Index

A

AboutDescriptionView (class in gpf_instance.views) abspath() (in module dae.utils.fs_utils) abstract (users_api.models.BaseVerificationCode.Meta attribute), [1] AbstractDuckDbImportStorage (class in dae.duckdb_storage.duckdb_import_storage) AbstractDuckDbStorage (class in dae.duckdb_storage.duckdb_genotype_storage) AbstractLiftoverAnnotator (class in dae.annotation.liftover_annotator) AbstractRunner (class in dae.tools.gpf_validation_runner) AbstractTaskGraphExecutor (class in dae.task_graph.executor) acgt_gpf() (in module dae.testing) (in module dae.testing.acgt_import) adapt() (dae.query_variants.query_runners.QueryRunner method) add() (dae.genomic_resources.aggregators.Aggregator method) (dae.genomic_resources.repository.Manifest method) add_annotator() (dae.annotation.annotation_pipeline.AnnotationPipeline method) add_arguments() (dae.task_graph.cli_tools.TaskGraphCli static method) (users_api.management.commands.dataset_groups.Command method) (users_api.management.commands.datasets_export.Command method) (users_api.management.commands.datasets_restore.Command method) (users_api.management.commands.groups_cleanup.Command method) (users_api.management.commands.unlock_user.Command method) (users_api.management.commands.user_create.Command method) (users_api.management.commands.user_set_name.Command method) (users_api.management.commands.user_setpasswd.Command method) (users_api.management.commands.users_add.Command method) (users_api.management.commands.users_export.Command method) (users_api.management.commands.users_group_add.Command method) (users_api.management.commands.users_group_remove.Command method) (users_api.management.commands.users_remove.Command method) (users_api.management.commands.users_restore.Command method) (users_api.management.commands.users_show.Command method) add_context_arguments() (dae.annotation.context.CLIAnnotationContext static method) (dae.genomic_resources.genomic_context.CLIGenomicContext static method) add_gene() (dae.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) add_group_perm_to_dataset() (in module datasets_api.permissions) add_group_perm_to_user() (in module datasets_api.permissions) add_measure_task() (dae.pheno.prepare_data.PreparePhenoBrowserBase method) add_members() (dae.pedigrees.family.Family method) add_missing_members() (dae.pedigrees.pedigrees.FamilyConnections static method) add_missing_parquet_fields() (in module dae.parquet.parquet_writer) add_page() (dae.pedigrees.drawing.PDFLayoutDrawer method) add_parent() (dae.studies.study.GenotypeData method) add_pheno_common_inference() (in module dae.pheno.pheno_import) add_rank() (dae.pedigrees.pedigrees.Individual method) add_ranks() (dae.pedigrees.pedigrees.FamilyConnections method) add_record_to_annotable_arguments() (in module dae.annotation.record_to_annotatable) add_relation() (datasets_api.models.DatasetHierarchy class method) add_score_aggregator_documentation() (dae.annotation.score_annotator.GenomicScoreAnnotatorBase method) add_statistics_build_tasks() (dae.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation method) (dae.gene_scores.implementations.gene_scores_impl.GeneScoreImplementation method) (dae.gene_sets.gene_sets_db.GeneSetCollection method) (dae.genomic_resources.cnv_collection.CnvCollectionImplementation method) (dae.genomic_resources.implementations.annotation_pipeline_impl.AnnotationPipelineImplementation method) (dae.genomic_resources.implementations.gene_models_impl.GeneModelsImpl method) (dae.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation method) (dae.genomic_resources.implementations.liftover_chain_impl.LiftoverChainImplementation method) (dae.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeImplementation method) (dae.genomic_resources.resource_implementation.GenomicResourceImplementation method) add_tagger() (dae.pedigrees.family_tag_builder.FamilyTagsBuilder method) add_to_parser() (dae.variants_loaders.raw.loader.CLIArgument method) add_transcript_model() (dae.genomic_resources.gene_models.gene_models.GeneModels method) (dae.genomic_resources.gene_models.GeneModels method) add_unnest_in_join() (dae.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method) (dae.query_variants.sql.schema2.base_query_builder.Dialect static method) add_value() (dae.genomic_resources.histogram.CategoricalHistogram method) (dae.genomic_resources.histogram.NullHistogram method) (dae.genomic_resources.histogram.NumberHistogram method) (dae.genomic_resources.implementations.reference_genome_impl.ChromosomeStatistic method) (dae.genomic_resources.implementations.reference_genome_impl.GenomeStatistic method) (dae.genomic_resources.statistics.base_statistic.Statistic method) (dae.genomic_resources.statistics.min_max.MinMaxValue method) add_variant_count() (in module dae.gene_profile.generate_gene_profile) adjust_chrom_prefix() (in module dae.variants_loaders.raw.flexible_variant_loader) adjust_dataset() (dae.tools.gpf_instance_adjustments.EnableDisableStudies method) (dae.tools.gpf_instance_adjustments.StudyConfigsAdjustmentCommand method) adjust_study() (dae.tools.gpf_instance_adjustments.DefaultGenotypeStorage method) (dae.tools.gpf_instance_adjustments.EnableDisableStudies method) (dae.tools.gpf_instance_adjustments.StudyConfigsAdjustmentCommand method) adjust_zero_based_line() (in module dae.genomic_resources.genomic_position_table.table) AdjustDuckDbStorageCommand (class in dae.tools.gpf_instance_adjustments) AdjustImpalaStorageCommand (class in dae.tools.gpf_instance_adjustments) AdjustmentsCommand (class in dae.tools.gpf_instance_adjustments) affected (dae.variants.attributes.Status attribute) AFFECTED_DAD (dae.pedigrees.family.FamilyTag attribute) AFFECTED_MOM (dae.pedigrees.family.FamilyTag attribute) AFFECTED_PRB (dae.pedigrees.family.FamilyTag attribute) AFFECTED_SIB (dae.pedigrees.family.FamilyTag attribute) aggregate_gene_values() (dae.annotation.gene_score_annotator.GeneScoreAnnotator method) Aggregator (class in dae.genomic_resources.aggregators) align_na_results() (dae.pheno_tool.pheno_tool_adapter.PhenoToolAdapter static method) all (dae.enrichment_tool.event_counters.EnrichmentResult attribute) (dae.enrichment_tool.event_counters.EventCountersResult attribute) (dae.enrichment_tool.event_counters.EventsResult attribute) (dae.enrichment_tool.event_counters.VariantEventsResult attribute) all() (dae.query_variants.attributes_query.StringQueryToTreeTransformer method) (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) ALL_ATTRIBUTE_IDXS (dae.effect_annotation.cli.AnnotationAttributes attribute) all_count() (dae.pheno.graphs.GraphColumn method) all_labels() (dae.pedigrees.family.FamilyTag static method) all_region_bins() (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) all_regions() (dae.genomic_resources.gene_models.gene_models.TranscriptModel method) (dae.genomic_resources.gene_models.TranscriptModel method) all_regions_from_chrom() (in module dae.utils.regions) all_tag_labels() (dae.pedigrees.family.Person method) all_tags() (dae.pedigrees.family.FamilyTag static method) alla_gpf() (in module dae.testing) (in module dae.testing.alla_import) Allele (class in dae.variants.core) Allele.Type (class in dae.variants.core) allele_aggregator (dae.genomic_resources.genomic_scores.AlleleScoreAggr attribute) (dae.genomic_resources.genomic_scores.AlleleScoreQuery attribute) (dae.genomic_resources.genomic_scores.ScoreDef attribute) allele_count (dae.variants.family_variant.FamilyVariant property) (dae.variants.variant.SummaryVariant property) allele_events (dae.enrichment_tool.genotype_helper.VariantEvent attribute) allele_in_members (dae.variants.family_variant.FamilyAllele property) allele_in_roles (dae.variants.family_variant.FamilyAllele property) allele_in_sexes (dae.variants.family_variant.FamilyAllele property) allele_in_statuses (dae.variants.family_variant.FamilyAllele property) allele_index (dae.variants.family_variant.FamilyAllele property) (dae.variants.variant.SummaryAllele property) allele_indexes (dae.variants.family_variant.FamilyVariant property) allele_type (dae.variants.core.Allele property) (dae.variants.family_variant.FamilyAllele property) allele_type_from_cshl_variant() (in module dae.variants.variant) allele_type_from_name() (in module dae.variants.variant) AlleleEffects (class in dae.effect_annotation.effect) AlleleEvent (class in dae.enrichment_tool.genotype_helper) AlleleParquetSerializer (class in dae.parquet.schema2.serializers) alleles (dae.variants.family_variant.FamilyVariant property) (dae.variants.variant.SummaryVariant property) AlleleScore (class in dae.genomic_resources.genomic_scores)

AlleleScoreAggr (class in dae.genomic_resources.genomic_scores) AlleleScoreAnnotator (class in dae.annotation.score_annotator) AlleleScoreQuery (class in dae.genomic_resources.genomic_scores) AllMemberDetailsView (class in family_api.views) allow_multiple_values() (dae.genomic_resources.genomic_scores.GenomicScore method) allowed_datasets (users_api.models.WdaeUser property), [1] alt (dae.annotation.annotatable.VCFAllele property) (dae.genomic_resources.genomic_position_table.Line attribute) (dae.genomic_resources.genomic_position_table.line.Line attribute) (dae.genomic_resources.genomic_position_table.line.LineBase attribute) ALT (dae.genomic_resources.genomic_position_table.table.GenomicPositionTable attribute) alt (dae.genomic_resources.genomic_scores.ScoreLine property) alt_alleles (dae.variants.variant.SummaryVariant property) alt_key (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) alternative (dae.annotation.annotatable.VCFAllele property) (dae.variants.core.Allele property) (dae.variants.family_variant.FamilyAllele property) (dae.variants.variant.SummaryVariant property) ancestor (datasets_api.models.Dataset attribute) (datasets_api.models.DatasetHierarchy attribute) ancestor_id (datasets_api.models.DatasetHierarchy attribute) AndNode (class in dae.query_variants.attributes_query) AndNode() (dae.query_variants.attributes_query.QueryTreeToBitwiseLambdaTransformer method) (dae.query_variants.attributes_query.QueryTreeToLambdaTransformer method) (dae.query_variants.attributes_query.QueryTreeToSQLBitwiseTransformer static method) Annotatable (class in dae.annotation.annotatable) Annotatable.Type (class in dae.annotation.annotatable) annotate() (dae.annotation.annotate_columns.AnnotateColumnsTool static method) (dae.annotation.annotate_vcf.AnnotateVCFTool static method) (dae.annotation.annotation_pipeline.AnnotationPipeline method) (dae.annotation.annotation_pipeline.Annotator method) (dae.annotation.annotation_pipeline.InputAnnotableAnnotatorDecorator method) (dae.annotation.annotation_pipeline.ReannotationPipeline method) (dae.annotation.annotation_pipeline.ValueTransformAnnotatorDecorator method) (dae.annotation.annotator_base.AnnotatorBase method) (dae.annotation.cnv_collection_annotator.CnvCollectionAnnotator method) (dae.annotation.debug_annotator.HelloWorldAnnotator method) (dae.annotation.gene_score_annotator.GeneScoreAnnotator method) (dae.annotation.score_annotator.AlleleScoreAnnotator method) (dae.annotation.score_annotator.PositionScoreAnnotatorBase method) (dae.effect_annotation.annotator.EffectAnnotator method) annotate_allele() (dae.effect_annotation.annotator.EffectAnnotator method) annotate_cnv() (dae.effect_annotation.annotator.EffectAnnotator method) annotate_parquet() (in module dae.annotation.parquet) annotate_region() (dae.effect_annotation.annotator.EffectAnnotator method) annotate_summary_allele() (dae.annotation.annotation_pipeline.ReannotationPipeline method) annotate_variant() (dae.effect_annotation.annotator.EffectAnnotator static method) AnnotateColumnsTool (class in dae.annotation.annotate_columns) AnnotateSchema2ParquetTool (class in dae.annotation.annotate_schema2_parquet) AnnotateVCFTool (class in dae.annotation.annotate_vcf) annotation_schema (dae.variants_loaders.raw.loader.AnnotationPipelineDecorator property) (dae.variants_loaders.raw.loader.VariantsLoader property) (dae.variants_loaders.raw.loader.VariantsLoaderDecorator property) AnnotationAttributes (class in dae.effect_annotation.cli) AnnotationConfigParser (class in dae.annotation.annotation_config) AnnotationConfigurationError AnnotationDecorator (class in dae.variants_loaders.raw.loader) AnnotationDependencyGraph (dae.annotation.annotation_pipeline.ReannotationPipeline attribute) AnnotationEffect (class in dae.effect_annotation.effect) AnnotationPipeline (class in dae.annotation.annotation_pipeline) AnnotationPipelineDecorator (class in dae.variants_loaders.raw.loader) AnnotationPipelineImplementation (class in dae.genomic_resources.implementations.annotation_pipeline_impl) AnnotationPreamble (class in dae.annotation.annotation_config) AnnotationRequestFactory (class in dae.effect_annotation.annotator) AnnotationTool (class in dae.annotation.annotate_utils) Annotator (class in dae.annotation.annotation_pipeline) annotator_id (dae.annotation.annotation_config.AnnotatorInfo attribute) AnnotatorBase (class in dae.annotation.annotator_base) AnnotatorDecorator (class in dae.annotation.annotation_pipeline) AnnotatorInfo (class in dae.annotation.annotation_config) annotators (dae.annotation.annotation_config.RawFullConfig attribute) any() (dae.query_variants.attributes_query.StringQueryToTreeTransformer method) (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) append() (dae.genomic_resources.genomic_position_table.line.LineBuffer method) (dae.genomic_resources.genomic_position_table.LineBuffer method) (dae.tools.gpf_validation_runner.TestSuite method) append_family_allele() (dae.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) append_meta_to_parquet() (in module dae.parquet.parquet_writer) append_summary_allele() (dae.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) apply() (dae.person_filters.FamilyFilter method) (dae.person_filters.person_filters.CriteriaFilter method) (dae.person_filters.person_filters.FamilyFilter method) (dae.person_filters.person_filters.PersonFilter method) (dae.person_filters.person_filters.PhenoFilter method) (dae.person_filters.PersonFilter method) (dae.person_filters.PhenoFilter method) apply_family_heuristics() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) apply_summary_heuristics() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) apply_to_df() (dae.person_filters.FamilyFilter method) (dae.person_filters.person_filters.FamilyFilter method) (dae.person_filters.person_filters.PersonFilter method) (dae.person_filters.person_filters.PersonFilterRange method) (dae.person_filters.person_filters.PersonFilterSet method) (dae.person_filters.PersonFilter method) (dae.person_filters.PersonFilterRange method) (dae.person_filters.PersonFilterSet method) apply_to_family() (dae.pedigrees.layout.Layout method) are_mates() (dae.pedigrees.pedigrees.Individual method) are_siblings() (dae.pedigrees.pedigrees.Individual method) arg() (dae.query_variants.attributes_query.BitwiseTreeTransformer method) (dae.query_variants.attributes_query.StringQueryToTreeTransformer method) args (dae.task_graph.graph.Task attribute) ARGUMENT (dae.variants_loaders.raw.loader.ArgumentType attribute) ArgumentType (class in dae.variants_loaders.raw.loader) array_item_suffix() (dae.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method) (dae.query_variants.sql.schema2.base_query_builder.Dialect static method) atom() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) atomlist() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) AttributeInfo (class in dae.annotation.annotation_config) attributes (dae.annotation.annotation_config.AnnotatorInfo attribute) (dae.annotation.annotation_pipeline.Annotator property) (dae.genomic_resources.cnv_collection.CNV attribute) (dae.variants.family_variant.FamilyAllele property) (dae.variants.variant.SummaryAllele property) (dae.variants.variant.SummaryVariant property) augment_accessibility() (in module datasets_api.views) augment_with_groups() (in module datasets_api.views) augment_with_parents() (in module datasets_api.views) auth_token (users_api.models.WdaeUser attribute), [1] authenticate() (utils.authentication.GPFOAuth2Authentication method) (utils.authentication.SessionAuthenticationWithUnauthenticatedCSRF method) authentication_classes (groups_api.views.GroupsViewSet attribute) (query_base.query_base.QueryBaseView attribute) (users_api.views.FederationCredentials attribute), [1] (users_api.views.UserViewSet attribute), [1] AuthenticationLog (class in users_api.models), [1] AuthenticationLog.DoesNotExist, [1] AuthenticationLog.MultipleObjectsReturned, [1] autosomal (dae.variants.attributes.GeneticModel attribute) autosomal_broken (dae.variants.attributes.GeneticModel attribute)

