members_index()
      • Family.redefine()
      • Family.samples_index
      • Family.set_tag()
      • Family.tag_labels
      • Family.tags
      • Family.to_json()
      • Family.trios
      • Family.unset_tag()
    • FamilyTag
      • FamilyTag.AFFECTED_DAD
      • FamilyTag.AFFECTED_MOM
      • FamilyTag.AFFECTED_PRB
      • FamilyTag.AFFECTED_SIB
      • FamilyTag.CONTROL
      • FamilyTag.FEMALE_PRB
      • FamilyTag.MALE_PRB
      • FamilyTag.MISSING_DAD
      • FamilyTag.MISSING_MOM
      • FamilyTag.MULTIPLEX
      • FamilyTag.NUCLEAR
      • FamilyTag.QUAD
      • FamilyTag.SIMPLEX
      • FamilyTag.TRIO
      • FamilyTag.UNAFFECTED_DAD
      • FamilyTag.UNAFFECTED_MOM
      • FamilyTag.UNAFFECTED_PRB
      • FamilyTag.UNAFFECTED_SIB
      • FamilyTag.all_labels()
      • FamilyTag.all_tags()
      • FamilyTag.from_label()
      • FamilyTag.label
    • Person
      • Person.all_tag_labels()
      • Person.diff()
      • Person.family_bin
      • Person.generated
      • Person.get_attr()
      • Person.has_attr()
      • Person.has_tag()
      • Person.layout
      • Person.member_index
      • Person.missing
      • Person.not_sequenced
      • Person.redefine()
      • Person.role
      • Person.sample_index
      • Person.set_attr()
      • Person.set_tag()
      • Person.sex
      • Person.status
      • Person.tags
      • Person.to_json()
      • Person.unset_tag()
    • get_pedigree_column_names()
  • gpf.pedigrees.family_role_builder module
    • FamilyRoleBuilder
      • FamilyRoleBuilder.build_roles()
    • Mating
      • Mating.build_id()
      • Mating.parents_id()
  • gpf.pedigrees.family_tag_builder module
    • FamilyTagsBuilder
      • FamilyTagsBuilder.TAGS
      • FamilyTagsBuilder.add_tagger()
      • FamilyTagsBuilder.clear_tags()
      • FamilyTagsBuilder.tag_family()
      • FamilyTagsBuilder.tag_family_type()
    • check_affected_dad_family()
    • check_affected_mom_family()
    • check_affected_prb_family()
    • check_affected_sib_family()
    • check_control_family()
    • check_family_tags_query()
    • check_female_prb_family()
    • check_male_prb_family()
    • check_missing_dad_family()
    • check_missing_mom_family()
    • check_multiplex_family()
    • check_nuclear_family()
    • check_quad_family()
    • check_simplex_family()
    • check_tag()
    • check_trio_family()
    • check_unaffected_dad_family()
    • check_unaffected_mom_family()
    • check_unaffected_prb_family()
    • check_unaffected_sib_family()
    • set_attr()
    • set_tag()
    • tag_affected_dad_family()
    • tag_affected_mom_family()
    • tag_affected_prb_family()
    • tag_affected_sib_family()
    • tag_control_family()
    • tag_female_prb_family()
    • tag_male_prb_family()
    • tag_missing_dad_family()
    • tag_missing_mom_family()
    • tag_multiplex_family()
    • tag_nuclear_family()
    • tag_quad_family()
    • tag_simplex_family()
    • tag_trio_family()
    • tag_unaffected_dad_family()
    • tag_unaffected_mom_family()
    • tag_unaffected_prb_family()
    • tag_unaffected_sib_family()
    • unset_tag()
  • gpf.pedigrees.layout module
    • IndividualWithCoordinates
      • IndividualWithCoordinates.SIZE
      • IndividualWithCoordinates.x_center
      • IndividualWithCoordinates.y_center
    • Layout
      • Layout.BBox
      • Layout.apply_to_family()
      • Layout.from_family()
      • Layout.from_family_layout()
      • Layout.get_bbox()
      • Layout.id_to_position
      • Layout.individuals_by_rank
      • Layout.scale()
      • Layout.translate()
    • Line
      • Line.curve_p0()
      • Line.curve_p1()
      • Line.curve_p2()
      • Line.curve_p3()
      • Line.curve_y_at()
      • Line.curved
      • Line.inverse_curve_p1()
      • Line.inverse_curve_p2()
      • Line.inverse_curve_y_at()
    • Point
      • Point.x
      • Point.y
    • layout_parser()
  • gpf.pedigrees.loader module
    • FamiliesLoader
      • FamiliesLoader.build_families_data_from_pedigree()
      • FamiliesLoader.flexible_pedigree_read()
      • FamiliesLoader.load()
      • FamiliesLoader.load_pedigree_file()
      • FamiliesLoader.load_simple_families_file()
      • FamiliesLoader.parse_cli_arguments()
      • FamiliesLoader.save_families()
      • FamiliesLoader.save_pedigree()
      • FamiliesLoader.to_tsv()
  • gpf.pedigrees.pedigrees module
    • FamilyConnections
      • FamilyConnections.add_missing_members()
      • FamilyConnections.add_ranks()
      • FamilyConnections.connected_components()
      • FamilyConnections.create_sandwich_instance()
      • FamilyConnections.from_family()
      • FamilyConnections.get_graph()
      • FamilyConnections.get_individual()
      • FamilyConnections.get_individuals()
      • FamilyConnections.get_individuals_with_rank()
      • FamilyConnections.get_mating_units()
      • FamilyConnections.get_sibship_units()
      • FamilyConnections.is_connected()
      • FamilyConnections.is_valid_family()
      • FamilyConnections.max_rank()
      • FamilyConnections.members
    • Individual
      • Individual.NO_RANK
      • Individual.add_rank()
      • Individual.are_mates()
      • Individual.are_siblings()
      • Individual.children_set()
      • Individual.individual_set()
      • Individual.is_individual()
    • IndividualGroup
      • IndividualGroup.children_set()
      • IndividualGroup.generation_ranks()
      • IndividualGroup.individual_set()
      • IndividualGroup.is_individual()
    • Interval
      • Interval.intersection()
    • IntervalForVertex
    • MatingUnit
      • MatingUnit.children_set()
      • MatingUnit.individual_set()
      • MatingUnit.other_parent()
    • Realization
      • Realization.can_extend()
      • Realization.copy()
      • Realization.dangling()
      • Realization.dangling_set()
      • Realization.degree()
      • Realization.extend()
      • Realization.force_extend()
      • Realization.get_active_vertex_edges()
      • Realization.get_active_vertices()
      • Realization.get_interval()
      • Realization.get_maximal_set()
      • Realization.is_active_vertex()
      • Realization.is_in_interval_order()
      • Realization.is_maximal()
    • SandwichInstance
      • SandwichInstance.from_sets()
    • SandwichSolver
      • SandwichSolver.solve()
      • SandwichSolver.try_solve()
    • SibshipUnit
      • SibshipUnit.children_set()
      • SibshipUnit.individual_set()
    • copy_graph()
  • gpf.pedigrees.testing module
    • build_families_data()
    • build_family()
  • Module contents
• gpf.person_filters package
  • Submodules
  • gpf.person_filters.person_filters module
    • CriteriaFilter
      • CriteriaFilter.apply()
    • FamilyFilter
      • FamilyFilter.apply()
      • FamilyFilter.apply_to_df()
    • PersonFilter
      • PersonFilter.apply()
      • PersonFilter.apply_to_df()
    • PersonFilterRange
      • PersonFilterRange.apply_to_df()
    • PersonFilterSet
      • PersonFilterSet.apply_to_df()
    • PhenoFilter
      • PhenoFilter.apply()
    • PhenoFilterRange
    • PhenoFilterSet
    • make_pedigree_filter()
    • make_pheno_filter()
    • make_pheno_filter_beta()
  • Module contents
    • FamilyFilter
      • FamilyFilter.apply()
      • FamilyFilter.apply_to_df()
    • PersonFilter
      • PersonFilter.apply()
      • PersonFilter.apply_to_df()
    • PersonFilterRange
      • PersonFilterRange.apply_to_df()
    • PersonFilterSet
      • PersonFilterSet.apply_to_df()
    • PhenoFilter
      • PhenoFilter.apply()
    • PhenoFilterRange
    • PhenoFilterSet
    • make_pedigree_filter()
    • make_pheno_filter()
    • make_pheno_filter_beta()
• gpf.person_sets package
  • Submodules
  • gpf.person_sets.person_sets module
    • AttributeQueriesUnsupportedException
    • ChildrenBySex
      • ChildrenBySex.female
      • ChildrenBySex.male
      • ChildrenBySex.unspecified
    • ChildrenStats
      • ChildrenStats.female
      • ChildrenStats.male
      • ChildrenStats.total
      • ChildrenStats.unspecified
    • PSCQuery
      • PSCQuery.psc_id
      • PSCQuery.selected_person_sets
    • PersonSet
      • PersonSet.from_json()
      • PersonSet.get_children()
      • PersonSet.get_children_by_sex()
      • PersonSet.get_children_count()
      • PersonSet.get_children_stats()
      • PersonSet.to_json()
    • PersonSetCollection
      • PersonSetCollection.collect_person_collection_attributes()
      • PersonSetCollection.combine()
      • PersonSetCollection.config_json()
      • PersonSetCollection.domain_json()
      • PersonSetCollection.from_families()
      • PersonSetCollection.get_person_color()
      • PersonSetCollection.get_person_set()
      • PersonSetCollection.get_person_set_of_person()
      • PersonSetCollection.get_query_person_set_ids()
      • PersonSetCollection.get_stats()
      • PersonSetCollection.is_pedigree_only()
      • PersonSetCollection.legend_json()
      • PersonSetCollection.merge_configs()
      • PersonSetCollection.query_fpids()
      • PersonSetCollection.query_person_ids()
      • PersonSetCollection.remove_empty_person_sets()
      • PersonSetCollection.transform_ps_query_to_attribute_queries()
    • PersonSetCollectionConfig
      • PersonSetCollectionConfig.default
      • PersonSetCollectionConfig.domain
      • PersonSetCollectionConfig.id
      • PersonSetCollectionConfig.model_computed_fields
      • PersonSetCollectionConfig.model_config
      • PersonSetCollectionConfig.model_fields
      • PersonSetCollectionConfig.name
      • PersonSetCollectionConfig.sources
    • PersonSetConfig
      • PersonSetConfig.color
      • PersonSetConfig.id
      • PersonSetConfig.model_computed_fields
      • PersonSetConfig.model_config
      • PersonSetConfig.model_fields
      • PersonSetConfig.name
      • PersonSetConfig.values
    • SourceConfig
      • SourceConfig.from_
      • SourceConfig.model_computed_fields
      • SourceConfig.model_config
      • SourceConfig.model_fields
      • SourceConfig.source
    • parse_person_set_collection_config()
    • parse_person_set_collections_study_config()
    • parse_person_set_config()
  • Module contents
    • ChildrenBySex
      • ChildrenBySex.female
      • ChildrenBySex.male
      • ChildrenBySex.unspecified
    • ChildrenStats
      • ChildrenStats.female
      • ChildrenStats.male
      • ChildrenStats.total
      • ChildrenStats.unspecified
    • PSCQuery
      • PSCQuery.psc_id
      • PSCQuery.selected_person_sets
    • PersonSet
      • PersonSet.from_json()
      • PersonSet.get_children()
      • PersonSet.get_children_by_sex()
      • PersonSet.get_children_count()
      • PersonSet.get_children_stats()
      • PersonSet.to_json()
    • PersonSetCollection
      • PersonSetCollection.collect_person_collection_attributes()
      • PersonSetCollection.combine()
      • PersonSetCollection.config_json()
      • PersonSetCollection.domain_json()
      • PersonSetCollection.from_families()
      • PersonSetCollection.get_person_color()
      • PersonSetCollection.get_person_set()
      • PersonSetCollection.get_person_set_of_person()
      • PersonSetCollection.get_query_person_set_ids()
      • PersonSetCollection.get_stats()
      • PersonSetCollection.is_pedigree_only()
      • PersonSetCollection.legend_json()
      • PersonSetCollection.merge_configs()
      • PersonSetCollection.query_fpids()
      • PersonSetCollection.query_person_ids()
      • PersonSetCollection.remove_empty_person_sets()
      • PersonSetCollection.transform_ps_query_to_attribute_queries()
    • PersonSetCollectionConfig
      • PersonSetCollectionConfig.default
      • PersonSetCollectionConfig.domain
      • PersonSetCollectionConfig.id
      • PersonSetCollectionConfig.model_computed_fields