B

backend (dae.studies.study.GenotypeDataStudy property) background_id (dae.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground property) (dae.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property) background_type (dae.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground property) (dae.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property) backup_schema2_study() (in module dae.annotation.parquet) base_dir (dae.duckdb_storage.duckdb_storage_config.DuckDbConf attribute) (dae.duckdb_storage.duckdb_storage_config.DuckDbParquetConf attribute) (dae.schema2_storage.schema2_layout.Schema2DatasetLayout attribute) base_fields (users_api.forms.WdaeLoginForm attribute) (users_api.forms.WdaePasswordForgottenForm attribute) (users_api.forms.WdaeRegisterPasswordForm attribute) (users_api.forms.WdaeResetPasswordForm attribute) BaseAnnotationRequest (class in dae.effect_annotation.annotation_request) BaseDatasetPermissionsView (class in datasets_api.views) BaseEnrichmentBackground (class in dae.enrichment_tool.base_enrichment_background) BaseEnrichmentBuilder (class in dae.enrichment_tool.enrichment_builder) BaseEnrichmentResourceBackground (class in dae.enrichment_tool.base_enrichment_background) BaseGeneSetCollection (class in dae.gene_sets.gene_sets_db) BaseGenotypeBrowserRunner (class in dae.tools.gpf_validation_runner) basename (groups_api.views.GroupsViewSet attribute) (users_api.views.UserViewSet attribute), [1] BasePasswordView (class in users_api.views), [1] BaseQueryBuilder (class in dae.query_variants.sql.schema2.base_query_builder) BaseQueryTransformerMatcher (class in dae.query_variants.attributes_query) BaseTreeTransformer (class in dae.query_variants.attributes_query) BaseVerificationCode (class in users_api.models), [1] BaseVerificationCode.Meta (class in users_api.models), [1] basic_liftover_allele() (in module dae.annotation.liftover_annotator) basic_liftover_variant() (in module dae.annotation.liftover_annotator) BasicLiftoverAnnotator (class in dae.annotation.liftover_annotator) batch_annotate() (dae.annotation.annotate_columns.AnnotateColumnsTool static method) (dae.annotation.annotation_pipeline.AnnotationPipeline method) (dae.annotation.annotation_pipeline.Annotator method) (dae.annotation.annotator_base.AnnotatorBase method) BATCH_ROWS (dae.parquet.schema2.parquet_io.ContinuousParquetFileWriter attribute) BATCH_SIZE (dae.variants_loaders.parquet.loader.Reader attribute) bcf_liftover_allele() (in module dae.annotation.liftover_annotator) bcf_liftover_variant() (in module dae.annotation.liftover_annotator) BcfLiftoverAnnotator (class in dae.annotation.liftover_annotator) bedfile2regions() (in module dae.utils.regions) BedRegion (class in dae.utils.regions) begin (dae.utils.regions.BedRegion property) (dae.utils.regions.Region property) best2gt() (in module dae.utils.variant_utils) best_st (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) best_state (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) BigWigLine (class in dae.genomic_resources.genomic_position_table) (class in dae.genomic_resources.genomic_position_table.line) BigWigTable (class in dae.genomic_resources.genomic_position_table) (class in dae.genomic_resources.genomic_position_table.table_bigwig) bitmask2inheritance() (in module dae.variants.attributes) BitwiseTreeTransformer (class in dae.query_variants.attributes_query) bold_red (wdae.default_settings.CustomFormatter attribute) broken (datasets_api.models.Dataset attribute) broken_families (dae.pedigrees.families_data.FamiliesData property) browsable_figure_path() (dae.pheno.prepare_data.PreparePhenoBrowserBase class method) Bucket (class in dae.import_tools.import_tools) bucket_url (dae.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (dae.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute) BUFFER_MAXSIZE (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (dae.genomic_resources.genomic_position_table.table_tabix.TabixGenomicPositionTable attribute) build() (dae.annotation.record_to_annotatable.CSHLAlleleRecordToAnnotatable method) (dae.annotation.record_to_annotatable.RecordToAnnotable method) (dae.annotation.record_to_annotatable.RecordToCNVAllele method) (dae.annotation.record_to_annotatable.RecordToPosition method) (dae.annotation.record_to_annotatable.RecordToRegion method) (dae.annotation.record_to_annotatable.RecordToVcfAllele method) (dae.annotation.record_to_annotatable.VcfLikeRecordToVcfAllele method) (dae.enrichment_tool.enrichment_builder.BaseEnrichmentBuilder method) (dae.enrichment_tool.enrichment_builder.EnrichmentBuilder method) (dae.gpf_instance.gpf_instance.GPFInstance static method) (dae.gpf_instance.GPFInstance static method) (dae.pheno.graphs.GraphColumn static method) (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) build_aggregator() (in module dae.genomic_resources.aggregators) build_allele_score_annotator() (in module dae.annotation.score_annotator) build_and_save() (dae.studies.study.GenotypeData method) build_annotation_filename() (dae.variants_loaders.raw.loader.AnnotationDecorator static method) build_annotation_pipeline() (dae.import_tools.import_tools.ImportProject method) (in module dae.annotation.annotation_factory) build_annotator() (in module dae.annotation.debug_annotator) build_arguments_dict() (dae.variants_loaders.raw.loader.CLILoader method) (dae.variants_loaders.raw.loader.VariantsLoaderDecorator method) build_array_join() (dae.duckdb_storage.duckdb_variants.DuckDbQueryDialect method) (dae.query_variants.sql.schema2.base_query_builder.Dialect method) build_backend() (dae.duckdb_storage.duckdb_genotype_storage.AbstractDuckDbStorage method) (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) (dae.genotype_storage.genotype_storage.GenotypeStorage method) (dae.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage method) (dae.parquet_storage.storage.ParquetGenotypeStorage method) build_batch() (dae.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) build_browser() (in module dae.pheno.pheno_import) build_cache() (dae.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) build_cli_arguments() (dae.variants_loaders.raw.loader.CLILoader class method) (dae.variants_loaders.raw.loader.VariantsLoaderDecorator class method) build_cnv_allele() (dae.variants.core.Allele static method) build_cnv_collection_annotator() (in module dae.annotation.cnv_collection_annotator) build_coding_length_background() (in module dae.enrichment_tool.build_coding_length_enrichment_background) build_collection() (dae.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection static method) (dae.gene_sets.denovo_gene_set_helpers.DenovoGeneSetHelpers class method) build_config() (dae.configuration.study_config_builder.StudyConfigBuilder method) build_configuration() (dae.gene_profile.db.GeneProfileDB class method) build_content_file() (dae.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) build_default_histogram_conf() (in module dae.genomic_resources.histogram) build_demo_graph() (in module dae.task_graph.demo_graphs_cli) build_dependency_graph() (dae.annotation.annotation_pipeline.ReannotationPipeline static method) build_descs_from_score() (dae.gene_scores.gene_scores.GeneScoresDb static method) build_effect_annotator() (dae.effect_annotation.cli.EffectAnnotatorBuilder method) (in module dae.annotation.effect_annotator) build_effect_types() (dae.effect_annotation.effect.EffectTypesMixin class method) build_effect_types_groups() (dae.effect_annotation.effect.EffectTypesMixin class method) build_effect_types_list() (dae.effect_annotation.effect.EffectTypesMixin class method) build_effect_types_naming() (dae.effect_annotation.effect.EffectTypesMixin class method) build_empty_histogram() (in module dae.genomic_resources.histogram) build_enrichment_event_counts_cache() (dae.enrichment_tool.enrichment_helper.EnrichmentHelper method)

build_families_data() (in module dae.pedigrees.testing) build_families_data_from_pedigree() (dae.pedigrees.loader.FamiliesLoader static method) build_families_report() (in module dae.tools.draw_pedigree) build_family() (in module dae.pedigrees.testing) build_family_allele_batch_dict() (dae.parquet.schema2.serializers.AlleleParquetSerializer method) build_family_layout() (in module dae.tools.draw_pedigree) build_family_schema() (dae.parquet.schema2.serializers.AlleleParquetSerializer class method) build_family_variants_query() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) build_family_variants_query_runner() (dae.duckdb_storage.duckdb2_variants.DuckDb2Variants method) (dae.inmemory_storage.raw_variants.RawFamilyVariants method) (dae.parquet_storage.storage.ParquetLoaderVariants method) (dae.query_variants.base_query_variants.QueryVariantsBase method) (dae.query_variants.sql.schema2.base_variants.SqlSchema2Variants method) build_filesystem_test_protocol() (in module dae.genomic_resources.testing) build_filesystem_test_repository() (in module dae.genomic_resources.testing) build_filesystem_test_resource() (in module dae.genomic_resources.testing) build_from_config() (dae.import_tools.import_tools.ImportProject static method) build_from_file() (dae.import_tools.import_tools.ImportProject static method) build_fsspec_protocol() (in module dae.genomic_resources.fsspec_protocol) build_gene_models_from_file() (in module dae.genomic_resources.gene_models) (in module dae.genomic_resources.gene_models.gene_models) build_gene_models_from_resource() (in module dae.genomic_resources.gene_models) (in module dae.genomic_resources.gene_models.gene_models) build_gene_models_from_resource_id() (in module dae.genomic_resources.gene_models) (in module dae.genomic_resources.gene_models.gene_models) build_gene_regions() (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) build_gene_score_annotator() (in module dae.annotation.gene_score_annotator) build_gene_score_from_resource() (in module dae.gene_scores.gene_scores) build_gene_score_from_resource_id() (in module dae.gene_scores.gene_scores) build_gene_score_implementation_from_resource() (in module dae.gene_scores.implementations.gene_scores_impl) build_gene_set_annotator() (in module dae.annotation.gene_set_annotator) build_gene_set_collection_from_file() (in module dae.gene_sets.gene_sets_db) build_gene_set_collection_from_resource() (in module dae.gene_sets.gene_sets_db) build_gene_set_collection_from_resource_id() (in module dae.gene_sets.gene_sets_db) build_gene_weights_enrichment_background() (in module dae.enrichment_tool.resource_implementations.enrichment_resource_impl) build_genomic_position_table() (in module dae.genomic_resources.genomic_position_table) (in module dae.genomic_resources.genomic_position_table.utils) build_genomic_resource() (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) build_genomic_resource_group_repository() (in module dae.genomic_resources.repository_factory) build_genomic_resource_repository() (in module dae.genomic_resources) (in module dae.genomic_resources.repository_factory) build_genomic_scores_registry() (dae.genomic_scores.scores.GenomicScoresRegistry static method) build_genotype_data_all_datasets() (studies.study_wrapper.StudyWrapperBase static method) build_genotype_data_description() (studies.study_wrapper.StudyWrapperBase static method) build_gtf_record() (in module dae.genomic_resources.gene_models.serialization) build_histogram_config() (in module dae.genomic_resources.histogram) build_http_test_protocol() (in module dae.genomic_resources.testing) build_id() (dae.pedigrees.family_role_builder.Mating static method) build_import_project() (in module dae.tools.simple_study_import) build_index_info() (dae.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) build_inheritance_query() (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) build_inmemory_protocol() (in module dae.genomic_resources.fsspec_protocol) build_inmemory_test_protocol() (in module dae.genomic_resources.testing) build_inmemory_test_repository() (in module dae.genomic_resources.testing) build_inmemory_test_resource() (in module dae.genomic_resources.testing) build_liftover_annotator() (in module dae.annotation.liftover_annotator) build_liftover_chain_from_resource() (in module dae.genomic_resources.liftover_chain) build_liftover_chain_from_resource_id() (in module dae.genomic_resources.liftover_chain) build_local_resource() (in module dae.genomic_resources.fsspec_protocol) build_manifest() (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) build_measures_count_query() (dae.pheno.db.PhenoDb method) build_measures_query() (dae.pheno.db.PhenoDb method) build_normalize_allele_annotator() (in module dae.annotation.normalize_allele_annotator) build_np_score_annotator() (in module dae.annotation.score_annotator) build_option() (dae.variants_loaders.raw.loader.CLIArgument method) build_pheno_browser() (in module dae.pheno.pheno_import) build_position_allele() (dae.variants.core.Allele static method) build_position_score_annotator() (in module dae.annotation.score_annotator) build_query() (dae.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder method) build_record_to_annotatable() (in module dae.annotation.record_to_annotatable) build_reference_genome_from_file() (in module dae.genomic_resources.reference_genome) build_reference_genome_from_resource() (in module dae.genomic_resources.reference_genome) build_reference_genome_from_resource_id() (in module dae.genomic_resources.reference_genome) build_regression() (dae.pheno.prepare_data.PreparePhenoBrowserBase class method) build_report() (dae.studies.study.GenotypeData method) build_report_description() (dae.pheno_tool.pheno_tool_adapter.PhenoToolAdapter method) build_resource_file_state() (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) build_resource_implementation() (in module dae.genomic_resources.repository_factory) build_results() (dae.enrichment_tool.enrichment_builder.EnrichmentBuilder method) build_roles() (dae.pedigrees.family_role_builder.FamilyRoleBuilder method) build_roles_query() (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) build_s3_test_bucket() (in module dae.genomic_resources.testing) build_s3_test_filesystem() (in module dae.genomic_resources.testing) build_s3_test_protocol() (in module dae.genomic_resources.testing) build_samocha_enrichment_background() (in module dae.enrichment_tool.resource_implementations.enrichment_resource_impl) build_schema() (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) build_score_aggregator_documentation() (dae.annotation.score_annotator.AlleleScoreAnnotator method) (dae.annotation.score_annotator.GenomicScoreAnnotatorBase method) (dae.annotation.score_annotator.NPScoreAnnotator method) (dae.annotation.score_annotator.PositionScoreAnnotator method) build_score_from_resource() (in module dae.genomic_resources.genomic_scores) build_score_from_resource_id() (in module dae.genomic_resources.genomic_scores) build_score_implementation_from_resource() (in module dae.genomic_resources.implementations.genomic_scores_impl) build_serializer() (dae.parquet.schema2.variant_serializers.VariantsDataSerializer static method) build_sexes_query() (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) build_simple_effect_annotator() (in module dae.annotation.simple_effect_annotator) build_statistics() (dae.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeStatistics static method) build_study_layout() (dae.duckdb_storage.duckdb_genotype_storage.AbstractDuckDbStorage method) (dae.duckdb_storage.duckdb_genotype_storage.DuckDbParquetStorage method) (dae.duckdb_storage.duckdb_genotype_storage.DuckDbS3ParquetStorage method) (dae.duckdb_storage.duckdb_genotype_storage.DuckDbS3Storage method) (dae.duckdb_storage.duckdb_genotype_storage.DuckDbStorage method) build_summary_allele_batch_dict() (dae.parquet.schema2.serializers.AlleleParquetSerializer method) build_summary_schema() (dae.parquet.schema2.serializers.AlleleParquetSerializer class method) build_summary_variants_query() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) build_summary_variants_query_runner() (dae.duckdb_storage.duckdb2_variants.DuckDb2Variants method) (dae.inmemory_storage.raw_variants.RawFamilyVariants method) (dae.parquet_storage.storage.ParquetLoaderVariants method) (dae.query_variants.base_query_variants.QueryVariantsBase method) (dae.query_variants.sql.schema2.base_variants.SqlSchema2Variants method) build_table() (dae.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) build_table_name() (dae.duckdb_storage.duckdb_variants.DuckDbQueryDialect method) (dae.query_variants.sql.schema2.base_query_builder.Dialect method) build_values_categorical_distribution() (dae.pheno.prepare_data.PreparePhenoBrowserBase class method) build_values_ordinal_distribution() (dae.pheno.prepare_data.PreparePhenoBrowserBase class method) build_values_violinplot() (dae.pheno.prepare_data.PreparePhenoBrowserBase class method) build_variant_row() (studies.response_transformer.ResponseTransformer method) build_variant_types_query() (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) build_variants_loader_pipeline() (dae.import_tools.import_tools.ImportProject method) build_vcf_allele() (dae.variants.core.Allele static method)

C

cache() (dae.task_graph.cache.FileTaskCache method) (dae.task_graph.cache.NoTaskCache method) (dae.task_graph.cache.TaskCache method) CACHE_LOCK (dae.pheno.registry.PhenoRegistry attribute) cache_resources() (in module dae.genomic_resources.cached_repository) CacheRecord (class in dae.task_graph.cache) CacheRecordType (class in dae.task_graph.cache) CacheResource (class in dae.genomic_resources.cached_repository) CachingProtocol (class in dae.genomic_resources.cached_repository) calc() (dae.pheno_tool.tool.PhenoTool method) calc_alleles() (dae.variants.family_variant.FamilyVariant static method) calc_alt_alleles() (dae.variants.family_variant.FamilyVariant static method) calc_batched_heuristics() (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) calc_bin_begin() (in module dae.utils.regions) calc_bin_end() (in module dae.utils.regions) calc_bin_index() (in module dae.utils.regions) calc_by_effect() (dae.pheno_tool.pheno_tool_adapter.PhenoToolAdapter method) (dae.pheno_tool.pheno_tool_adapter.PhenoToolAdapterBase method) calc_coding_bins() (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) calc_enrichment_test() (dae.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground method) (dae.enrichment_tool.enrichment_helper.EnrichmentHelper method) (dae.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground method) (dae.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground method) (dae.enrichment_tool.samocha_background.SamochaEnrichmentBackground method) calc_expected_observed_pvalue() (dae.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground static method) (dae.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground static method) calc_family_bins() (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) calc_frame_for_gtf_cds_feature() (in module dae.genomic_resources.gene_models.serialization) calc_frames() (dae.genomic_resources.gene_models.gene_models.TranscriptModel method) (dae.genomic_resources.gene_models.TranscriptModel method) calc_frequency_bins() (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) calc_heuristics() (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) calc_info_hash() (dae.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation method) (dae.gene_scores.implementations.gene_scores_impl.GeneScoreImplementation method) (dae.gene_sets.gene_sets_db.GeneSetCollection method) (dae.genomic_resources.cnv_collection.CnvCollectionImplementation method) (dae.genomic_resources.implementations.annotation_pipeline_impl.AnnotationPipelineImplementation method) (dae.genomic_resources.implementations.gene_models_impl.GeneModelsImpl method) (dae.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation method) (dae.genomic_resources.implementations.liftover_chain_impl.LiftoverChainImplementation method) (dae.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeImplementation method) (dae.genomic_resources.resource_implementation.GenomicResourceImplementation method) calc_inheritance_trio() (dae.variants.family_variant.FamilyAllele class method) calc_region_bins() (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) calc_statistics_hash() (dae.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation method) (dae.gene_scores.implementations.gene_scores_impl.GeneScoreImplementation method) (dae.gene_sets.gene_sets_db.GeneSetCollection method) (dae.genomic_resources.cnv_collection.CnvCollectionImplementation method) (dae.genomic_resources.implementations.annotation_pipeline_impl.AnnotationPipelineImplementation method) (dae.genomic_resources.implementations.gene_models_impl.GeneModelsImpl method) (dae.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation method) (dae.genomic_resources.implementations.liftover_chain_impl.LiftoverChainImplementation method) (dae.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeImplementation method) (dae.genomic_resources.resource_implementation.GenomicResourceImplementation method) calc_variants() (dae.pheno_tool.pheno_tool_adapter.PhenoToolAdapter method) (dae.pheno_tool.pheno_tool_adapter.PhenoToolAdapterBase method) calculate_simple_best_state() (in module dae.variants.family_variant) calculate_table_values() (in module dae.gene_profile.generate_gene_profile) call_region() (dae.annotation.simple_effect_annotator.SimpleEffectAnnotator method) camelize_string() (in module dae.utils.helpers) can_extend() (dae.pedigrees.pedigrees.Realization method) categorical (dae.pheno.common.InferenceConfig attribute) (dae.pheno.common.MeasureType attribute) CategoricalHistogram (class in dae.genomic_resources.histogram) CategoricalHistogramConfig (class in dae.genomic_resources.histogram) cds_intron_regions() (dae.annotation.simple_effect_annotator.SimpleEffectAnnotator method) cds_len() (dae.genomic_resources.gene_models.gene_models.TranscriptModel method) (dae.genomic_resources.gene_models.TranscriptModel method) cds_regions() (dae.effect_annotation.annotation_request.BaseAnnotationRequest method) (dae.genomic_resources.gene_models.gene_models.TranscriptModel method) (dae.genomic_resources.gene_models.TranscriptModel method) cds_to_dictlist() (genomes_api.views.GeneModels method) change_environment() (in module dae.utils.fixtures) change_password() (in module users_api.views), [1] (users_api.models.WdaeUser static method), [1] check_affected_dad_family() (in module dae.pedigrees.family_tag_builder) check_affected_mom_family() (in module dae.pedigrees.family_tag_builder) check_affected_prb_family() (in module dae.pedigrees.family_tag_builder) check_affected_sib_family() (in module dae.pedigrees.family_tag_builder) check_control_family() (in module dae.pedigrees.family_tag_builder) check_denovo_trio() (dae.variants.family_variant.FamilyAllele static method) check_family_tags_query() (in module dae.pedigrees.family_tag_builder) check_female_prb_family() (in module dae.pedigrees.family_tag_builder) check_for_repeated_attributes_in_annotator() (in module dae.annotation.annotation_factory) check_for_repeated_attributes_in_pipeline() (in module dae.annotation.annotation_factory) check_for_unused_parameters() (in module dae.annotation.annotation_factory) check_if_new_stop() (dae.effect_annotation.effect_checkers.frame_shift.FrameShiftEffectChecker method) check_inheritance_denovo_only() (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) check_inheritance_query_value() (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) check_male_prb_family() (in module dae.pedigrees.family_tag_builder) check_mendelian_trio() (dae.variants.family_variant.FamilyAllele static method) check_missing_dad_family() (in module dae.pedigrees.family_tag_builder) check_missing_mom_family() (in module dae.pedigrees.family_tag_builder) check_multiplex_family() (in module dae.pedigrees.family_tag_builder) check_nuclear_family() (in module dae.pedigrees.family_tag_builder) check_omission_trio() (dae.variants.family_variant.FamilyAllele static method) check_phenotype_data_config() (in module dae.pheno.common) check_quad_family() (in module dae.pedigrees.family_tag_builder) check_roles_denovo_only() (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) check_roles_query_value() (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) check_sexes_query_value() (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) check_simplex_family() (in module dae.pedigrees.family_tag_builder) check_stop_codon() (dae.effect_annotation.effect_checkers.frame_shift.FrameShiftEffectChecker method) (dae.effect_annotation.effect_checkers.utr.UTREffectChecker method) check_tag() (in module dae.pedigrees.family_tag_builder) check_trio_family() (in module dae.pedigrees.family_tag_builder) check_unaffected_dad_family() (in module dae.pedigrees.family_tag_builder) check_unaffected_mom_family() (in module dae.pedigrees.family_tag_builder) check_unaffected_prb_family() (in module dae.pedigrees.family_tag_builder) check_unaffected_sib_family() (in module dae.pedigrees.family_tag_builder) check_update_manifest() (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) check_variant_types_value() (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) CHECK_VERBOSITY (dae.query_variants.query_runners.QueryResult attribute) check_verif_code() (in module users_api.views), [1] checkConsistency() (in module dae.tools.phase) checkers (dae.configuration.gpf_config_parser.GPFConfigValidator attribute) child (dae.variants.attributes.Role attribute) children_set() (dae.pedigrees.pedigrees.Individual method) (dae.pedigrees.pedigrees.IndividualGroup method) (dae.pedigrees.pedigrees.MatingUnit method) (dae.pedigrees.pedigrees.SibshipUnit method) ChildrenBySex (class in dae.person_sets) (class in dae.person_sets.person_sets) ChildrenStats (class in dae.person_sets) (class in dae.person_sets.person_sets) choose_bin_lin() (dae.genomic_resources.histogram.NumberHistogram method) choose_bin_log() (dae.genomic_resources.histogram.NumberHistogram method) chrom (dae.annotation.annotatable.Annotatable property) (dae.genomic_resources.cnv_collection.CNV attribute) (dae.genomic_resources.genomic_position_table.Line attribute) (dae.genomic_resources.genomic_position_table.line.Line attribute) (dae.genomic_resources.genomic_position_table.line.LineBase attribute) CHROM (dae.genomic_resources.genomic_position_table.table.GenomicPositionTable attribute) (dae.genomic_resources.genomic_position_table.table_vcf.VCFGenomicPositionTable attribute) (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) chrom (dae.genomic_resources.genomic_scores.ScoreLine property) (dae.variants.core.Allele property) (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) (dae.variants.variant.SummaryVariant property) chrom_count (dae.genomic_resources.implementations.reference_genome_impl.GenomeStatistic property) chrom_key (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) chrom_map (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) chrom_order (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) chrom_prefix (dae.genomic_resources.reference_genome.ReferenceGenome property) chromosome (dae.annotation.annotatable.Annotatable property) (dae.variants.core.Allele property) (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) (dae.variants.variant.SummaryVariant property) chromosomes (dae.genomic_resources.reference_genome.ReferenceGenome property) (dae.variants_loaders.cnv.loader.CNVLoader property) (dae.variants_loaders.dae.loader.DaeTransmittedLoader property) (dae.variants_loaders.dae.loader.DenovoLoader property) (dae.variants_loaders.raw.loader.VariantsLoader property) (dae.variants_loaders.raw.loader.VariantsLoaderDecorator property) (dae.variants_loaders.vcf.loader.SingleVcfLoader property) (dae.variants_loaders.vcf.loader.VcfLoader property) ChromosomeStatistic (class in dae.genomic_resources.implementations.reference_genome_impl) CHUNK_SIZE (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol attribute) classification_reference_impl() (in module dae.pheno.prepare.measure_classifier) ClassifierReport (class in dae.pheno.prepare.measure_classifier) classify() (dae.pheno.prepare.measure_classifier.MeasureClassifier method) clean() (users_api.forms.WdaeLoginForm method) clean_new_password2() (users_api.forms.WdaeResetPasswordForm method) CLEAN_UP_COLUMNS (dae.variants_loaders.raw.loader.AnnotationDecorator attribute) cleanup_groups() (users_api.management.commands.groups_cleanup.Command method) cleanup_users() (users_api.management.commands.groups_cleanup.Command method) cleanup_wdae_datasets() (users_api.management.commands.groups_cleanup.Command method) clear() (dae.genomic_resources.aggregators.Aggregator method) (dae.genomic_resources.genomic_position_table.line.LineBuffer method) (dae.genomic_resources.genomic_position_table.LineBuffer method) (datasets_api.models.DatasetHierarchy class method) clear_tags() (dae.pedigrees.family_tag_builder.FamilyTagsBuilder method) cli() (in module dae.annotation.annotate_columns) (in module dae.annotation.annotate_doc) (in module dae.annotation.annotate_schema2_parquet) (in module dae.annotation.annotate_vcf) (in module dae.annotation.reannotate_instance) (in module dae.enrichment_tool.build_coding_length_enrichment_background) (in module dae.enrichment_tool.build_ur_synonymous_enrichment_background) (in module dae.enrichment_tool.enrichment_cache_builder) (in module dae.tools.annotate_variants) (in module dae.tools.gpf_instance_adjustments) (in module wdae.wgpf) cli_arguments() (dae.variants_loaders.raw.loader.CLILoader class method) (dae.variants_loaders.raw.loader.VariantsLoaderDecorator class method) (in module dae.tools.simple_study_import) cli_browse() (in module dae.genomic_resources.cli) cli_cache_repo() (in module dae.tools.grr_cache_repo) cli_columns() (in module dae.effect_annotation.cli) cli_defaults() (dae.variants_loaders.raw.loader.CLILoader class method) (dae.variants_loaders.raw.loader.VariantsLoaderDecorator class method) cli_export() (in module dae.gene_profile.exporter) cli_genome_options() (in module dae.tools.annotate_variants) cli_manage() (in module dae.genomic_resources.cli) cli_variants_options() (in module dae.tools.annotate_variants) cli_vcf() (in module dae.effect_annotation.cli) (in module dae.tools.annotate_variants) CLIAnnotationContext (class in dae.annotation.context) CLIArgument (class in dae.variants_loaders.raw.loader) CLIGenomicContext (class in dae.genomic_resources.genomic_context) CLILoader (class in dae.variants_loaders.raw.loader) close() (dae.annotation.annotation_pipeline.AnnotationPipeline method) (dae.annotation.annotation_pipeline.Annotator method) (dae.annotation.annotation_pipeline.AnnotatorDecorator method) (dae.annotation.cnv_collection_annotator.CnvCollectionAnnotator method) (dae.annotation.effect_annotator.EffectAnnotatorAdapter method) (dae.annotation.liftover_annotator.AbstractLiftoverAnnotator method) (dae.annotation.normalize_allele_annotator.NormalizeAlleleAnnotator method) (dae.annotation.score_annotator.GenomicScoreAnnotatorBase method) (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) (dae.effect_annotation.cli.VariantColumnInputFile method) (dae.effect_annotation.cli.VariantColumnOutputFile method) (dae.genomic_resources.cnv_collection.CnvCollection method) (dae.genomic_resources.genomic_position_table.BigWigTable method) (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table.GenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table_bigwig.BigWigTable method) (dae.genomic_resources.genomic_position_table.table_inmemory.InmemoryGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table_tabix.TabixGenomicPositionTable method) (dae.genomic_resources.genomic_scores.GenomicScore method) (dae.genomic_resources.liftover_chain.LiftoverChain method) (dae.genomic_resources.reference_genome.ReferenceGenome method) (dae.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) (dae.parquet.schema2.parquet_io.VariantsParquetWriter method) (dae.query_variants.query_runners.QueryResult method) (dae.query_variants.query_runners.QueryRunner method) (dae.studies.study.GenotypeData method) (dae.task_graph.executor.AbstractTaskGraphExecutor method) (dae.task_graph.executor.DaskExecutor method) (dae.task_graph.executor.TaskGraphExecutor method) (dae.task_graph.logging.FsspecHandler method) (dae.tools.gpf_instance_adjustments.AdjustmentsCommand method) (dae.utils.debug_closing.closing method) (dae.variants_loaders.cnv.loader.CNVLoader method) (dae.variants_loaders.dae.loader.DaeTransmittedLoader method) (dae.variants_loaders.dae.loader.DenovoLoader method) (dae.variants_loaders.parquet.loader.MultiReader method) (dae.variants_loaders.parquet.loader.Reader method) (dae.variants_loaders.raw.loader.AnnotationPipelineDecorator method) (dae.variants_loaders.raw.loader.EffectAnnotationDecorator method) (dae.variants_loaders.raw.loader.VariantsLoader method) (dae.variants_loaders.raw.loader.VariantsLoaderDecorator method) (dae.variants_loaders.vcf.loader.SingleVcfLoader method) (dae.variants_loaders.vcf.loader.VcfLoader method)