      • PersonSetCollectionConfig.model_config
      • PersonSetCollectionConfig.model_fields
      • PersonSetCollectionConfig.name
      • PersonSetCollectionConfig.sources
    • PersonSetConfig
      • PersonSetConfig.color
      • PersonSetConfig.id
      • PersonSetConfig.model_computed_fields
      • PersonSetConfig.model_config
      • PersonSetConfig.model_fields
      • PersonSetConfig.name
      • PersonSetConfig.values
    • SourceConfig
      • SourceConfig.from_
      • SourceConfig.model_computed_fields
      • SourceConfig.model_config
      • SourceConfig.model_fields
      • SourceConfig.source
    • parse_person_set_collection_config()
    • parse_person_set_collections_study_config()
    • parse_person_set_config()
• gpf.pheno package
  • Subpackages
    • gpf.pheno.prepare package
      • Submodules
      • gpf.pheno.prepare.measure_classifier module
      • Module contents
    • gpf.pheno.utils package
      • Submodules
      • gpf.pheno.utils.commons module
      • gpf.pheno.utils.lin_regress module
      • Module contents
  • Submodules
  • gpf.pheno.browser module
    • PhenoBrowser
      • PhenoBrowser.PAGE_SIZE
      • PhenoBrowser.close()
      • PhenoBrowser.count_measures()
      • PhenoBrowser.create_browser_tables()
      • PhenoBrowser.has_instrument_descriptions
      • PhenoBrowser.has_measure_descriptions
      • PhenoBrowser.regression_display_names
      • PhenoBrowser.regression_display_names_with_ids
      • PhenoBrowser.regression_ids
      • PhenoBrowser.save()
      • PhenoBrowser.save_descriptions()
      • PhenoBrowser.save_regression()
      • PhenoBrowser.save_regression_values()
      • PhenoBrowser.search_measures()
  • gpf.pheno.build_pheno_browser module
    • build_pheno_browser()
    • main()
    • pheno_cli_parser()
  • gpf.pheno.common module
    • DataDictionaryConfig
      • DataDictionaryConfig.delimiter
      • DataDictionaryConfig.description_column
      • DataDictionaryConfig.instrument
      • DataDictionaryConfig.instrument_column
      • DataDictionaryConfig.measure_column
      • DataDictionaryConfig.model_computed_fields
      • DataDictionaryConfig.model_config
      • DataDictionaryConfig.model_fields
      • DataDictionaryConfig.path
    • DestinationConfig
      • DestinationConfig.model_computed_fields
      • DestinationConfig.model_config
      • DestinationConfig.model_fields
      • DestinationConfig.storage_dir
      • DestinationConfig.storage_id
    • GPFInstanceConfig
      • GPFInstanceConfig.model_computed_fields
      • GPFInstanceConfig.model_config
      • GPFInstanceConfig.model_fields
      • GPFInstanceConfig.path
    • ImportManifest
      • ImportManifest.create_table()
      • ImportManifest.from_row()
      • ImportManifest.from_table()
      • ImportManifest.import_config
      • ImportManifest.is_older_than()
      • ImportManifest.model_computed_fields
      • ImportManifest.model_config
      • ImportManifest.model_fields
      • ImportManifest.unix_timestamp
      • ImportManifest.write_to_db()
    • InferenceConfig
      • InferenceConfig.categorical
      • InferenceConfig.continuous
      • InferenceConfig.histogram_type
      • InferenceConfig.min_individuals
      • InferenceConfig.model_computed_fields
      • InferenceConfig.model_config
      • InferenceConfig.model_fields
      • InferenceConfig.non_numeric_cutoff
      • InferenceConfig.ordinal
      • InferenceConfig.skip
      • InferenceConfig.value_max_len
      • InferenceConfig.value_type
    • InstrumentConfig
      • InstrumentConfig.delimiter
      • InstrumentConfig.instrument
      • InstrumentConfig.model_computed_fields
      • InstrumentConfig.model_config
      • InstrumentConfig.model_fields
      • InstrumentConfig.path
      • InstrumentConfig.person_column
    • InstrumentDescriptionsConfig
      • InstrumentDescriptionsConfig.dictionary
      • InstrumentDescriptionsConfig.files
      • InstrumentDescriptionsConfig.model_computed_fields
      • InstrumentDescriptionsConfig.model_config
      • InstrumentDescriptionsConfig.model_fields
    • InstrumentDictionaryConfig
      • InstrumentDictionaryConfig.delimiter
      • InstrumentDictionaryConfig.description_column
      • InstrumentDictionaryConfig.instrument
      • InstrumentDictionaryConfig.instrument_column
      • InstrumentDictionaryConfig.model_computed_fields
      • InstrumentDictionaryConfig.model_config
      • InstrumentDictionaryConfig.model_fields
      • InstrumentDictionaryConfig.path
    • MeasureDescriptionsConfig
      • MeasureDescriptionsConfig.dictionary
      • MeasureDescriptionsConfig.files
      • MeasureDescriptionsConfig.model_computed_fields
      • MeasureDescriptionsConfig.model_config
      • MeasureDescriptionsConfig.model_fields
    • MeasureHistogramConfigs
      • MeasureHistogramConfigs.categorical_config
      • MeasureHistogramConfigs.model_computed_fields
      • MeasureHistogramConfigs.model_config
      • MeasureHistogramConfigs.model_fields
      • MeasureHistogramConfigs.number_config
    • MeasureType
      • MeasureType.categorical
      • MeasureType.continuous
      • MeasureType.from_str()
      • MeasureType.is_numeric()
      • MeasureType.is_text()
      • MeasureType.ordinal
      • MeasureType.other
      • MeasureType.raw
      • MeasureType.skipped
      • MeasureType.text
    • PhenoImportConfig
      • PhenoImportConfig.data_dictionary
      • PhenoImportConfig.delimiter
      • PhenoImportConfig.destination
      • PhenoImportConfig.gpf_instance
      • PhenoImportConfig.histogram_configs
      • PhenoImportConfig.id
      • PhenoImportConfig.inference_config
      • PhenoImportConfig.input_dir
      • PhenoImportConfig.instrument_dictionary
      • PhenoImportConfig.instrument_files
      • PhenoImportConfig.model_computed_fields
      • PhenoImportConfig.model_config