closing (class in dae.utils.debug_closing) CNV (class in dae.genomic_resources.cnv_collection) cnv (dae.testing.import_helpers.StudyInputLayout attribute) (dae.testing.StudyInputLayout attribute) (dae.variants.core.Allele.Type attribute) cnv_import() (in module dae.testing) (in module dae.testing.import_helpers) cnv_study() (in module dae.testing) (in module dae.testing.import_helpers) cnv_variant_type() (in module dae.utils.cnv_utils) CNVAllele (class in dae.annotation.annotatable) CnvCollection (class in dae.genomic_resources.cnv_collection) CnvCollectionAnnotator (class in dae.annotation.cnv_collection_annotator) CnvCollectionImplementation (class in dae.genomic_resources.cnv_collection) CNVLoader (class in dae.variants_loaders.cnv.loader) coalesce() (in module dae.utils.regions) cod2aa() (dae.effect_annotation.annotation_request.BaseAnnotationRequest method) (dae.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) code_type (users_api.views.BasePasswordView attribute), [1] (users_api.views.ResetPassword attribute), [1] (users_api.views.SetPassword attribute), [1] coding_bins (dae.query_variants.sql.schema2.sql_query_builder.QueryHeuristics attribute) coding_bins() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) CodingEffectChecker (class in dae.effect_annotation.effect_checkers.coding) CodonsAa (dae.effect_annotation.gene_codes.NuclearCode attribute) CodonsAaKeys (dae.effect_annotation.gene_codes.NuclearCode attribute) coercers (dae.configuration.gpf_config_parser.GPFConfigValidator attribute) collapse() (in module dae.utils.regions) collapse_no_chrom() (in module dae.utils.regions) collect_all_resources() (dae.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) collect_cds_regions() (in module dae.genomic_resources.gene_models.serialization) collect_denovo_events() (dae.enrichment_tool.genotype_helper.GenotypeHelper static method) collect_directory_configs() (dae.configuration.gpf_config_parser.GPFConfigParser class method) collect_dvc_entries() (in module dae.genomic_resources.cli) collect_expectations() (dae.tools.gpf_validation_runner.MainRunner static method) collect_families() (common_reports_api.views.FamiliesDataDownloadView class method) collect_genotype_data_backgrounds() (dae.enrichment_tool.enrichment_helper.EnrichmentHelper method) collect_gtf_cds_regions() (in module dae.genomic_resources.gene_models.serialization) collect_gtf_start_codon_regions() (in module dae.genomic_resources.gene_models.serialization) collect_gtf_stop_codon_regions() (in module dae.genomic_resources.gene_models.serialization) collect_instruments() (in module dae.pheno.pheno_import) collect_pedigree_parquet_schema() (in module dae.parquet.parquet_writer) collect_person_collection_attributes() (dae.person_sets.person_sets.PersonSetCollection method) (dae.person_sets.PersonSetCollection method) collect_resource_entries() (dae.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) collect_variant_counts() (in module dae.gene_profile.generate_gene_profile) CollectionConfigsView (class in person_sets_api.views) CollectionDomainView (class in person_sets_api.views) collections_descriptions (dae.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb property) (dae.gene_sets.gene_sets_db.GeneSetsDb property) CollectionStatsView (class in person_sets_api.views) color (dae.person_sets.person_sets.PersonSetConfig attribute) (dae.person_sets.PersonSetConfig attribute) column_counts() (in module dae.pheno.graphs) column_name (dae.common_reports.denovo_report.EffectCell property) combine() (dae.pedigrees.families_data.FamiliesData static method) (dae.person_sets.person_sets.PersonSetCollection static method) (dae.person_sets.PersonSetCollection static method) (dae.variants.variant.VariantDesc static method) (in module dae.annotation.annotate_columns) (in module dae.annotation.annotate_vcf) Command (class in users_api.management.commands.dataset_groups) (class in users_api.management.commands.datasets_export) (class in users_api.management.commands.datasets_restore) (class in users_api.management.commands.datasets_show) (class in users_api.management.commands.groups_cleanup) (class in users_api.management.commands.unlock_user) (class in users_api.management.commands.user_create) (class in users_api.management.commands.user_set_name) (class in users_api.management.commands.user_setpasswd) (class in users_api.management.commands.users_add) (class in users_api.management.commands.users_export) (class in users_api.management.commands.users_group_add) (class in users_api.management.commands.users_group_remove) (class in users_api.management.commands.users_remove) (class in users_api.management.commands.users_restore) (class in users_api.management.commands.users_show) common_reports_api module common_reports_api.urls module common_reports_api.views module CommonReport (class in dae.common_reports.common_report) complement() (dae.effect_annotation.annotation_request.NegativeStrandAnnotationRequest static method) (in module dae.utils.variant_utils) COMPLEX (dae.annotation.annotatable.Annotatable.Type attribute) complex (dae.variants.core.Allele.Type attribute) compute_md5_sum() (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) COMPUTED (dae.task_graph.cache.CacheRecordType attribute) ConcatAggregator (class in dae.genomic_resources.aggregators) config_columns (studies.study_wrapper.StudyWrapper property) config_json() (dae.person_sets.person_sets.PersonSetCollection method) (dae.person_sets.PersonSetCollection method) ConfigDumper (class in dae.configuration.study_config_builder) ConfigurationView (class in gene_profiles_api.views) configure_argument_parser() (in module dae.annotation.annotate_doc) configure_task_logging() (in module dae.task_graph.logging) ConfigView (class in gene_view.views) confirm_login_allowed() (users_api.forms.WdaeLoginForm method) connect() (dae.duckdb_storage.duckdb_connection_factory.DuckDbConnectionFactory method) (dae.duckdb_storage.duckdb_genotype_storage.AbstractDuckDbStorage method) (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) connected_component() (in module dae.utils.regions) connected_components() (dae.pedigrees.pedigrees.FamilyConnections method) construct_import_annotation_pipeline() (in module dae.import_tools.import_tools) construct_import_annotation_pipeline_config() (in module dae.import_tools.import_tools) containing_path() (in module dae.utils.fs_utils) contains() (dae.genomic_resources.gene_models.Exon method) (dae.genomic_resources.gene_models.gene_models.Exon method) (dae.genomic_resources.genomic_position_table.line.LineBuffer method) (dae.genomic_resources.genomic_position_table.LineBuffer method) (dae.utils.regions.Region method) ContainsNode (class in dae.query_variants.attributes_query) ContainsNode() (dae.query_variants.attributes_query.QueryTreeToBitwiseLambdaTransformer method) (dae.query_variants.attributes_query.QueryTreeToLambdaTransformer method) (dae.query_variants.attributes_query.QueryTreeToSQLBitwiseTransformer method) CONTENT_ID (gpf_instance.views.AboutDescriptionView attribute) (gpf_instance.views.DescriptionView attribute) (gpf_instance.views.MarkdownFileView attribute) context_builder() (dae.annotation.context.CLIAnnotationContext static method) (dae.genomic_resources.genomic_context.CLIGenomicContext static method) (dae.genomic_resources.genomic_context.DefaultRepositoryContextProvider static method) (dae.gpf_instance_plugin.gpf_instance_context_plugin.GPFInstanceGenomicContextProvider static method) continuous (dae.pheno.common.InferenceConfig attribute) (dae.pheno.common.MeasureType attribute) ContinuousParquetFileWriter (class in dae.parquet.schema2.parquet_io) CONTROL (dae.pedigrees.family.FamilyTag attribute) convert() (in module utils.streaming_response_util) convert_coordinate() (dae.genomic_resources.liftover_chain.LiftoverChain method) convert_size() (in module dae.utils.helpers) convert_to_numeric() (in module dae.pheno.prepare.measure_classifier) convert_to_string() (in module dae.pheno.prepare.measure_classifier) convert_to_tab_separated() (in module dae.genomic_resources.testing) (in module dae.testing) Convertible (class in dae.pheno.prepare.measure_classifier) copy() (dae.pedigrees.families_data.FamiliesData method) (dae.pedigrees.pedigrees.Realization method) (in module dae.utils.fs_utils) copy_annotation_pipeline() (in module dae.annotation.annotation_factory) copy_graph() (in module dae.pedigrees.pedigrees) copy_proto_genomic_resources() (in module dae.genomic_resources.testing) copy_reannotation_pipeline() (in module dae.annotation.annotation_factory) copy_resource() (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) copy_resource_file() (dae.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) count (dae.gene_sets.gene_sets_db.GeneSet attribute) count_measure_ids() (pheno_browser_api.views.PhenoMeasuresDownload method) count_measures() (dae.pheno.db.PhenoDb method) (dae.pheno.pheno_data.PhenotypeData method) (dae.pheno.pheno_data.PhenotypeGroup method) (dae.pheno.pheno_data.PhenotypeStudy method) count_variant() (dae.common_reports.denovo_report.EffectCell method) (dae.common_reports.denovo_report.EffectRow method) (in module dae.gene_profile.generate_gene_profile) counter() (dae.tools.gpf_validation_runner.AbstractRunner method) (dae.tools.gpf_validation_runner.MainRunner method) CounterBase (class in dae.enrichment_tool.event_counters) CountError CreatableSlugRelatedField (class in users_api.serializers), [1] create() (dae.task_graph.cache.TaskCache static method) (groups_api.serializers.GroupCreateSerializer method) (users_api.models.BaseVerificationCode class method), [1] (users_api.models.WdaeUserManager method), [1] (users_api.serializers.DatasetSerializer method), [1] (users_api.serializers.UserSerializer method), [1] (users_api.views.UserViewSet method), [1] create_aggregator() (in module dae.genomic_resources.aggregators) create_aggregator_definition() (in module dae.genomic_resources.aggregators) create_annotation_request() (dae.effect_annotation.annotator.AnnotationRequestFactory static method) create_background() (dae.enrichment_tool.enrichment_helper.EnrichmentHelper method) create_counter() (dae.enrichment_tool.enrichment_helper.EnrichmentHelper method) create_database_connection() (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) (in module dae.duckdb_storage.duckdb_storage_helpers) create_denovo_gene_set_spec() (in module dae.gene_sets.denovo_gene_sets_config) create_df() (dae.pheno_tool.tool.PhenoTool method) create_duckdb_tables() (in module dae.duckdb_storage.duckdb_storage_helpers) create_effect() (dae.effect_annotation.effect.EffectFactory class method) (dae.effect_annotation.effect_checkers.frame_shift.FrameShiftEffectChecker method) (dae.effect_annotation.effect_checkers.promoter.PromoterEffectChecker method) (dae.effect_annotation.effect_checkers.utr.UTREffectChecker method) create_effect_details() (dae.effect_annotation.effect.AnnotationEffect method) create_effect_with_aa_change() (dae.effect_annotation.effect.EffectFactory class method) create_effect_with_prot_length() (dae.effect_annotation.effect.EffectFactory class method) create_effect_with_prot_pos() (dae.effect_annotation.effect.EffectFactory class method) create_effect_with_request() (dae.effect_annotation.effect.EffectFactory class method) create_effect_with_tm() (dae.effect_annotation.effect.EffectFactory class method) create_empty_collection() (dae.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection static method) create_executor() (dae.task_graph.cli_tools.TaskGraphCli static method) create_import_tasks() (in module dae.pheno.pheno_import) create_intronic_effect() (dae.effect_annotation.effect.EffectFactory class method) create_intronic_non_coding_effect() (dae.effect_annotation.effect.EffectFactory class method) create_memory_connection() (in module dae.duckdb_storage.duckdb_storage_helpers) create_negative_strand_effect() (dae.effect_annotation.effect_checkers.promoter.PromoterEffectChecker method) create_parquet_scans_layout_from_layout() (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage static method) create_parquet_scans_layout_relative() (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) create_positive_strand_effect() (dae.effect_annotation.effect_checkers.promoter.PromoterEffectChecker method) create_reference_allele() (dae.variants.variant.SummaryAllele static method) create_regions_from_genes() (in module dae.genomic_resources.gene_models) (in module dae.genomic_resources.gene_models.gene_models) create_relative_parquet_scans_layout() (in module dae.duckdb_storage.duckdb_storage_helpers) create_s3_attach_db_clause() (in module dae.duckdb_storage.duckdb_storage_helpers) create_s3_filesystem() (in module dae.duckdb_storage.duckdb_storage_helpers) create_s3_secret_clause() (in module dae.duckdb_storage.duckdb_storage_helpers) create_sandwich_instance() (dae.pedigrees.pedigrees.FamilyConnections method) create_schema2_dataset_layout() (in module dae.schema2_storage.schema2_layout) create_study_parquet_tables_layout() (in module dae.duckdb_storage.duckdb_storage_helpers) create_superuser() (users_api.models.WdaeUserManager method), [1] create_table() (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) create_table_layout() (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage static method) (in module dae.duckdb_storage.duckdb_storage_helpers) create_table_partitioned() (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) create_tables() (in module dae.pheno.pheno_import) create_task() (dae.task_graph.graph.TaskGraph method) create_user() (users_api.models.WdaeUserManager method), [1] create_utr_effect() (dae.effect_annotation.effect_checkers.utr.UTREffectChecker method) created_at (users_api.models.BaseVerificationCode attribute), [1] (users_api.models.ResetPasswordCode attribute), [1] (users_api.models.SetPasswordCode attribute), [1] CriteriaFilter (class in dae.person_filters.person_filters) criterias (dae.gene_sets.denovo_gene_sets_config.DGSSpec attribute) cshl2cnv_variant() (in module dae.utils.cnv_utils) cshl2vcf_variant() (in module dae.utils.dae_utils) cshl_format() (in module dae.variants.variant) cshl_location (dae.variants.variant.SummaryAllele property) (dae.variants.variant.SummaryVariant property) cshl_position (dae.variants.variant.SummaryAllele property) cshl_variant (dae.variants.variant.SummaryAllele property) (dae.variants.variant.SummaryVariant property) cshl_variant_full (dae.variants.variant.SummaryAllele property) (dae.variants.variant.SummaryVariant property) CSHLAlleleRecordToAnnotatable (class in dae.annotation.record_to_annotatable) csrf_clear() (in module users_api.models), [1] csv_value_iterator() (pheno_browser_api.views.PhenoMeasuresDownload method) current_idx (dae.variants_loaders.parquet.loader.MultiReader property) (dae.variants_loaders.parquet.loader.Reader property) curve_p0() (dae.pedigrees.layout.Line method) curve_p1() (dae.pedigrees.layout.Line method) curve_p2() (dae.pedigrees.layout.Line method) curve_p3() (dae.pedigrees.layout.Line method) curve_y_at() (dae.pedigrees.layout.Line method) curved (dae.pedigrees.layout.Line property) CustomFormatter (class in wdae.default_settings)

D

dad (dae.variants.attributes.Role attribute) dae module dae (dae.testing.import_helpers.StudyInputLayout attribute) (dae.testing.StudyInputLayout attribute) dae.annotation module dae.annotation.annotatable module dae.annotation.annotate_columns module dae.annotation.annotate_doc module dae.annotation.annotate_schema2_parquet module dae.annotation.annotate_utils module dae.annotation.annotate_vcf module dae.annotation.annotation_config module dae.annotation.annotation_factory module dae.annotation.annotation_pipeline module dae.annotation.annotator_base module dae.annotation.cnv_collection_annotator module dae.annotation.context module dae.annotation.debug_annotator module dae.annotation.effect_annotator module dae.annotation.gene_score_annotator module dae.annotation.gene_set_annotator module dae.annotation.liftover_annotator module dae.annotation.normalize_allele_annotator module dae.annotation.parquet module dae.annotation.reannotate_instance module dae.annotation.record_to_annotatable module dae.annotation.score_annotator module dae.annotation.simple_effect_annotator module dae.common_reports module dae.common_reports.common_report module dae.common_reports.denovo_report module dae.common_reports.family_counter module dae.common_reports.family_report module dae.common_reports.generate_common_report module dae.common_reports.people_counter module dae.configuration module dae.configuration.gpf_config_parser module dae.configuration.schemas module dae.configuration.schemas.dae_conf module dae.configuration.schemas.gene_profile module dae.configuration.schemas.gene_weights_db module dae.configuration.schemas.import_config module dae.configuration.schemas.person_sets module dae.configuration.schemas.phenotype_data module dae.configuration.schemas.study_config module dae.configuration.study_config_builder module dae.configuration.utils module dae.conftest module dae.dask module dae.dask.config module dae.dask.named_cluster module dae.duckdb_storage module dae.duckdb_storage.duckdb2_variants module dae.duckdb_storage.duckdb_connection_factory module dae.duckdb_storage.duckdb_genotype_storage module dae.duckdb_storage.duckdb_import_storage module dae.duckdb_storage.duckdb_legacy_genotype_storage module dae.duckdb_storage.duckdb_storage_config module dae.duckdb_storage.duckdb_storage_helpers module dae.duckdb_storage.duckdb_variants module dae.effect_annotation module dae.effect_annotation.annotation_effects module dae.effect_annotation.annotation_request module dae.effect_annotation.annotator module dae.effect_annotation.cli module dae.effect_annotation.effect module dae.effect_annotation.effect_checkers module dae.effect_annotation.effect_checkers.coding module dae.effect_annotation.effect_checkers.effect_checker module dae.effect_annotation.effect_checkers.frame_shift module dae.effect_annotation.effect_checkers.intron module dae.effect_annotation.effect_checkers.promoter module dae.effect_annotation.effect_checkers.protein_change module dae.effect_annotation.effect_checkers.splice_site module dae.effect_annotation.effect_checkers.start_loss module dae.effect_annotation.effect_checkers.stop_loss module dae.effect_annotation.effect_checkers.utr module dae.effect_annotation.gene_codes module dae.effect_annotation.variant module dae.enrichment_tool module dae.enrichment_tool.base_enrichment_background module dae.enrichment_tool.build_coding_length_enrichment_background module dae.enrichment_tool.build_ur_synonymous_enrichment_background module dae.enrichment_tool.enrichment_builder module dae.enrichment_tool.enrichment_cache_builder module dae.enrichment_tool.enrichment_helper module dae.enrichment_tool.enrichment_serializer module dae.enrichment_tool.event_counters module dae.enrichment_tool.gene_weights_background module dae.enrichment_tool.genotype_helper module dae.enrichment_tool.resource_implementations module dae.enrichment_tool.resource_implementations.enrichment_resource_impl module dae.enrichment_tool.samocha_background module dae.gene_profile module dae.gene_profile.db module dae.gene_profile.exporter module dae.gene_profile.generate_gene_profile module dae.gene_profile.statistic module dae.gene_scores module dae.gene_scores.gene_scores module dae.gene_scores.implementations module dae.gene_scores.implementations.gene_scores_impl module dae.gene_sets module dae.gene_sets.denovo_gene_set_collection module dae.gene_sets.denovo_gene_set_helpers module dae.gene_sets.denovo_gene_sets_config module dae.gene_sets.denovo_gene_sets_db module dae.gene_sets.gene_sets_db module dae.gene_sets.gene_term module dae.gene_sets.generate_denovo_gene_sets module dae.genomic_resources module dae.genomic_resources.aggregators module dae.genomic_resources.cached_repository module dae.genomic_resources.cli module dae.genomic_resources.cnv_collection module dae.genomic_resources.draw_score_histograms module dae.genomic_resources.fsspec_protocol module dae.genomic_resources.gene_models module dae.genomic_resources.gene_models.gene_models module dae.genomic_resources.gene_models.parsing module dae.genomic_resources.gene_models.serialization module dae.genomic_resources.genomic_context module dae.genomic_resources.genomic_position_table module dae.genomic_resources.genomic_position_table.line module dae.genomic_resources.genomic_position_table.table module dae.genomic_resources.genomic_position_table.table_bigwig module dae.genomic_resources.genomic_position_table.table_inmemory module dae.genomic_resources.genomic_position_table.table_tabix module dae.genomic_resources.genomic_position_table.table_vcf module dae.genomic_resources.genomic_position_table.utils module dae.genomic_resources.genomic_scores module dae.genomic_resources.group_repository module dae.genomic_resources.histogram module dae.genomic_resources.implementations module dae.genomic_resources.implementations.annotation_pipeline_impl module dae.genomic_resources.implementations.gene_models_impl module dae.genomic_resources.implementations.genomic_scores_impl module dae.genomic_resources.implementations.liftover_chain_impl module dae.genomic_resources.implementations.reference_genome_impl module dae.genomic_resources.liftover_chain module dae.genomic_resources.reference_genome module dae.genomic_resources.repository module dae.genomic_resources.repository_factory module dae.genomic_resources.resource_implementation module dae.genomic_resources.statistics module dae.genomic_resources.statistics.base_statistic module dae.genomic_resources.statistics.min_max module dae.genomic_resources.testing module dae.genomic_resources.variant_utils module dae.genomic_scores module dae.genomic_scores.scores module dae.genotype_storage module dae.genotype_storage.genotype_storage module dae.genotype_storage.genotype_storage_registry module dae.gpf_instance module dae.gpf_instance.gpf_instance module dae.gpf_instance_plugin module dae.gpf_instance_plugin.gpf_instance_context_plugin module dae.import_tools module dae.import_tools.cli module dae.import_tools.import_tools module dae.inmemory_storage module dae.inmemory_storage.inmemory_genotype_storage module dae.inmemory_storage.inmemory_import_storage module dae.inmemory_storage.raw_variants module dae.parquet module dae.parquet.helpers module dae.parquet.parquet_writer module dae.parquet.partition_descriptor module dae.parquet.schema2 module dae.parquet.schema2.parquet_io module dae.parquet.schema2.serializers module dae.parquet.schema2.variant_serializers module dae.parquet_storage module dae.parquet_storage.storage module dae.pedigrees module dae.pedigrees.drawing module dae.pedigrees.families_data module dae.pedigrees.family module dae.pedigrees.family_role_builder module dae.pedigrees.family_tag_builder module dae.pedigrees.generate_families_cache module dae.pedigrees.layout module dae.pedigrees.loader module dae.pedigrees.pedigrees module dae.pedigrees.testing module dae.person_filters module dae.person_filters.person_filters module dae.person_sets module dae.person_sets.person_sets module dae.pheno module dae.pheno.common module dae.pheno.db module dae.pheno.graphs module dae.pheno.pheno_data module dae.pheno.pheno_import module dae.pheno.prepare module dae.pheno.prepare.measure_classifier module dae.pheno.prepare_data module dae.pheno.registry module dae.pheno.utils module dae.pheno.utils.commons module dae.pheno.utils.lin_regress module dae.pheno_tool module dae.pheno_tool.pheno_tool_adapter module dae.pheno_tool.tool module

dae.query_variants module dae.query_variants.attributes_query module dae.query_variants.attributes_query_inheritance module dae.query_variants.base_query_variants module dae.query_variants.query_runners module dae.query_variants.sql module dae.query_variants.sql.schema2 module dae.query_variants.sql.schema2.base_query_builder module dae.query_variants.sql.schema2.base_variants module dae.query_variants.sql.schema2.family_builder module dae.query_variants.sql.schema2.sql_query_builder module dae.query_variants.sql.schema2.summary_builder module dae.schema2_storage module dae.schema2_storage.schema2_import_storage module dae.schema2_storage.schema2_layout module dae.studies module dae.studies.dataset_helpers module dae.studies.study module dae.studies.variants_db module dae.task_graph module dae.task_graph.cache module dae.task_graph.cli_tools module dae.task_graph.demo_graphs_cli module dae.task_graph.executor module dae.task_graph.graph module dae.task_graph.logging module dae.testing module dae.testing.acgt_import module dae.testing.alla_import module dae.testing.foobar_import module dae.testing.import_helpers module dae.testing.setup_helpers module dae.testing.t4c8_import module dae.tools module dae.tools.annotate_variants module dae.tools.cnv_liftover module dae.tools.cshl2vcf module dae.tools.dae_liftover module dae.tools.denovo_liftover module dae.tools.draw_pedigree module dae.tools.gpf_convert_study_config module dae.tools.gpf_instance_adjustments module dae.tools.gpf_validation_runner module dae.tools.grr_cache_repo module dae.tools.ped2ped module dae.tools.phase module dae.tools.simple_family2pedigree module dae.tools.simple_study_import module dae.tools.stats_liftover module dae.tools.to_gpf_gene_models_format module dae.tools.vcf_liftover module dae.tools.vcfinfo_extractor module dae.utils module dae.utils.cnv_utils module dae.utils.dae_utils module dae.utils.debug_closing module dae.utils.dict_utils module dae.utils.filehash module dae.utils.fixtures module dae.utils.fs_utils module dae.utils.helpers module dae.utils.progress module dae.utils.regions module dae.utils.sql_utils module dae.utils.statistics module dae.utils.variant_utils module dae.utils.verbosity_configuration module dae.variants module dae.variants.attributes module dae.variants.core module dae.variants.family_variant module dae.variants.variant module dae.variants_loaders module dae.variants_loaders.cnv module dae.variants_loaders.cnv.flexible_cnv_loader module dae.variants_loaders.cnv.loader module dae.variants_loaders.dae module dae.variants_loaders.dae.loader module dae.variants_loaders.parquet module dae.variants_loaders.parquet.loader module dae.variants_loaders.raw module dae.variants_loaders.raw.flexible_variant_loader module dae.variants_loaders.raw.loader module dae.variants_loaders.vcf module dae.variants_loaders.vcf.loader module dae2vcf_variant() (in module dae.utils.dae_utils) dae_import() (in module dae.testing.import_helpers) dae_study() (in module dae.testing.import_helpers) DaeTransmittedFamiliesGenotypes (class in dae.variants_loaders.dae.loader) DaeTransmittedLoader (class in dae.variants_loaders.dae.loader) dangling() (dae.pedigrees.pedigrees.Realization method) dangling_set() (dae.pedigrees.pedigrees.Realization method) DaskExecutor (class in dae.task_graph.executor) data (query_state_save.models.QueryState attribute) (users_api.models.GpUserState attribute), [1] data_reset() (dae.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) Dataset (class in datasets_api.models) Dataset.DoesNotExist Dataset.MultipleObjectsReturned dataset_family_partition() (dae.parquet.partition_descriptor.PartitionDescriptor method) dataset_id (datasets_api.models.Dataset attribute) dataset_name (datasets_api.models.Dataset attribute) dataset_summary_partition() (dae.parquet.partition_descriptor.PartitionDescriptor method) DatasetAccessRightsView (class in query_base.query_base) DatasetBaseMixin (class in users_api.management.commands.dataset_mixin) DatasetConfigView (class in datasets_api.views) DatasetDescriptionView (class in datasets_api.views) DatasetDetailsView (class in datasets_api.views) DatasetHelpers (class in dae.studies.dataset_helpers) DatasetHierarchy (class in datasets_api.models) DatasetHierarchy.DoesNotExist DatasetHierarchy.MultipleObjectsReturned DatasetHierarchyView (class in datasets_api.views) DatasetPedigreeView (class in datasets_api.views) DatasetPermissionsSingleView (class in datasets_api.views) DatasetPermissionsView (class in datasets_api.views) datasets_api module datasets_api.migrations module datasets_api.migrations.0001_initial module datasets_api.migrations.0002_dataset_groups module datasets_api.migrations.0003_alter_dataset_options module datasets_api.migrations.0004_dataset_broken module datasets_api.migrations.0005_dataset_dataset_name module datasets_api.migrations.0006_datasethierarchy module datasets_api.migrations.0007_datasethierarchy_direct module datasets_api.migrations.0008_datasethierarchy_instance_id module datasets_api.models module datasets_api.permissions module datasets_api.urls module datasets_api.views module DatasetSerializer (class in users_api.serializers), [1] DatasetView (class in datasets_api.views) date_joined (users_api.models.WdaeUser attribute), [1] db (dae.duckdb_storage.duckdb_storage_config.DuckDbConf attribute) (dae.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (dae.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute) Db2Layout (class in dae.query_variants.sql.schema2.sql_query_builder) db_filename (dae.pheno.common.ImportConfig attribute) dd() (in module dae.gene_sets.gene_term) deauthenticate() (users_api.models.WdaeUser method), [1] declared_fields (users_api.forms.WdaeLoginForm attribute) (users_api.forms.WdaePasswordForgottenForm attribute) (users_api.forms.WdaeRegisterPasswordForm attribute) (users_api.forms.WdaeResetPasswordForm attribute) decorate() (dae.annotation.annotation_pipeline.InputAnnotableAnnotatorDecorator static method) (dae.annotation.annotation_pipeline.ValueTransformAnnotatorDecorator static method) (dae.variants_loaders.raw.loader.StoredAnnotationDecorator static method) default (dae.person_sets.person_sets.PersonSetCollectionConfig attribute) (dae.person_sets.PersonSetCollectionConfig attribute) DEFAULT_AGGREGATOR_TYPE (dae.annotation.gene_score_annotator.GeneScoreAnnotator attribute) DEFAULT_COMPRESSION (dae.parquet.schema2.parquet_io.ContinuousParquetFileWriter attribute) default_config() (dae.genomic_resources.histogram.CategoricalHistogramConfig static method) (dae.genomic_resources.histogram.NullHistogramConfig static method) (dae.genomic_resources.histogram.NumberHistogramConfig static method) (in module dae.pheno.common) default_groups (datasets_api.models.Dataset property) default_inference (dae.pheno.common.ImportConfig attribute) default_setters (dae.configuration.gpf_config_parser.GPFConfigValidator attribute) DefaultBox (class in dae.configuration.gpf_config_parser) DefaultGeneModelsId (class in genomes_api.views) DefaultGenotypeStorage (class in dae.tools.gpf_instance_adjustments) DefaultRepositoryContextProvider (class in dae.genomic_resources.genomic_context) definition (dae.genomic_resources.repository.GenomicResourceRepo property) degree() (dae.pedigrees.pedigrees.Realization method) del_loader_prefix() (dae.import_tools.import_tools.ImportProject static method) delete() (users_api.views.FederationCredentials method), [1] delete_resource_file() (dae.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) denovo (dae.testing.import_helpers.StudyInputLayout attribute) (dae.testing.StudyInputLayout attribute) (dae.variants.attributes.Inheritance attribute) (dae.variants.attributes.TransmissionType attribute) denovo() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) denovo_gene_set_cache_file() (dae.gene_sets.denovo_gene_set_helpers.DenovoGeneSetHelpers static method) denovo_gene_sets_db (dae.gpf_instance.gpf_instance.GPFInstance property) (dae.gpf_instance.GPFInstance property) denovo_gene_sets_types (dae.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb property) denovo_import() (in module dae.testing) (in module dae.testing.import_helpers) denovo_study() (in module dae.testing) (in module dae.testing.import_helpers) DenovoFamiliesGenotypes (class in dae.variants_loaders.dae.loader) DenovoGeneSetCollection (class in dae.gene_sets.denovo_gene_set_collection) DenovoGeneSetHelpers (class in dae.gene_sets.denovo_gene_set_helpers) DenovoGeneSetsConfig (class in dae.gene_sets.denovo_gene_sets_config) DenovoGeneSetsDb (class in dae.gene_sets.denovo_gene_sets_db) DenovoGeneSetsTypesView (class in gene_sets.views) DenovoLoader (class in dae.variants_loaders.dae.loader) DenovoReport (class in dae.common_reports.denovo_report) DenovoReportTable (class in dae.common_reports.denovo_report) dependencies (datasets_api.migrations.0001_initial.Migration attribute) (datasets_api.migrations.0002_dataset_groups.Migration attribute) (datasets_api.migrations.0003_alter_dataset_options.Migration attribute) (datasets_api.migrations.0004_dataset_broken.Migration attribute) (datasets_api.migrations.0005_dataset_dataset_name.Migration attribute) (datasets_api.migrations.0006_datasethierarchy.Migration attribute) (datasets_api.migrations.0007_datasethierarchy_direct.Migration attribute) (datasets_api.migrations.0008_datasethierarchy_instance_id.Migration attribute) (query_state_save.migrations.0001_initial.Migration attribute) (query_state_save.migrations.0002_auto_20190205_0736.Migration attribute) (user_queries.migrations.0001_initial.Migration attribute) (users_api.migrations.0001_initial.Migration attribute) (users_api.migrations.0002_auto_20190424_0751.Migration attribute) (users_api.migrations.0003_authenticationlog.Migration attribute) (users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more.Migration attribute) (users_api.migrations.0005_gpuserstate.Migration attribute) deps (dae.task_graph.graph.Task attribute) desc (dae.gene_scores.gene_scores.ScoreDef attribute) (dae.gene_sets.gene_sets_db.GeneSet attribute) (dae.genomic_resources.genomic_scores.ScoreDef attribute) descendant (datasets_api.models.Dataset attribute) (datasets_api.models.DatasetHierarchy attribute) descendant_id (datasets_api.models.DatasetHierarchy attribute) description (dae.annotation.annotation_config.AnnotationPreamble attribute) (dae.annotation.annotation_config.AttributeInfo attribute) (dae.annotation.annotation_config.RawPreamble attribute) (dae.gene_scores.gene_scores.ScoreDesc attribute) (dae.gene_sets.gene_term.GeneInfo attribute) (dae.genomic_resources.statistics.base_statistic.Statistic attribute) (dae.genomic_scores.scores.ScoreDesc attribute) (dae.studies.study.GenotypeData property) (groups_api.views.GroupsViewSet attribute) (studies.study_wrapper.StudyWrapperBase property) (user_queries.models.UserQuery attribute) (users_api.views.UserViewSet attribute), [1] DescriptionView (class in gpf_instance.views) deserialize() (dae.genomic_resources.histogram.CategoricalHistogram static method) (dae.genomic_resources.histogram.NullHistogram static method) (dae.genomic_resources.histogram.NumberHistogram static method) (dae.genomic_resources.implementations.gene_models_impl.GeneModelsStatistics static method) (dae.genomic_resources.implementations.reference_genome_impl.ChromosomeStatistic static method) (dae.genomic_resources.implementations.reference_genome_impl.GenomeStatistic static method) (dae.genomic_resources.statistics.base_statistic.Statistic static method) (dae.genomic_resources.statistics.min_max.MinMaxValue static method) deserialize_family_record() (dae.parquet.schema2.variant_serializers.JsonVariantsDataSerializer method) (dae.parquet.schema2.variant_serializers.VariantsDataSerializer method) deserialize_family_variant() (dae.query_variants.base_query_variants.QueryVariantsBase method) deserialize_summary_record() (dae.parquet.schema2.variant_serializers.JsonVariantsDataSerializer method) (dae.parquet.schema2.variant_serializers.VariantsDataSerializer method) deserialize_summary_variant() (dae.query_variants.base_query_variants.QueryVariantsBase method) destroy() (users_api.views.UserViewSet method), [1] detail (groups_api.views.GroupsViewSet attribute) (users_api.views.UserViewSet attribute), [1] details (dae.variants.family_variant.FamilyAllele property) (dae.variants.variant.SummaryAllele property) (dae.variants.variant.SummaryVariant property) DGSCQuery (class in dae.gene_sets.denovo_gene_sets_config) DGSSpec (class in dae.gene_sets.denovo_gene_sets_config) Dialect (class in dae.query_variants.sql.schema2.base_query_builder) DictAggregator (class in dae.genomic_resources.aggregators) diff() (dae.pedigrees.family.Person method) difference() (in module dae.utils.regions) direct (datasets_api.models.DatasetHierarchy attribute) disable_study_config() (dae.studies.dataset_helpers.DatasetHelpers method) display_name (dae.variants.attributes.Role property) display_values (dae.genomic_resources.histogram.CategoricalHistogram property) displayed_values_count (dae.genomic_resources.histogram.CategoricalHistogramConfig attribute) displayed_values_percent (dae.genomic_resources.histogram.CategoricalHistogramConfig attribute) DISTRIBUTION_CUTOFF (dae.pheno.prepare.measure_classifier.ClassifierReport attribute) do_annotate_variant() (dae.effect_annotation.annotator.EffectAnnotator method) do_measure_build() (dae.pheno.prepare_data.PreparePhenoBrowserBase class method) do_study_config() (dae.duckdb_storage.duckdb_import_storage.AbstractDuckDbImportStorage class method) documentation (dae.annotation.annotation_config.AnnotatorInfo attribute) (dae.annotation.annotation_config.AttributeInfo property) domain (dae.person_sets.person_sets.PersonSetCollectionConfig attribute) (dae.person_sets.PersonSetCollectionConfig attribute) (dae.pheno.pheno_data.Measure property) domain_json() (dae.person_sets.person_sets.PersonSetCollection method) (dae.person_sets.PersonSetCollection method) DOWNLOAD_LIMIT (gene_view.views.DownloadSummaryVariantsView attribute) DownloadSummaryVariantsView (class in gene_view.views) draw() (dae.pedigrees.drawing.OffsetLayoutDrawer method) draw_categorical_violin_distribution() (in module dae.pheno.graphs) draw_distribution() (in module dae.pheno.graphs) draw_families() (in module dae.tools.draw_pedigree) draw_families_report() (in module dae.tools.draw_pedigree) draw_linregres() (in module dae.pheno.graphs) draw_measure_violinplot() (in module dae.pheno.graphs) draw_ordinal_violin_distribution() (in module dae.pheno.graphs) draw_pedigree() (in module dae.tools.draw_pedigree) drop_gp_table() (dae.gene_profile.db.GeneProfileDB method) DuckDb2Runner (class in dae.duckdb_storage.duckdb2_variants) DuckDb2Variants (class in dae.duckdb_storage.duckdb2_variants) duckdb_connect() (in module dae.duckdb_storage.duckdb_legacy_genotype_storage) duckdb_parquet_storage_factory() (in module dae.duckdb_storage.duckdb_genotype_storage) duckdb_s3_parquet_storage_factory() (in module dae.duckdb_storage.duckdb_genotype_storage) duckdb_s3_storage_factory() (in module dae.duckdb_storage.duckdb_genotype_storage) duckdb_storage_factory() (in module dae.duckdb_storage.duckdb_genotype_storage) DuckDbBaseConf (class in dae.duckdb_storage.duckdb_storage_config) DuckDbConf (class in dae.duckdb_storage.duckdb_storage_config) DuckDbConnectionFactory (class in dae.duckdb_storage.duckdb_connection_factory) DuckDbImportStorage (class in dae.duckdb_storage.duckdb_import_storage) DuckDbLegacyImportStorage (class in dae.duckdb_storage.duckdb_import_storage) DuckDbLegacyStorage (class in dae.duckdb_storage.duckdb_legacy_genotype_storage) DuckDbParquetConf (class in dae.duckdb_storage.duckdb_storage_config) DuckDbParquetImportStorage (class in dae.duckdb_storage.duckdb_import_storage) DuckDbParquetStorage (class in dae.duckdb_storage.duckdb_genotype_storage) DuckDbQueryDialect (class in dae.duckdb_storage.duckdb_variants) DuckDbRunner (class in dae.duckdb_storage.duckdb_variants) DuckDbS3Conf (class in dae.duckdb_storage.duckdb_storage_config) DuckDbS3ImportStorage (class in dae.duckdb_storage.duckdb_import_storage) DuckDbS3ParquetConf (class in dae.duckdb_storage.duckdb_storage_config) DuckDbS3ParquetImportStorage (class in dae.duckdb_storage.duckdb_import_storage) DuckDbS3ParquetStorage (class in dae.duckdb_storage.duckdb_genotype_storage) DuckDbS3Storage (class in dae.duckdb_storage.duckdb_genotype_storage) DuckDbStorage (class in dae.duckdb_storage.duckdb_genotype_storage) DuckDbVariants (class in dae.duckdb_storage.duckdb_variants) dump_browser_variable() (dae.pheno.prepare_data.PreparePhenoBrowserBase method) dump_config() (in module dae.pheno.common)