      • PhenoImportConfig.model_fields
      • PhenoImportConfig.pedigree
      • PhenoImportConfig.person_column
      • PhenoImportConfig.skip_pedigree_measures
      • PhenoImportConfig.study_config
      • PhenoImportConfig.work_dir
    • RankRange
      • RankRange.max_rank
      • RankRange.min_rank
      • RankRange.model_computed_fields
      • RankRange.model_config
      • RankRange.model_fields
    • RegressionMeasure
      • RegressionMeasure.display_name
      • RegressionMeasure.instrument_name
      • RegressionMeasure.jitter
      • RegressionMeasure.measure_names
      • RegressionMeasure.model_computed_fields
      • RegressionMeasure.model_config
      • RegressionMeasure.model_fields
    • StudyConfig
      • StudyConfig.common_report
      • StudyConfig.model_computed_fields
      • StudyConfig.model_config
      • StudyConfig.model_fields
      • StudyConfig.person_set_collections
      • StudyConfig.regressions
  • gpf.pheno.db module
    • PhenoDb
      • PhenoDb.find_instrument_values_tables()
      • PhenoDb.get_measures_df()
      • PhenoDb.get_pedigree_df()
      • PhenoDb.get_people_measure_values()
      • PhenoDb.get_people_measure_values_df()
      • PhenoDb.get_persons_df()
      • PhenoDb.save_descriptions()
    • generate_instrument_table_name()
    • safe_db_name()
  • gpf.pheno.graphs module
    • GraphColumn
      • GraphColumn.all_count()
      • GraphColumn.build()
      • GraphColumn.females_count()
      • GraphColumn.label
      • GraphColumn.males_count()
    • column_counts()
    • draw_categorical_violin_distribution()
    • draw_linregres()
    • draw_measure_violinplot()
    • draw_ordinal_violin_distribution()
    • gender_palette()
    • gender_palette_light()
    • get_columns_to_draw()
    • male_female_legend()
    • role_labels()
    • set_figure_size()
  • gpf.pheno.import_tools module
    • main()
    • pheno_cli_parser()
  • gpf.pheno.pheno_data module
    • Instrument
    • Measure
      • Measure.domain
      • Measure.from_json()
      • Measure.from_record()
      • Measure.to_json()
    • PhenotypeData
      • PhenotypeData.browser
      • PhenotypeData.build_and_save()
      • PhenotypeData.build_report()
      • PhenotypeData.close()
      • PhenotypeData.count_measures()
      • PhenotypeData.create_browser()
      • PhenotypeData.families
      • PhenotypeData.generate_import_manifests()
      • PhenotypeData.get_children_ids()
      • PhenotypeData.get_common_report()
      • PhenotypeData.get_image()
      • PhenotypeData.get_instrument_measures()
      • PhenotypeData.get_instruments()
      • PhenotypeData.get_measure()
      • PhenotypeData.get_measure_description()
      • PhenotypeData.get_measures()
      • PhenotypeData.get_measures_info()
      • PhenotypeData.get_pedigree_df()
      • PhenotypeData.get_people_measure_values()
      • PhenotypeData.get_people_measure_values_df()
      • PhenotypeData.get_person_roles()
      • PhenotypeData.get_person_set_collection()
      • PhenotypeData.get_persons()
      • PhenotypeData.get_persons_df()
      • PhenotypeData.get_regressions()
      • PhenotypeData.has_measure()
      • PhenotypeData.instruments
      • PhenotypeData.is_browser_outdated()
      • PhenotypeData.is_group
      • PhenotypeData.measures
      • PhenotypeData.person_set_collections
      • PhenotypeData.pheno_id
      • PhenotypeData.search_measures()
    • PhenotypeGroup
      • PhenotypeGroup.count_measures()
      • PhenotypeGroup.families
      • PhenotypeGroup.generate_import_manifests()
      • PhenotypeGroup.get_children_ids()
      • PhenotypeGroup.get_leaves()
      • PhenotypeGroup.get_measures_info()
      • PhenotypeGroup.get_pedigree_df()
      • PhenotypeGroup.get_people_measure_values()
      • PhenotypeGroup.get_people_measure_values_df()
      • PhenotypeGroup.get_person_roles()
      • PhenotypeGroup.get_persons_df()
      • PhenotypeGroup.get_regressions()
      • PhenotypeGroup.is_group
      • PhenotypeGroup.person_set_collections
    • PhenotypeStudy
      • PhenotypeStudy.count_measures()
      • PhenotypeStudy.families
      • PhenotypeStudy.generate_import_manifests()
      • PhenotypeStudy.get_children_ids()
      • PhenotypeStudy.get_measures_info()
      • PhenotypeStudy.get_pedigree_df()
      • PhenotypeStudy.get_people_measure_values()
      • PhenotypeStudy.get_people_measure_values_df()
      • PhenotypeStudy.get_persons_df()
      • PhenotypeStudy.get_regressions()
      • PhenotypeStudy.person_set_collections
    • get_pheno_browser_images_dir()
    • get_pheno_db_dir()
  • gpf.pheno.pheno_import module
    • ImportInstrument
      • ImportInstrument.delimiter
      • ImportInstrument.files
      • ImportInstrument.name
      • ImportInstrument.person_column
    • MeasureReport
      • MeasureReport.db_name
      • MeasureReport.inference_report
      • MeasureReport.instrument_name
      • MeasureReport.measure_name
      • MeasureReport.measure_type
      • MeasureReport.model_computed_fields
      • MeasureReport.model_config
      • MeasureReport.model_fields
    • add_pheno_common_inference()
    • collect_instruments()
    • create_import_tasks()
    • create_tables()
    • determine_destination()
    • generate_phenotype_data_config()
    • get_gpf_instance()
    • get_output_parquet_files_dir()
    • handle_measure_inference_tasks()
    • import_pheno_data()
    • infer_measures()
    • load_histogram_configs()
    • load_inference_configs()
    • load_instrument_description_file()
    • load_instrument_descriptions()
    • load_measure_description_file()
    • load_measure_descriptions()
    • main()
    • merge_histogram_configs()
    • merge_inference_configs()
    • open_file()
    • pheno_cli_parser()
    • read_and_classify_measure()
    • read_instrument_measure_names()
    • read_pedigree()
    • transform_cli_args()
    • write_descriptions()
    • write_reports_to_parquet()
    • write_results()
    • write_to_parquet()
  • gpf.pheno.prepare_data module
    • PreparePhenoBrowserBase
      • PreparePhenoBrowserBase.LARGE_DPI
      • PreparePhenoBrowserBase.SMALL_DPI
      • PreparePhenoBrowserBase.add_measure_task()
      • PreparePhenoBrowserBase.browsable_figure_path()
      • PreparePhenoBrowserBase.build_regression()
      • PreparePhenoBrowserBase.build_values_categorical_distribution()
      • PreparePhenoBrowserBase.build_values_ordinal_distribution()
      • PreparePhenoBrowserBase.build_values_violinplot()
      • PreparePhenoBrowserBase.close()
      • PreparePhenoBrowserBase.collect_child_configs()
      • PreparePhenoBrowserBase.do_measure_build()
      • PreparePhenoBrowserBase.figure_filepath()
      • PreparePhenoBrowserBase.get_regression_measures()
      • PreparePhenoBrowserBase.run()
      • PreparePhenoBrowserBase.save_fig()
  • gpf.pheno.registry module
    • PhenoRegistry
      • PhenoRegistry.CACHE_LOCK
      • PhenoRegistry.get_all_phenotype_data()
      • PhenoRegistry.get_phenotype_data()
      • PhenoRegistry.get_phenotype_data_config()
      • PhenoRegistry.get_phenotype_data_ids()
      • PhenoRegistry.has_phenotype_data()
      • PhenoRegistry.register_phenotype_data()
      • PhenoRegistry.shutdown()
  • gpf.pheno.storage module
    • PhenotypeStorage
      • PhenotypeStorage.build_phenotype_study()
      • PhenotypeStorage.from_config()
      • PhenotypeStorage.shutdown()
    • PhenotypeStorageRegistry
      • PhenotypeStorageRegistry.get_all_phenotype_storage_ids()
      • PhenotypeStorageRegistry.get_all_phenotype_storages()
      • PhenotypeStorageRegistry.get_default_phenotype_storage()
      • PhenotypeStorageRegistry.get_phenotype_storage()
      • PhenotypeStorageRegistry.register_default_storage()
      • PhenotypeStorageRegistry.register_phenotype_storage()
      • PhenotypeStorageRegistry.register_storage_config()
      • PhenotypeStorageRegistry.register_storages_configs()
      • PhenotypeStorageRegistry.shutdown()
  • gpf.pheno.update_pheno_descriptions module
    • main()
    • pheno_cli_parser()
    • save_descriptions()
  • Module contents
• gpf.pheno_tool package
  • Submodules
  • gpf.pheno_tool.pheno_tool_adapter module
    • PhenoToolAdapter
      • PhenoToolAdapter.align_na_results()
      • PhenoToolAdapter.build_report_description()
      • PhenoToolAdapter.calc_by_effect()
      • PhenoToolAdapter.calc_variants()
      • PhenoToolAdapter.get_result_by_sex()
    • PhenoToolAdapterBase
      • PhenoToolAdapterBase.calc_by_effect()
      • PhenoToolAdapterBase.calc_variants()
  • gpf.pheno_tool.tool module
    • PhenoResult
      • PhenoResult.set_negative_stats()
      • PhenoResult.set_positive_stats()
    • PhenoTool
      • PhenoTool.calc()
      • PhenoTool.create_df()
      • PhenoTool.get_normalize_measure_id()
      • PhenoTool.init_normalize_measures()
      • PhenoTool.join_pheno_df_with_variants()
    • PhenoToolHelper
      • PhenoToolHelper.genotype_data_persons()
      • PhenoToolHelper.genotype_data_variants()
  • Module contents
• gpf.query_variants package
  • Subpackages
    • gpf.query_variants.sql package
      • Subpackages
      • Module contents
  • Submodules
  • gpf.query_variants.attribute_queries module
    • AttributeQueryNotSupported
    • AttributeQueryTransformer
    • AttributeQueryTransformerFunction
      • AttributeQueryTransformerFunction.and_()
      • AttributeQueryTransformerFunction.compound()
      • AttributeQueryTransformerFunction.grouping()
      • AttributeQueryTransformerFunction.literal()
      • AttributeQueryTransformerFunction.neg()
      • AttributeQueryTransformerFunction.or_()
    • AttributeQueryTransformerSQL
      • AttributeQueryTransformerSQL.and_()
      • AttributeQueryTransformerSQL.compound()
      • AttributeQueryTransformerSQL.grouping()
      • AttributeQueryTransformerSQL.literal()
      • AttributeQueryTransformerSQL.neg()
      • AttributeQueryTransformerSQL.or_()
    • AttributeQueryTransformerSQLLegacy
      • AttributeQueryTransformerSQLLegacy.compound()
      • AttributeQueryTransformerSQLLegacy.literal()
    • CompoundStripTransformer
      • CompoundStripTransformer.compound()
    • Matcher
    • QueryCompoundAdditionTransformer
      • QueryCompoundAdditionTransformer.all()
      • QueryCompoundAdditionTransformer.and_()
      • QueryCompoundAdditionTransformer.any()
      • QueryCompoundAdditionTransformer.compound()
      • QueryCompoundAdditionTransformer.grouping()
      • QueryCompoundAdditionTransformer.literal()
      • QueryCompoundAdditionTransformer.neg()
      • QueryCompoundAdditionTransformer.or_()
    • SyntaxSugarTransformer
      • SyntaxSugarTransformer.all()
      • SyntaxSugarTransformer.any()
    • create_and_node()
    • create_or_node()
    • transform_attribute_query_to_function()
    • transform_attribute_query_to_sql_expression()
    • transform_attribute_query_to_sql_expression_schema1()
    • update_attribute_query_with_compounds()
  • gpf.query_variants.base_query_variants module
    • QueryVariants
      • QueryVariants.build_family_variants_query_runner()
      • QueryVariants.build_summary_variants_query_runner()
      • QueryVariants.families
      • QueryVariants.has_affected_status_queries()
      • QueryVariants.tags_to_family_ids()
      • QueryVariants.transform_roles_to_single_role_string()
    • QueryVariantsBase
      • QueryVariantsBase.RUNNER_CLASS
      • QueryVariantsBase.deserialize_family_variant()
      • QueryVariantsBase.deserialize_summary_variant()
      • QueryVariantsBase.has_affected_status_queries()
  • gpf.query_variants.query_runners module
    • QueryResult
      • QueryResult.CHECK_DONE_VERBOSITY
      • QueryResult.close()
      • QueryResult.is_done()
      • QueryResult.start()
    • QueryRunner