E

effect (dae.enrichment_tool.genotype_helper.GeneEffect attribute) effect_gene_symbols (dae.variants.variant.SummaryAllele property) (dae.variants.variant.SummaryVariant property) effect_genes (dae.enrichment_tool.genotype_helper.AlleleEvent attribute) (dae.variants.variant.SummaryAllele property) EFFECT_GROUPS (dae.effect_annotation.effect.EffectTypesMixin attribute) effect_severity() (dae.effect_annotation.effect.AnnotationEffect class method) EFFECT_TYPES (dae.effect_annotation.effect.EffectTypesMixin attribute) effect_types (dae.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) (dae.variants.variant.SummaryAllele property) (dae.variants.variant.SummaryVariant property) effect_types() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) EFFECT_TYPES_MAPPING (dae.effect_annotation.effect.EffectTypesMixin attribute) EFFECT_TYPES_UI_NAMING (dae.effect_annotation.effect.EffectTypesMixin attribute) EffectAnnotationDecorator (class in dae.variants_loaders.raw.loader) EffectAnnotator (class in dae.effect_annotation.annotator) EffectAnnotatorAdapter (class in dae.annotation.effect_annotator) EffectAnnotatorBuilder (class in dae.effect_annotation.cli) EffectCell (class in dae.common_reports.denovo_report) EffectChecker (class in dae.effect_annotation.effect_checkers.effect_checker) EffectFactory (class in dae.effect_annotation.effect) EffectGene (class in dae.effect_annotation.effect) EffectRow (class in dae.common_reports.denovo_report) effects (dae.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (dae.gene_sets.denovo_gene_sets_config.EffectsCriteria attribute) (dae.variants.family_variant.FamilyAllele property) (dae.variants.variant.SummaryAllele property) (dae.variants.variant.SummaryVariant property) effects_description() (dae.effect_annotation.effect.AnnotationEffect class method) EffectsCriteria (class in dae.gene_sets.denovo_gene_sets_config) EffectTranscript (class in dae.effect_annotation.effect) EffectTypesMixin (class in dae.effect_annotation.effect) ElementOfNode (class in dae.query_variants.attributes_query) ElementOfNode() (dae.query_variants.attributes_query.QueryTreeToLambdaTransformer method) email (users_api.models.AuthenticationLog attribute), [1] (users_api.models.WdaeUser attribute), [1] email_user() (users_api.models.WdaeUser method), [1] enabled (dae.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) EnableDisableStudies (class in dae.tools.gpf_instance_adjustments) end (dae.gene_sets.denovo_gene_sets_config.RecurrencyCriteriaBase attribute) (dae.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute) (dae.gene_sets.denovo_gene_sets_config.SingleCriteria attribute) (dae.gene_sets.denovo_gene_sets_config.TripleCriteria attribute) (dae.utils.regions.BedRegion property) (dae.utils.regions.Region property) end_position (dae.annotation.annotatable.Annotatable property) (dae.variants.core.Allele property) (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) (dae.variants.variant.SummaryVariant property) endpoint_url (dae.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (dae.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute) enforce_csrf() (utils.authentication.SessionAuthenticationWithoutCSRF method) enforce_type (dae.genomic_resources.histogram.CategoricalHistogramConfig attribute) enrichment_api module

enrichment_api.urls module enrichment_api.views module enrichment_description() (enrichment_api.views.EnrichmentTestView method) EnrichmentBackgroundResourceImplementation (class in dae.enrichment_tool.resource_implementations.enrichment_resource_impl) EnrichmentBuilder (class in dae.enrichment_tool.enrichment_builder) EnrichmentHelper (class in dae.enrichment_tool.enrichment_helper) EnrichmentModelsView (class in enrichment_api.views) EnrichmentResult (class in dae.enrichment_tool.event_counters) EnrichmentSerializer (class in dae.enrichment_tool.enrichment_serializer) EnrichmentSingleResult (class in dae.enrichment_tool.event_counters) EnrichmentTestView (class in enrichment_api.views) ensure_log_dir() (in module dae.task_graph.logging) entries_to_delete (dae.genomic_resources.repository.ManifestUpdate attribute) entries_to_update (dae.genomic_resources.repository.ManifestUpdate attribute) ENUM_PROPERTIES (dae.parquet.schema2.serializers.AlleleParquetSerializer attribute) EqualsNode (class in dae.query_variants.attributes_query) EqualsNode() (dae.query_variants.attributes_query.QueryTreeToLambdaTransformer method) error (dae.task_graph.cache.CacheRecord property) ERROR (dae.task_graph.cache.CacheRecordType attribute) (dae.tools.gpf_validation_runner.TestStatus attribute) error_case_count (dae.tools.gpf_validation_runner.AbstractRunner property) error_messages (users_api.forms.WdaeLoginForm attribute) (users_api.forms.WdaeResetPasswordForm attribute) errors_case_count (dae.tools.gpf_validation_runner.MainRunner property) escape_char() (dae.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method) (dae.query_variants.sql.schema2.base_query_builder.Dialect static method) escape_quote_char() (dae.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method) (dae.query_variants.sql.schema2.base_query_builder.Dialect static method) event_counts() (dae.enrichment_tool.event_counters.CounterBase method) EventCountersResult (class in dae.enrichment_tool.event_counters) events() (dae.enrichment_tool.event_counters.CounterBase method) (dae.enrichment_tool.event_counters.EventsCounter method) (dae.enrichment_tool.event_counters.GeneEventsCounter method) EventsCounter (class in dae.enrichment_tool.event_counters) EventsResult (class in dae.enrichment_tool.event_counters) execute() (dae.task_graph.executor.AbstractTaskGraphExecutor method) (dae.task_graph.executor.TaskGraphExecutor method) (dae.tools.gpf_instance_adjustments.AdjustDuckDbStorageCommand method) (dae.tools.gpf_instance_adjustments.AdjustImpalaStorageCommand method) (dae.tools.gpf_instance_adjustments.AdjustmentsCommand method) (dae.tools.gpf_instance_adjustments.DefaultGenotypeStorage method) (dae.tools.gpf_instance_adjustments.EnableDisableStudies method) (dae.tools.gpf_instance_adjustments.InstanceIdCommand method) exists() (in module dae.utils.fs_utils) Exon (class in dae.genomic_resources.gene_models) (class in dae.genomic_resources.gene_models.gene_models) exon_to_dict() (genomes_api.views.GeneModels method) expand_effect_types() (in module dae.effect_annotation.effect) expand_gene_set() (in module utils.expand_gene_set) expand_gene_syms() (in module utils.expand_gene_set) ExportUsersBase (class in users_api.management.commands.export_base) Expression (class in dae.query_variants.attributes_query_inheritance) expression() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) extend() (dae.pedigrees.pedigrees.Realization method) extract_resource_ids_from_annotation() (in module dae.tools.grr_cache_repo)

F

F (dae.variants.attributes.Sex attribute) FAIL (dae.tools.gpf_validation_runner.TestStatus attribute) failed_attempt (users_api.models.AuthenticationLog attribute), [1] failed_case_count (dae.tools.gpf_validation_runner.AbstractRunner property) (dae.tools.gpf_validation_runner.MainRunner property) families (dae.parquet_storage.storage.ParquetLoaderVariants property) (dae.studies.study.GenotypeData property) (dae.studies.study.GenotypeDataGroup property) (dae.studies.study.GenotypeDataStudy property) (studies.response_transformer.ResponseTransformer property) (studies.study_wrapper.StudyWrapper property) families_of_persons() (dae.pedigrees.families_data.FamiliesData method) FamiliesData (class in dae.pedigrees.families_data) FamiliesDataDownloadView (class in common_reports_api.views) FamiliesGenotypes (class in dae.variants_loaders.raw.loader) FamiliesGroupCounters (class in dae.common_reports.family_counter) FamiliesLoader (class in dae.pedigrees.loader) FamiliesReport (class in dae.common_reports.family_report) Family (class in dae.pedigrees.family) family (dae.common_reports.family_counter.FamilyCounter property) (dae.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute) (dae.schema2_storage.schema2_layout.Schema2DatasetLayout attribute) FAMILY_ALLELE_BASE_SCHEMA (dae.parquet.schema2.serializers.AlleleParquetSerializer attribute) family_allele_indexes (dae.variants.family_variant.FamilyVariant property) family_alleles (dae.variants.family_variant.FamilyVariant property) family_alt_alleles (dae.variants.family_variant.FamilyVariant property) family_api module family_api.urls module family_api.views module family_attributes (dae.variants.family_variant.FamilyAllele property) family_base() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) family_best_state (dae.variants.family_variant.FamilyVariant property) family_bin (dae.pedigrees.family.Person property) family_bins (dae.query_variants.sql.schema2.sql_query_builder.QueryHeuristics attribute) family_bins() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) FAMILY_COLUMNS (dae.variants_loaders.parquet.loader.ParquetLoader attribute) family_genotype (dae.variants.family_variant.FamilyVariant property) family_genotype_iterator() (dae.variants_loaders.dae.loader.DaeTransmittedFamiliesGenotypes method) (dae.variants_loaders.dae.loader.DenovoFamiliesGenotypes method) (dae.variants_loaders.raw.loader.FamiliesGenotypes method) (dae.variants_loaders.vcf.loader.VcfFamiliesGenotypes method) family_id (dae.enrichment_tool.genotype_helper.VariantEvent attribute) (dae.variants.family_variant.FamilyDelegate property) family_ids() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) family_index (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) family_partition() (dae.parquet.partition_descriptor.PartitionDescriptor method) family_query() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) family_variant_filter_duplicate_function() (dae.inmemory_storage.raw_variants.RawFamilyVariants class method) family_variant_filter_function() (dae.inmemory_storage.raw_variants.RawFamilyVariants class method) family_variants() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) family_variants_iterator() (dae.inmemory_storage.raw_variants.RawFamilyVariants method) (dae.variants_loaders.raw.loader.VariantsLoader method) FamilyAllele (class in dae.variants.family_variant) FamilyConnections (class in dae.pedigrees.pedigrees) FamilyCounter (class in dae.common_reports.family_counter) FamilyCounterDownloadView (class in common_reports_api.views) FamilyCounterListView (class in common_reports_api.views) FamilyDelegate (class in dae.variants.family_variant) FamilyDetailsView (class in family_api.views) FamilyFilter (class in dae.person_filters) (class in dae.person_filters.person_filters) FamilyQueryBuilder (class in dae.query_variants.sql.schema2.family_builder) FamilyRoleBuilder (class in dae.pedigrees.family_role_builder) FamilyTag (class in dae.pedigrees.family) FamilyTagsBuilder (class in dae.pedigrees.family_tag_builder) FamilyVariant (class in dae.variants.family_variant) favicon() (in module gpfjs.views) fchrom (dae.genomic_resources.genomic_position_table.Line attribute) (dae.genomic_resources.genomic_position_table.line.Line attribute) (dae.genomic_resources.genomic_position_table.line.LineBase attribute) FederationCredentials (class in users_api.views), [1] female (dae.enrichment_tool.event_counters.EnrichmentResult attribute) (dae.enrichment_tool.event_counters.EventCountersResult attribute) (dae.enrichment_tool.event_counters.EventsResult attribute) (dae.enrichment_tool.event_counters.VariantEventsResult attribute) (dae.person_sets.ChildrenBySex attribute) (dae.person_sets.ChildrenStats attribute) (dae.person_sets.person_sets.ChildrenBySex attribute) (dae.person_sets.person_sets.ChildrenStats attribute) (dae.variants.attributes.Sex attribute) FEMALE_PRB (dae.pedigrees.family.FamilyTag attribute) females_count() (dae.pheno.graphs.GraphColumn method) fetch() (dae.genomic_resources.genomic_position_table.line.LineBuffer method) (dae.genomic_resources.genomic_position_table.LineBuffer method) (dae.genomic_resources.reference_genome.ReferenceGenome method) fetch_annotation() (dae.duckdb_storage.duckdb2_variants.DuckDb2Variants method) fetch_cnvs() (dae.genomic_resources.cnv_collection.CnvCollection method) fetch_family_variants() (dae.variants_loaders.parquet.loader.ParquetLoader method) fetch_region() (dae.genomic_resources.genomic_scores.NPScoreBase method) (dae.genomic_resources.genomic_scores.PositionScore method) fetch_scores() (dae.genomic_resources.genomic_scores.NPScoreBase method) (dae.genomic_resources.genomic_scores.PositionScore method) fetch_scores_agg() (dae.genomic_resources.genomic_scores.AlleleScore method) (dae.genomic_resources.genomic_scores.NPScore method) (dae.genomic_resources.genomic_scores.PositionScore method) fetch_summary_variants() (dae.variants_loaders.parquet.loader.ParquetLoader method) fetch_variants() (dae.variants_loaders.parquet.loader.ParquetLoader method) fgt2str() (in module dae.utils.variant_utils) fields (groups_api.serializers.GroupCreateSerializer.Meta attribute) (groups_api.serializers.GroupRetrieveSerializer.Meta attribute) (groups_api.serializers.GroupSerializer.Meta attribute) (query_state_save.serializers.QueryStateSerializer.Meta attribute) (users_api.serializers.UserSerializer.Meta attribute), [1] (users_api.serializers.UserWithoutEmailSerializer.Meta attribute), [1] figure_filepath() (dae.pheno.prepare_data.PreparePhenoBrowserBase class method) file_exists() (dae.genomic_resources.cached_repository.CachingProtocol method) (dae.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) filename (dae.enrichment_tool.base_enrichment_background.BaseEnrichmentResourceBackground property) (dae.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property) (dae.genomic_resources.repository.ResourceFileState attribute) files (dae.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation property) (dae.gene_scores.gene_scores.GeneScore property) (dae.gene_sets.gene_sets_db.GeneSetCollection property) (dae.genomic_resources.cnv_collection.CnvCollectionImplementation property) (dae.genomic_resources.implementations.annotation_pipeline_impl.AnnotationPipelineImplementation property) (dae.genomic_resources.implementations.gene_models_impl.GeneModelsImpl property) (dae.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation property) (dae.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeImplementation property) (dae.genomic_resources.liftover_chain.LiftoverChain property) (dae.genomic_resources.resource_implementation.GenomicResourceImplementation property) FileTaskCache (class in dae.task_graph.cache) filetype_parsers (dae.configuration.gpf_config_parser.GPFConfigParser attribute) fill_family_bins() (in module dae.parquet.parquet_writer) fill_query_parameters() (in module dae.utils.sql_utils) filter_allele() (dae.inmemory_storage.raw_variants.RawFamilyVariants class method) filter_backends (groups_api.views.GroupsViewSet attribute) (users_api.views.UserViewSet attribute), [1] filter_denovo_one_event_per_family() (in module dae.enrichment_tool.event_counters) filter_denovo_one_gene_per_events() (in module dae.enrichment_tool.event_counters) filter_denovo_one_gene_per_recurrent_events() (in module dae.enrichment_tool.event_counters) filter_family_variant() (dae.inmemory_storage.raw_variants.RawFamilyVariants class method)