      • QueryRunner.NOBODY_INTEREST_LOG_INTERVAL
      • QueryRunner.NOBODY_INTEREST_THRESHOLD
      • QueryRunner.adapt()
      • QueryRunner.close()
      • QueryRunner.is_closed()
      • QueryRunner.is_done()
      • QueryRunner.is_started()
      • QueryRunner.put_value_in_result_queue()
      • QueryRunner.result_queue
      • QueryRunner.run()
      • QueryRunner.set_result_queue()
      • QueryRunner.set_study_id()
      • QueryRunner.start()
  • Module contents
• gpf.schema2_storage package
  • Submodules
  • gpf.schema2_storage.schema2_import_storage module
    • Schema2ImportStorage
      • Schema2ImportStorage.BATCH_SIZE
      • Schema2ImportStorage.generate_import_task_graph()
      • Schema2ImportStorage.generate_reannotate_task_graph()
      • Schema2ImportStorage.load_meta()
    • schema2_project_dataset_layout()
  • gpf.schema2_storage.schema2_layout module
    • Schema2DatasetLayout
      • Schema2DatasetLayout.base_dir
      • Schema2DatasetLayout.family
      • Schema2DatasetLayout.has_variants()
      • Schema2DatasetLayout.meta
      • Schema2DatasetLayout.pedigree
      • Schema2DatasetLayout.study
      • Schema2DatasetLayout.summary
    • create_schema2_dataset_layout()
    • load_schema2_dataset_layout()
  • Module contents
• gpf.studies package
  • Submodules
  • gpf.studies.study module
    • CommonStudyMixin
      • CommonStudyMixin.description
    • GenotypeData
      • GenotypeData.add_parent()
      • GenotypeData.build_and_save()
      • GenotypeData.build_report()
      • GenotypeData.close()
      • GenotypeData.families
      • GenotypeData.get_children_ids()
      • GenotypeData.get_common_report()
      • GenotypeData.get_leaf_children()
      • GenotypeData.get_person_set_collection()
      • GenotypeData.get_query_leaf_studies()
      • GenotypeData.get_studies_ids()
      • GenotypeData.has_cnv
      • GenotypeData.has_complex
      • GenotypeData.has_denovo
      • GenotypeData.has_transmitted
      • GenotypeData.has_zygosity
      • GenotypeData.is_group
      • GenotypeData.name
      • GenotypeData.parents
      • GenotypeData.person_set_collections
      • GenotypeData.phenotype
      • GenotypeData.pub_med
      • GenotypeData.query_summary_variants()
      • GenotypeData.query_variants()
      • GenotypeData.study_id
      • GenotypeData.study_type
      • GenotypeData.year
    • GenotypeDataGroup
      • GenotypeDataGroup.families
      • GenotypeDataGroup.get_children_ids()
      • GenotypeDataGroup.get_studies_ids()
      • GenotypeDataGroup.has_denovo
      • GenotypeDataGroup.has_transmitted
      • GenotypeDataGroup.is_group
      • GenotypeDataGroup.rebuild_families()
    • GenotypeDataStudy
      • GenotypeDataStudy.backend
      • GenotypeDataStudy.families
      • GenotypeDataStudy.get_children_ids()
      • GenotypeDataStudy.get_studies_ids()
      • GenotypeDataStudy.is_group
      • GenotypeDataStudy.study_phenotype
    • PSCQueryAdjustments
      • PSCQueryAdjustments.affected_statues
      • PSCQueryAdjustments.person_ids
      • PSCQueryAdjustments.roles
      • PSCQueryAdjustments.sexes
  • gpf.studies.variants_db module
    • VariantsDb
      • VariantsDb.get()
      • VariantsDb.get_all_genotype_data()
      • VariantsDb.get_all_genotype_group_ids()
      • VariantsDb.get_all_genotype_groups()
      • VariantsDb.get_all_genotype_studies()
      • VariantsDb.get_all_genotype_study_ids()
      • VariantsDb.get_genotype_group()
      • VariantsDb.get_genotype_group_config()
      • VariantsDb.get_genotype_study()
      • VariantsDb.get_genotype_study_config()
      • VariantsDb.register_genotype_data()
      • VariantsDb.reload()
      • VariantsDb.unregister_genotype_data()
  • Module contents
• gpf.testing package
  • Submodules
  • gpf.testing.acgt_import module
    • acgt_gpf()
  • gpf.testing.alla_import module
    • alla_gpf()
  • gpf.testing.foobar_import module
    • foobar_gpf()
  • gpf.testing.import_helpers module
    • StudyInputLayout
      • StudyInputLayout.cnv
      • StudyInputLayout.dae
      • StudyInputLayout.denovo
      • StudyInputLayout.pedigree
      • StudyInputLayout.study_id
      • StudyInputLayout.vcf
    • cnv_import()
    • cnv_study()
    • dae_import()
    • dae_study()
    • denovo_import()
    • denovo_study()
    • pedigree_import()
    • setup_dataset()
    • setup_dataset_config()
    • setup_import_project()
    • setup_import_project_config()
    • study_update()
    • update_study_config()
    • vcf_import()
    • vcf_study()
  • gpf.testing.setup_helpers module
    • setup_gpf_instance()
  • gpf.testing.t4c8_import module
    • t4c8_gpf()
  • Module contents
• gpf.tools package
  • Submodules
  • gpf.tools.dae2vcf module
    • main()
    • parse_cli_arguments()
  • gpf.tools.dataset_helpers module
    • DatasetHelpers
      • DatasetHelpers.disable_study_config()
      • DatasetHelpers.find_genotype_data_config()
      • DatasetHelpers.find_genotype_data_config_file()
      • DatasetHelpers.get_genotype_storage()
      • DatasetHelpers.remove_study_config()
      • DatasetHelpers.rename_study_config()
  • gpf.tools.denovo2vcf module
    • main()
    • parse_cli_arguments()
  • gpf.tools.draw_pedigree module
    • build_families_report()
    • build_family_layout()
    • draw_families()
    • draw_families_report()
    • draw_pedigree()
    • main()
  • gpf.tools.generate_common_report module
    • main()
  • gpf.tools.generate_denovo_gene_sets module
    • main()
  • gpf.tools.gpf_convert_study_config module
    • load_study_config()
    • main()
  • gpf.tools.gpf_validation_runner module
    • AbstractRunner
      • AbstractRunner.counter()
      • AbstractRunner.error_case_count
      • AbstractRunner.failed_case_count
      • AbstractRunner.passed_case_count
    • BaseGenotypeBrowserRunner
    • GenotypeBrowserRunner
      • GenotypeBrowserRunner.run()