filter_gene_effects() (dae.effect_annotation.effect.AnnotationEffect class method) (dae.inmemory_storage.raw_variants.RawFamilyVariants static method) filter_genes() (dae.gene_sets.gene_term.GeneTerms method) filter_overlapping_events() (in module dae.enrichment_tool.event_counters) filter_real_attr() (dae.inmemory_storage.raw_variants.RawFamilyVariants static method) filter_regions() (dae.inmemory_storage.raw_variants.RawFamilyVariants static method) FILTER_RENAMES_MAP (studies.query_transformer.QueryTransformer attribute) filter_summary_allele() (dae.inmemory_storage.raw_variants.RawFamilyVariants class method) filter_summary_variant() (dae.inmemory_storage.raw_variants.RawFamilyVariants class method) find_dataset_id_in_dict() (in module utils.datasets) find_dataset_id_in_request() (in module utils.datasets) find_directory_with_a_file() (in module dae.utils.fs_utils) find_exon_cds_region_for_gtf_cds_feature() (in module dae.genomic_resources.gene_models.serialization) find_genotype_data_config() (dae.studies.dataset_helpers.DatasetHelpers method) find_genotype_data_config_file() (dae.studies.dataset_helpers.DatasetHelpers method) find_index() (dae.genomic_resources.genomic_position_table.line.LineBuffer method) (dae.genomic_resources.genomic_position_table.LineBuffer method) find_instrument_values_tables() (dae.pheno.db.PhenoDb method) find_resource() (dae.genomic_resources.cached_repository.GenomicResourceCachedRepo method) (dae.genomic_resources.group_repository.GenomicResourceGroupRepo method) (dae.genomic_resources.repository.GenomicResourceProtocolRepo method) (dae.genomic_resources.repository.GenomicResourceRepo method) (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) finish() (dae.genomic_resources.implementations.reference_genome_impl.ChromosomeStatistic method) (dae.genomic_resources.implementations.reference_genome_impl.GenomeStatistic method) (dae.genomic_resources.statistics.base_statistic.Statistic method) fit() (dae.pheno.utils.lin_regress.LinearRegression method) flexible_cnv_loader() (in module dae.variants_loaders.cnv.flexible_cnv_loader) flexible_denovo_load() (dae.variants_loaders.dae.loader.DenovoLoader method) flexible_pedigree_read() (dae.pedigrees.loader.FamiliesLoader static method) flexible_variant_loader() (in module dae.variants_loaders.raw.flexible_variant_loader) float_type() (dae.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method) (dae.query_variants.sql.schema2.base_query_builder.Dialect static method) fmt_invert (wdae.default_settings.CustomFormatter attribute) fmt_normal (wdae.default_settings.CustomFormatter attribute) foobar_genes() (in module dae.testing.foobar_import) foobar_genome() (in module dae.testing.foobar_import) foobar_gpf() (in module dae.testing) (in module dae.testing.foobar_import) force_extend() (dae.pedigrees.pedigrees.Realization method) ForgotPassword (class in users_api.views), [1] form (users_api.views.BasePasswordView attribute), [1] (users_api.views.ResetPassword attribute), [1] (users_api.views.SetPassword attribute), [1] format() (wdae.default_settings.CustomFormatter method) FORMAT_DEF (dae.genomic_resources.genomic_position_table.table_inmemory.InmemoryGenomicPositionTable attribute) FORMATS (wdae.default_settings.CustomFormatter attribute) FrameShiftEffectChecker (class in dae.effect_annotation.effect_checkers.frame_shift) frequencies (dae.variants.variant.SummaryVariant property) frequency (dae.variants.variant.SummaryAllele property) frequency() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) frequency_bins (dae.query_variants.sql.schema2.sql_query_builder.QueryHeuristics attribute) frequency_bins() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) from_ (dae.person_sets.person_sets.SourceConfig attribute) (dae.person_sets.SourceConfig attribute) from_cnv() (dae.variants.variant.VariantDetails static method) from_dict() (dae.configuration.study_config_builder.TOMLDict static method) (dae.genomic_resources.histogram.CategoricalHistogram static method) (dae.genomic_resources.histogram.CategoricalHistogramConfig static method) (dae.genomic_resources.histogram.NullHistogram static method) (dae.genomic_resources.histogram.NullHistogramConfig static method) (dae.genomic_resources.histogram.NumberHistogram static method) (dae.genomic_resources.histogram.NumberHistogramConfig static method) from_effect_transcripts() (dae.effect_annotation.effect.EffectTranscript class method) from_effects() (dae.effect_annotation.effect.AlleleEffects class method) from_events_result() (dae.enrichment_tool.event_counters.EventCountersResult static method) from_families() (dae.common_reports.family_counter.FamiliesGroupCounters static method) (dae.pedigrees.families_data.FamiliesData static method) (dae.person_sets.person_sets.PersonSetCollection static method) (dae.person_sets.PersonSetCollection static method) from_families_data() (dae.common_reports.family_report.FamiliesReport static method) from_family() (dae.common_reports.family_counter.FamilyCounter static method) (dae.pedigrees.layout.Layout static method) (dae.pedigrees.pedigrees.FamilyConnections class method) from_family_layout() (dae.pedigrees.layout.Layout static method) from_family_persons() (dae.pedigrees.families_data.FamiliesData static method) from_file_content() (dae.genomic_resources.repository.Manifest static method) from_gene_effects() (dae.effect_annotation.effect.EffectGene class method) from_genotype_study() (dae.common_reports.denovo_report.DenovoReport static method) (dae.common_reports.family_report.FamiliesReport static method) from_json() (dae.genomic_scores.scores.ScoreDesc static method) (dae.person_sets.person_sets.PersonSet static method) (dae.person_sets.PersonSet static method) (dae.pheno.pheno_data.Measure class method) from_label() (dae.pedigrees.family.FamilyTag static method) from_list() (dae.configuration.study_config_builder.TOMLList static method) from_manifest_entries() (dae.genomic_resources.repository.Manifest static method) from_name() (dae.variants.attributes.Inheritance static method) (dae.variants.attributes.Role static method) (dae.variants.attributes.Sex static method) (dae.variants.attributes.Status static method) from_pedigree_df() (dae.pedigrees.families_data.FamiliesData static method) from_person_set() (dae.common_reports.people_counter.PeopleCounter static method) from_person_set_collection() (dae.common_reports.people_counter.PeopleCounters static method) from_person_set_collections() (dae.common_reports.people_counter.PeopleReport static method) from_persons() (dae.pedigrees.family.Family static method) from_record() (dae.pheno.pheno_data.Measure class method) from_records() (dae.pedigrees.family.Family static method) from_sets() (dae.pedigrees.pedigrees.SandwichInstance static method) from_simplified_effects() (dae.effect_annotation.effect.AlleleEffects class method) from_str() (dae.pheno.common.MeasureType static method) (dae.utils.regions.BedRegion static method) (dae.utils.regions.Region static method) from_string() (dae.annotation.annotatable.Annotatable static method) (dae.annotation.annotatable.Annotatable.Type static method) (dae.annotation.annotatable.CNVAllele static method) (dae.annotation.annotatable.Position static method) (dae.annotation.annotatable.Region static method) (dae.annotation.annotatable.VCFAllele static method) (dae.effect_annotation.effect.AlleleEffects static method) (dae.effect_annotation.effect.EffectGene static method) (dae.effect_annotation.effect.EffectTranscript static method) from_tuple() (dae.effect_annotation.effect.EffectGene class method) (dae.effect_annotation.effect.EffectTranscript class method) from_value() (dae.variants.attributes.Inheritance static method) (dae.variants.attributes.Role static method) (dae.variants.attributes.Sex static method) (dae.variants.attributes.Status static method) from_variants() (dae.common_reports.denovo_report.DenovoReportTable static method) from_vcf() (dae.variants.variant.VariantDetails static method) FrozenBox (class in dae.configuration.gpf_config_parser) FsspecHandler (class in dae.task_graph.logging) FsspecReadOnlyProtocol (class in dae.genomic_resources.fsspec_protocol) FsspecReadWriteProtocol (class in dae.genomic_resources.fsspec_protocol) full_members (dae.pedigrees.family.Family property) full_variants (dae.inmemory_storage.raw_variants.RawMemoryVariants property) full_variants_iterator() (dae.inmemory_storage.raw_variants.RawFamilyVariants method) (dae.inmemory_storage.raw_variants.RawMemoryVariants method) (dae.variants_loaders.cnv.loader.CNVLoader method) (dae.variants_loaders.dae.loader.DenovoLoader method) (dae.variants_loaders.raw.loader.AnnotationPipelineDecorator method) (dae.variants_loaders.raw.loader.EffectAnnotationDecorator method) (dae.variants_loaders.raw.loader.StoredAnnotationDecorator method) (dae.variants_loaders.raw.loader.VariantsGenotypesLoader method) (dae.variants_loaders.raw.loader.VariantsLoader method) FullReannotationPipeline (class in dae.annotation.annotation_pipeline) func (dae.task_graph.graph.Task attribute) fvuid (dae.enrichment_tool.genotype_helper.VariantEvent attribute) (dae.variants.family_variant.FamilyVariant property)