      • GenotypeBrowserRunner.store_results()
    • MainRunner
      • MainRunner.collect_expectations()
      • MainRunner.counter()
      • MainRunner.errors_case_count
      • MainRunner.failed_case_count
      • MainRunner.main()
      • MainRunner.make_validation_runner()
      • MainRunner.passed_case_count
      • MainRunner.store_junit_results()
      • MainRunner.store_results()
      • MainRunner.summary()
    • TestResult
      • TestResult.to_xml_element()
    • TestStatus
      • TestStatus.ERROR
      • TestStatus.FAIL
      • TestStatus.NOTSET
      • TestStatus.PASSED
    • TestSuite
      • TestSuite.append()
      • TestSuite.to_xml_element()
    • main()
  • gpf.tools.grr_cache_repo module
    • cli_cache_repo()
  • gpf.tools.liftover_tools module
    • CNVLiftoverTool
      • CNVLiftoverTool.build_cli_arguments_parser()
      • CNVLiftoverTool.liftover_variants()
    • DaeLiftoverTool
      • DaeLiftoverTool.build_cli_arguments_parser()
      • DaeLiftoverTool.liftover_variants()
    • DenovoLiftoverTool
      • DenovoLiftoverTool.build_cli_arguments_parser()
      • DenovoLiftoverTool.liftover_variants()
    • LiftoverTool
      • LiftoverTool.build_cli_arguments_parser()
      • LiftoverTool.build_liftover_pipeline()
      • LiftoverTool.liftover_variants()
      • LiftoverTool.run()
    • VCFLiftoverTool
      • VCFLiftoverTool.build_cli_arguments_parser()
      • VCFLiftoverTool.liftover_variants()
      • VCFLiftoverTool.report_variant()
      • VCFLiftoverTool.report_vcf_variant()
    • cnv_liftover_main()
    • dae_liftover_main()
    • denovo_liftover_main()
    • vcf_liftover_main()
  • gpf.tools.ped2ped module
    • main()
  • gpf.tools.reannotate_instance module
    • ReannotateInstanceTool
      • ReannotateInstanceTool.get_argument_parser()
      • ReannotateInstanceTool.run()
    • cli()
  • gpf.tools.simple_study_import module
    • build_import_project()
    • cli_arguments()
    • main()
  • gpf.tools.to_gpf_gene_models_format module
    • main()
  • gpf.tools.vcf2tsv module
    • main()
    • parse_cli_arguments()
  • Module contents
• gpf.utils package
  • Submodules
  • gpf.utils.testing module
    • setup_t4c8_instance()
  • gpf.utils.variant_utils module
    • BitmaskEnumTranslator
      • BitmaskEnumTranslator.apply_mask()
    • best2gt()
    • fgt2str()
    • get_interval_locus_ploidy()
    • get_locus_ploidy()
    • gt2str()
    • is_all_reference_genotype()
    • is_all_unknown_genotype()
    • is_reference_genotype()
    • is_unknown_genotype()
    • mat2str()
    • reference_genotype()
    • str2fgt()
    • str2gt()
    • str2lists()
    • str2mat()
    • str2mat_adjust_colsep()
  • Module contents
• gpf.variants package
  • Submodules
  • gpf.variants.attributes module
    • GeneticModel
      • GeneticModel.X
      • GeneticModel.X_broken
      • GeneticModel.autosomal
      • GeneticModel.autosomal_broken
      • GeneticModel.pseudo_autosomal
    • Inheritance
      • Inheritance.denovo
      • Inheritance.from_name()
      • Inheritance.from_value()
      • Inheritance.mendelian
      • Inheritance.missing
      • Inheritance.omission
      • Inheritance.other
      • Inheritance.possible_denovo
      • Inheritance.possible_omission
      • Inheritance.reference
      • Inheritance.unknown
    • Role
      • Role.child
      • Role.dad
      • Role.display_name
      • Role.from_name()
      • Role.from_value()
      • Role.half_sibling
      • Role.maternal_aunt
      • Role.maternal_cousin
      • Role.maternal_grandfather
      • Role.maternal_grandmother
      • Role.maternal_half_sibling
      • Role.maternal_uncle
      • Role.mom
      • Role.not_role()
      • Role.parent
      • Role.paternal_aunt
      • Role.paternal_cousin
      • Role.paternal_grandfather
      • Role.paternal_grandmother
      • Role.paternal_half_sibling
      • Role.paternal_uncle
      • Role.prb
      • Role.sib
      • Role.spouse
      • Role.step_dad
      • Role.step_mom
      • Role.to_name()
      • Role.to_value()
      • Role.unknown
    • Sex
      • Sex.F
      • Sex.M
      • Sex.U
      • Sex.aliases()
      • Sex.female
      • Sex.from_name()
      • Sex.from_value()
      • Sex.male
      • Sex.short()
      • Sex.to_name()
      • Sex.to_value()
      • Sex.unspecified
    • Status
      • Status.affected
      • Status.from_name()
      • Status.from_value()
      • Status.short()
      • Status.to_name()
      • Status.to_value()
      • Status.unaffected
      • Status.unspecified
    • TransmissionType
      • TransmissionType.denovo
      • TransmissionType.transmitted
      • TransmissionType.unknown
    • Zygosity
      • Zygosity.from_name()
      • Zygosity.from_value()
      • Zygosity.heterozygous
      • Zygosity.homozygous
      • Zygosity.undefined
    • bitmask2inheritance()
  • gpf.variants.core module
    • Allele
      • Allele.DISPLAY_NAME_TYPE
      • Allele.TYPE_DISPLAY_NAME
      • Allele.Type
      • Allele.allele_type
      • Allele.alternative
      • Allele.build_cnv_allele()
      • Allele.build_position_allele()
      • Allele.build_vcf_allele()
      • Allele.chrom
      • Allele.chromosome
      • Allele.end_position
      • Allele.get_annotatable()
      • Allele.position
      • Allele.reference
  • gpf.variants.family_variant module
    • FamilyAllele
      • FamilyAllele.allele_in_members
      • FamilyAllele.allele_in_roles
      • FamilyAllele.allele_in_sexes
      • FamilyAllele.allele_in_statuses
      • FamilyAllele.allele_index
      • FamilyAllele.allele_type
      • FamilyAllele.alternative
      • FamilyAllele.attributes
      • FamilyAllele.best_st
      • FamilyAllele.best_state
      • FamilyAllele.calc_inheritance_trio()
      • FamilyAllele.check_denovo_trio()
      • FamilyAllele.check_mendelian_trio()
      • FamilyAllele.check_omission_trio()
      • FamilyAllele.chrom
      • FamilyAllele.chromosome
      • FamilyAllele.details
      • FamilyAllele.effects
      • FamilyAllele.end_position
      • FamilyAllele.family_attributes
      • FamilyAllele.family_id
      • FamilyAllele.family_index
      • FamilyAllele.genetic_model
      • FamilyAllele.genotype
      • FamilyAllele.get_attribute()
      • FamilyAllele.gt_flatten()
      • FamilyAllele.has_attribute()
      • FamilyAllele.inheritance_in_members
      • FamilyAllele.member_fpids
      • FamilyAllele.member_ids
      • FamilyAllele.position
      • FamilyAllele.reference
      • FamilyAllele.summary_allele
      • FamilyAllele.summary_attributes
      • FamilyAllele.summary_index
      • FamilyAllele.transmission_type
      • FamilyAllele.update_attributes()
      • FamilyAllele.variant_in_member_fpids
      • FamilyAllele.variant_in_members
      • FamilyAllele.variant_in_roles
      • FamilyAllele.variant_in_sexes
      • FamilyAllele.variant_in_statuses
      • FamilyAllele.zygosity_in_roles
      • FamilyAllele.zygosity_in_sexes
      • FamilyAllele.zygosity_in_status
    • FamilyVariant
      • FamilyVariant.allele_count
      • FamilyVariant.allele_indexes
      • FamilyVariant.alleles
      • FamilyVariant.best_st
      • FamilyVariant.best_state
      • FamilyVariant.calc_alleles()
      • FamilyVariant.calc_alt_alleles()
      • FamilyVariant.chrom
      • FamilyVariant.chromosome
      • FamilyVariant.end_position
      • FamilyVariant.family_allele_indexes
      • FamilyVariant.family_alleles
      • FamilyVariant.family_alt_alleles
      • FamilyVariant.family_best_state
      • FamilyVariant.family_genotype
      • FamilyVariant.family_id
      • FamilyVariant.family_index
      • FamilyVariant.fvuid
      • FamilyVariant.genetic_model
      • FamilyVariant.genotype
      • FamilyVariant.gt_flatten()
      • FamilyVariant.is_reference()
      • FamilyVariant.is_unknown()
      • FamilyVariant.member_fpids
      • FamilyVariant.member_ids
      • FamilyVariant.position
      • FamilyVariant.reference
      • FamilyVariant.summary_index
      • FamilyVariant.to_record()
      • FamilyVariant.variant_in_members
      • FamilyVariant.zygosity_in_roles
      • FamilyVariant.zygosity_in_sexes
      • FamilyVariant.zygosity_in_status
    • calculate_simple_best_state()
  • gpf.variants.variant module
    • SummaryAllele
      • SummaryAllele.allele_index
      • SummaryAllele.attributes
      • SummaryAllele.create_reference_allele()
      • SummaryAllele.cshl_location
      • SummaryAllele.cshl_position
      • SummaryAllele.cshl_variant
      • SummaryAllele.cshl_variant_full
      • SummaryAllele.details
      • SummaryAllele.effect_gene_symbols
      • SummaryAllele.effect_genes
      • SummaryAllele.effect_types
      • SummaryAllele.effects
      • SummaryAllele.frequency
      • SummaryAllele.get_attribute()
      • SummaryAllele.has_attribute()
      • SummaryAllele.is_reference_allele
      • SummaryAllele.summary_index
      • SummaryAllele.to_record()
      • SummaryAllele.transmission_type
      • SummaryAllele.update_attributes()
      • SummaryAllele.variant_type
      • SummaryAllele.worst_effect
    • SummaryVariant
      • SummaryVariant.allele_count
      • SummaryVariant.alleles
      • SummaryVariant.alt_alleles
      • SummaryVariant.alternative
      • SummaryVariant.attributes
      • SummaryVariant.chrom
      • SummaryVariant.chromosome
      • SummaryVariant.cshl_location
      • SummaryVariant.cshl_variant
      • SummaryVariant.cshl_variant_full
      • SummaryVariant.details
      • SummaryVariant.effect_gene_symbols
      • SummaryVariant.effect_types
      • SummaryVariant.effects
      • SummaryVariant.end_position
      • SummaryVariant.frequencies
      • SummaryVariant.get_attribute()
      • SummaryVariant.has_attribute()
      • SummaryVariant.location
      • SummaryVariant.matched_alleles
      • SummaryVariant.matched_alleles_indexes
      • SummaryVariant.matched_gene_effects
      • SummaryVariant.position
      • SummaryVariant.ref_allele
      • SummaryVariant.reference
      • SummaryVariant.set_matched_alleles()
      • SummaryVariant.summary_index
      • SummaryVariant.svuid
      • SummaryVariant.to_record()
      • SummaryVariant.transmission_type
      • SummaryVariant.update_attributes()
      • SummaryVariant.variant_types
    • SummaryVariantFactory
      • SummaryVariantFactory.summary_allele_from_record()
      • SummaryVariantFactory.summary_variant_from_records()
      • SummaryVariantFactory.summary_variant_from_vcf()
    • VariantDesc
      • VariantDesc.combine()
      • VariantDesc.to_cshl_full()
      • VariantDesc.to_cshl_short()
    • VariantDetails
      • VariantDetails.from_cnv()
      • VariantDetails.from_vcf()
    • allele_type_from_cshl_variant()
    • allele_type_from_name()
    • cshl_format()
    • tandem_repeat()
    • vcf2cshl()
  • Module contents
• gpf.variants_loaders package
  • Subpackages
    • gpf.variants_loaders.cnv package
      • Submodules
      • gpf.variants_loaders.cnv.flexible_cnv_loader module
      • gpf.variants_loaders.cnv.loader module
      • Module contents
    • gpf.variants_loaders.dae package
      • Submodules
      • gpf.variants_loaders.dae.loader module
      • Module contents
    • gpf.variants_loaders.parquet package
      • Submodules
      • gpf.variants_loaders.parquet.loader module
      • Module contents
    • gpf.variants_loaders.raw package
      • Submodules
      • gpf.variants_loaders.raw.flexible_variant_loader module
      • gpf.variants_loaders.raw.loader module
      • Module contents
    • gpf.variants_loaders.vcf package
      • Submodules
      • gpf.variants_loaders.vcf.loader module
      • gpf.variants_loaders.vcf.serializer module
      • Module contents
  • Module contents

Module contents