G

GAP (dae.pedigrees.drawing.OffsetLayoutDrawer attribute) gd2str() (in module dae.effect_annotation.effect) ge2str() (in module dae.effect_annotation.effect) gender_palette() (in module dae.pheno.graphs) gender_palette_light() (in module dae.pheno.graphs) gene (dae.enrichment_tool.genotype_helper.GeneEffect attribute) gene_effect_get_genes() (in module dae.effect_annotation.effect) gene_effect_get_genes_worst() (in module dae.effect_annotation.effect) gene_effect_get_worst_effect() (in module dae.effect_annotation.effect) gene_effects() (dae.effect_annotation.effect.AnnotationEffect class method) gene_id (dae.gene_sets.gene_term.GeneInfo attribute) gene_models (dae.gpf_instance.gpf_instance.GPFInstance property) (dae.gpf_instance.GPFInstance property) gene_models_by_gene_name() (dae.genomic_resources.gene_models.gene_models.GeneModels method) (dae.genomic_resources.gene_models.GeneModels method) gene_models_by_location() (dae.genomic_resources.gene_models.gene_models.GeneModels method) (dae.genomic_resources.gene_models.GeneModels method) gene_models_to_gtf() (in module dae.genomic_resources.gene_models) (in module dae.genomic_resources.gene_models.serialization) gene_names() (dae.genomic_resources.gene_models.gene_models.GeneModels method) (dae.genomic_resources.gene_models.GeneModels method) gene_number (dae.genomic_resources.implementations.gene_models_impl.StatisticsData attribute) gene_profiles_api module gene_profiles_api.table_views module gene_profiles_api.urls module gene_profiles_api.views module GENE_REGIONS_HEURISTIC_CUTOFF (dae.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute) (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase attribute) GENE_REGIONS_HEURISTIC_EXTEND (dae.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute) (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase attribute) gene_scores module gene_scores.urls module gene_scores.views module gene_scores_db (dae.gpf_instance.gpf_instance.GPFInstance property) (dae.gpf_instance.GPFInstance property) gene_set_id (dae.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (dae.gene_sets.denovo_gene_sets_config.DGSSpec attribute) gene_sets module gene_sets.urls module gene_sets.views module gene_sets_db (dae.gpf_instance.gpf_instance.GPFInstance property) (dae.gpf_instance.GPFInstance property) gene_sets_ids (dae.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) gene_sym (dae.gene_sets.gene_term.GeneInfo attribute) gene_view module gene_view.urls module gene_view.views module GeneEffect (class in dae.enrichment_tool.genotype_helper) GeneEventsCounter (class in dae.enrichment_tool.event_counters) GeneInfo (class in dae.gene_sets.gene_term) GeneModels (class in dae.genomic_resources.gene_models) (class in dae.genomic_resources.gene_models.gene_models) (class in genomes_api.views) GeneModelsImpl (class in dae.genomic_resources.implementations.gene_models_impl) GeneModelsStatistics (class in dae.genomic_resources.implementations.gene_models_impl) GeneProfileDB (class in dae.gene_profile.db) generate_columns() (pheno_tool_api.views.PhenoToolDownload method) generate_gp() (in module dae.gene_profile.generate_gene_profile) generate_import_task_graph() (dae.duckdb_storage.duckdb_import_storage.AbstractDuckDbImportStorage method) (dae.import_tools.import_tools.ImportStorage method) (dae.inmemory_storage.inmemory_import_storage.InmemoryImportStorage method) (dae.parquet_storage.storage.ParquetImportStorage method) (dae.schema2_storage.schema2_import_storage.Schema2ImportStorage method) generate_instrument_table_name() (in module dae.pheno.db) generate_phenotype_data_config() (in module dae.pheno.pheno_import) generate_reannotate_task_graph() (dae.schema2_storage.schema2_import_storage.Schema2ImportStorage static method) generate_variants() (gene_view.views.DownloadSummaryVariantsView method) generated (dae.pedigrees.family.Person property) generation_ranks() (dae.pedigrees.pedigrees.IndividualGroup method) genes (dae.gene_sets.gene_term.NCBIGeneInfo attribute) genes() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) genes_prob() (dae.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground method) (dae.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground method) genes_weight() (dae.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground method) (dae.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground method) GeneScore (class in dae.gene_scores.gene_scores) GeneScoreAnnotator (class in dae.annotation.gene_score_annotator) GeneScoreEnrichmentBackground (class in dae.enrichment_tool.gene_weights_background) GeneScoreImplementation (class in dae.gene_scores.implementations.gene_scores_impl) GeneScoresDb (class in dae.gene_scores.gene_scores) GeneScoresDownloadView (class in gene_scores.views) GeneScoresListView (class in gene_scores.views) GeneScoresPartitionsView (class in gene_scores.views) GeneSet (class in dae.gene_sets.gene_sets_db) GeneSetAnnotator (class in dae.annotation.gene_set_annotator) GeneSetCollection (class in dae.gene_sets.gene_sets_db) GeneSetDownloadView (class in gene_sets.views) GeneSetsCollectionsView (class in gene_sets.views) GeneSetsDb (class in dae.gene_sets.gene_sets_db) GeneSetsHasDenovoView (class in gene_sets.views) GeneSetsView (class in gene_sets.views) GeneSymbolsSearch (class in genomes_api.views) GeneSymbolsView (class in gene_profiles_api.table_views) GeneTerms (class in dae.gene_sets.gene_term) genetic_model (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) GeneticModel (class in dae.variants.attributes) GeneWeightsEnrichmentBackground (class in dae.enrichment_tool.gene_weights_background) genomes_api module genomes_api.urls module genomes_api.views module GenomeStatistic (class in dae.genomic_resources.implementations.reference_genome_impl) GenomeStatisticsMixin (class in dae.genomic_resources.implementations.reference_genome_impl) genomic_scores (dae.gpf_instance.gpf_instance.GPFInstance property) (dae.gpf_instance.GPFInstance property) genomic_scores_api module genomic_scores_api.urls module genomic_scores_api.views module GenomicContext (class in dae.genomic_resources.genomic_context) GenomicContextProvider (class in dae.genomic_resources.genomic_context) GenomicPositionTable (class in dae.genomic_resources.genomic_position_table.table) GenomicResource (class in dae.genomic_resources) (class in dae.genomic_resources.repository) GenomicResourceCachedRepo (class in dae.genomic_resources.cached_repository) GenomicResourceGroupRepo (class in dae.genomic_resources.group_repository) GenomicResourceImplementation (class in dae.genomic_resources.resource_implementation) GenomicResourceProtocolRepo (class in dae.genomic_resources.repository) GenomicResourceRepo (class in dae.genomic_resources.repository) GenomicScore (class in dae.genomic_resources.genomic_scores) GenomicScoreAnnotatorBase (class in dae.annotation.score_annotator) GenomicScoreDescsView (class in genomic_scores_api.views) GenomicScoreImplementation (class in dae.genomic_resources.implementations.genomic_scores_impl) GenomicScoresRegistry (class in dae.genomic_scores.scores) GenomicScoresView (class in genomic_scores_api.views) genotype (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) genotype_browser module, [1] genotype_browser.urls module, [1] genotype_browser.views module, [1] genotype_data_persons() (dae.pheno_tool.tool.PhenoToolHelper method) genotype_data_variants() (dae.pheno_tool.tool.PhenoToolHelper method) genotype_storages (dae.gpf_instance.gpf_instance.GPFInstance property) (dae.gpf_instance.GPFInstance property) GenotypeBrowserQueryView (class in genotype_browser.views), [1] GenotypeBrowserRunner (class in dae.tools.gpf_validation_runner) GenotypeData (class in dae.studies.study) GenotypeDataGroup (class in dae.studies.study) GenotypeDataStudy (class in dae.studies.study) GenotypeHelper (class in dae.enrichment_tool.genotype_helper) GenotypeStorage (class in dae.genotype_storage.genotype_storage) GenotypeStorageRegistry (class in dae.genotype_storage.genotype_storage_registry) get() (common_reports_api.views.FamiliesDataDownloadView method) (common_reports_api.views.VariantReportsFullView method) (common_reports_api.views.VariantReportsView method) (dae.genomic_resources.genomic_position_table.BigWigLine method) (dae.genomic_resources.genomic_position_table.Line method) (dae.genomic_resources.genomic_position_table.line.BigWigLine method) (dae.genomic_resources.genomic_position_table.line.Line method) (dae.genomic_resources.genomic_position_table.line.LineBase method) (dae.genomic_resources.genomic_position_table.line.VCFLine method) (dae.genomic_resources.genomic_position_table.VCFLine method) (dae.pedigrees.families_data.FamiliesData method) (dae.query_variants.query_runners.QueryResult method) (dae.studies.variants_db.VariantsDb method) (datasets_api.views.DatasetConfigView method) (datasets_api.views.DatasetDescriptionView method) (datasets_api.views.DatasetDetailsView method) (datasets_api.views.DatasetHierarchyView method) (datasets_api.views.DatasetPedigreeView method) (datasets_api.views.DatasetPermissionsSingleView method) (datasets_api.views.DatasetPermissionsView method) (datasets_api.views.DatasetView method) (datasets_api.views.StudiesView method) (datasets_api.views.VisibleDatasetsView method) (enrichment_api.views.EnrichmentModelsView method) (family_api.views.AllMemberDetailsView method) (family_api.views.FamilyDetailsView method) (family_api.views.ListAllDetailsView method) (family_api.views.ListFamiliesView method) (family_api.views.ListMembersView method) (family_api.views.MemberDetailsView method) (family_api.views.TagsView method) (gene_profiles_api.table_views.GeneSymbolsView method) (gene_profiles_api.table_views.TableConfigurationView method) (gene_profiles_api.table_views.TableRowsView method) (gene_profiles_api.views.ConfigurationView method) (gene_profiles_api.views.ProfileView method) (gene_scores.views.GeneScoresDownloadView method) (gene_scores.views.GeneScoresListView method) (gene_scores.views.HistogramView method) (gene_sets.views.DenovoGeneSetsTypesView method) (gene_sets.views.GeneSetDownloadView method) (gene_sets.views.GeneSetsCollectionsView method) (gene_sets.views.GeneSetsHasDenovoView method) (gene_view.views.ConfigView method) (genomes_api.views.DefaultGeneModelsId method) (genomes_api.views.GeneModels method) (genomes_api.views.GeneSymbolsSearch method) (genomic_scores_api.views.GenomicScoreDescsView method) (genomic_scores_api.views.GenomicScoresView method) (gpf_instance.views.AboutDescriptionView method) (gpf_instance.views.DescriptionView method) (gpf_instance.views.MarkdownFileView method) (measures_api.views.PhenoMeasureRegressionsView method) (measures_api.views.PhenoMeasuresView method) (person_sets_api.views.CollectionConfigsView method) (person_sets_api.views.CollectionDomainView method) (person_sets_api.views.CollectionStatsView method) (pheno_browser_api.views.PhenoConfigView method) (pheno_browser_api.views.PhenoImagesView method) (pheno_browser_api.views.PhenoInstrumentsView method) (pheno_browser_api.views.PhenoMeasureDescriptionView method) (pheno_browser_api.views.PhenoMeasuresCount method) (pheno_browser_api.views.PhenoMeasuresDownload method) (pheno_browser_api.views.PhenoMeasuresInfoView method) (pheno_browser_api.views.PhenoMeasuresView method) (pheno_tool_api.views.PhenoToolInstruments method) (pheno_tool_api.views.PhenoToolMeasure method) (pheno_tool_api.views.PhenoToolMeasures method) (user_queries.views.UserQueryCollectView method) (users_api.views.BasePasswordView method), [1] (users_api.views.FederationCredentials method), [1] (users_api.views.ForgotPassword method), [1] (users_api.views.UserGpStateView method), [1] (users_api.views.WdaeLoginView method), [1] get_about_etag() (in module gpf_instance.views) get_active_vertex_edges() (dae.pedigrees.pedigrees.Realization method) get_active_vertices() (dae.pedigrees.pedigrees.Realization method) get_aggregator_class() (in module dae.genomic_resources.aggregators) get_all_chrom_lengths() (dae.genomic_resources.reference_genome.ReferenceGenome method) get_all_chromosomes() (dae.genomic_resources.genomic_scores.GenomicScore method) get_all_common_report_configs() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_all_context_objects() (dae.genomic_resources.genomic_context.SimpleGenomicContext method) get_all_gene_score_descs() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_all_gene_scores() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_all_gene_sets() (dae.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection class method) (dae.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) (dae.gene_sets.gene_sets_db.BaseGeneSetCollection method) (dae.gene_sets.gene_sets_db.GeneSetCollection method) (dae.gene_sets.gene_sets_db.GeneSetsDb method) get_all_genotype_data() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) (dae.studies.variants_db.VariantsDb method) get_all_genotype_group_configs() (dae.studies.variants_db.VariantsDb method) get_all_genotype_group_ids() (dae.studies.variants_db.VariantsDb method) get_all_genotype_groups() (dae.studies.variants_db.VariantsDb method) get_all_genotype_storage_ids() (dae.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) get_all_genotype_storages() (dae.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) get_all_genotype_studies() (dae.studies.variants_db.VariantsDb method) get_all_genotype_study_configs() (dae.studies.variants_db.VariantsDb method) get_all_genotype_study_ids() (dae.studies.variants_db.VariantsDb method) get_all_ids() (dae.studies.variants_db.VariantsDb method) get_all_phenotype_data() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) (dae.pheno.registry.PhenoRegistry method) get_all_records() (dae.genomic_resources.genomic_position_table.BigWigTable method) (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table.GenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table_bigwig.BigWigTable method) (dae.genomic_resources.genomic_position_table.table_inmemory.InmemoryGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table_tabix.TabixGenomicPositionTable method) get_all_resources() (dae.genomic_resources.cached_repository.CachingProtocol method) (dae.genomic_resources.cached_repository.GenomicResourceCachedRepo method) (dae.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (dae.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (dae.genomic_resources.group_repository.GenomicResourceGroupRepo method) (dae.genomic_resources.repository.GenomicResourceProtocolRepo method) (dae.genomic_resources.repository.GenomicResourceRepo method) (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) get_all_scores() (dae.gene_scores.gene_scores.GeneScore method) (dae.genomic_resources.genomic_scores.GenomicScore method) get_allowed_genotype_studies() (in module datasets_api.permissions) get_amino_acids() (dae.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) (dae.effect_annotation.annotation_request.PositiveStrandAnnotationRequest method) get_annotatable() (dae.variants.core.Allele method) get_annotation_pipeline() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_annotation_pipeline_config() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) (dae.import_tools.import_tools.ImportProject method) get_annotator_by_attribute_info() (dae.annotation.annotation_pipeline.AnnotationPipeline method) get_annotator_factory() (in module dae.annotation.annotation_factory) get_argument_parser() (dae.annotation.annotate_columns.AnnotateColumnsTool method) (dae.annotation.annotate_schema2_parquet.AnnotateSchema2ParquetTool method) (dae.annotation.annotate_utils.AnnotationTool method) (dae.annotation.annotate_vcf.AnnotateVCFTool method) (dae.annotation.reannotate_instance.ReannotateInstanceTool method) get_attr() (dae.pedigrees.family.Person method) get_attribute() (dae.variants.family_variant.FamilyAllele method) (dae.variants.variant.SummaryAllele method) (dae.variants.variant.SummaryVariant method) (dae.variants_loaders.raw.loader.VariantsLoader method) (dae.variants_loaders.raw.loader.VariantsLoaderDecorator method) get_attribute_info() (dae.annotation.annotation_pipeline.AnnotationPipeline method) get_attributes() (dae.annotation.annotation_pipeline.AnnotationPipeline method) (dae.annotation.annotation_pipeline.ReannotationPipeline method) get_available_annotator_types() (in module dae.annotation.annotation_factory) get_available_scores() (dae.genomic_resources.genomic_scores.ScoreLine method) get_base_dir() (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) get_base_resource_schema() (in module dae.genomic_resources.resource_implementation) get_bbox() (dae.pedigrees.layout.Layout method) get_bit_and_str() (in module dae.query_variants.attributes_query) get_browser_measure() (dae.pheno.db.PhenoDb method) get_children() (dae.person_sets.person_sets.PersonSet method) (dae.person_sets.PersonSet method) (datasets_api.models.DatasetHierarchy class method) get_children_by_sex() (dae.person_sets.person_sets.PersonSet method) (dae.person_sets.PersonSet method) get_children_count() (dae.person_sets.person_sets.PersonSet method) (dae.person_sets.PersonSet method) get_children_stats() (dae.person_sets.person_sets.PersonSet method) (dae.person_sets.PersonSet method) get_chrom_file() (dae.genomic_resources.implementations.reference_genome_impl.GenomeStatisticsMixin static method) get_chrom_length() (dae.genomic_resources.reference_genome.ReferenceGenome method) get_chromosome_length() (dae.genomic_resources.genomic_position_table.BigWigTable method) (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table.GenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table_bigwig.BigWigTable method) (dae.genomic_resources.genomic_position_table.table_inmemory.InmemoryGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table_tabix.TabixGenomicPositionTable method) get_chromosome_length_tabix() (in module dae.utils.regions) get_chromosomes() (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table.GenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table_tabix.TabixGenomicPositionTable method) get_clean_gene_id() (in module dae.gene_sets.gene_term) get_code() (users_api.models.BaseVerificationCode class method), [1] get_coding_left() (dae.effect_annotation.annotation_request.BaseAnnotationRequest method) get_coding_region_for_pos() (dae.effect_annotation.annotation_request.BaseAnnotationRequest method) get_coding_right() (dae.effect_annotation.annotation_request.BaseAnnotationRequest method) get_codons() (dae.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) (dae.effect_annotation.annotation_request.PositiveStrandAnnotationRequest method) get_codons_left() (dae.effect_annotation.annotation_request.BaseAnnotationRequest method) get_codons_right() (dae.effect_annotation.annotation_request.BaseAnnotationRequest method) get_collection_types_legend() (dae.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) get_column_key() (dae.genomic_resources.genomic_position_table.table.GenomicPositionTable method) get_columns() (dae.pedigrees.family.Family method) get_columns_as_sources() (studies.study_wrapper.StudyWrapperBase static method) get_columns_to_draw() (in module dae.pheno.graphs) get_common_report() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) (dae.studies.study.GenotypeData method) get_config() (dae.genomic_resources.genomic_scores.GenomicScore method) (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) (dae.genomic_resources.resource_implementation.GenomicResourceImplementation method) (dae.studies.variants_db.VariantsDb method) get_config_histograms() (dae.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation method) get_context_keys() (dae.genomic_resources.genomic_context.GenomicContext method) (dae.genomic_resources.genomic_context.PriorityGenomicContext method) (dae.genomic_resources.genomic_context.SimpleGenomicContext method) (dae.gpf_instance_plugin.gpf_instance_context_plugin.GPFInstanceGenomicContext method) get_context_object() (dae.genomic_resources.genomic_context.GenomicContext method) (dae.genomic_resources.genomic_context.PriorityGenomicContext method) (dae.genomic_resources.genomic_context.SimpleGenomicContext method) (dae.gpf_instance_plugin.gpf_instance_context_plugin.GPFInstanceGenomicContext method) get_context_provider_priority() (dae.genomic_resources.genomic_context.GenomicContextProvider method) (dae.genomic_resources.genomic_context.SimpleGenomicContextProvider method) get_context_provider_type() (dae.genomic_resources.genomic_context.GenomicContextProvider method) (dae.genomic_resources.genomic_context.SimpleGenomicContextProvider method) get_contexts() (dae.genomic_resources.genomic_context.GenomicContextProvider method) (dae.genomic_resources.genomic_context.SimpleGenomicContextProvider method) get_count() (pheno_browser_api.views.PhenoMeasuresCount method) get_data_dir() (dae.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage method) get_dataset() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) (users_api.management.commands.dataset_mixin.DatasetBaseMixin method) get_dataset_groups() (in module datasets_api.permissions) get_dataset_info() (in module datasets_api.permissions) get_datasets() (groups_api.serializers.GroupRetrieveSerializer method) get_db() (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) get_db_filename() (dae.duckdb_storage.duckdb_genotype_storage.DuckDbS3Storage method) (dae.duckdb_storage.duckdb_genotype_storage.DuckDbStorage method) (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) get_default_annotation_attribute() (dae.genomic_resources.genomic_scores.GenomicScore method) get_default_annotation_attributes() (dae.genomic_resources.genomic_scores.GenomicScore method) get_default_application() (in module users_api.models), [1] get_default_background_model() (dae.enrichment_tool.enrichment_helper.EnrichmentHelper static method) get_default_counting_model() (dae.enrichment_tool.enrichment_helper.EnrichmentHelper static method) get_default_genotype_storage() (dae.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) get_default_grr_definition() (in module dae.genomic_resources.repository_factory) get_default_grr_definition_path() (in module dae.genomic_resources.repository_factory) get_denovo_events() (dae.enrichment_tool.genotype_helper.GenotypeHelper method) get_denovo_gene_set_spec() (in module utils.gene_sets) get_dependencies_for() (dae.annotation.annotation_pipeline.ReannotationPipeline method) get_dependents_for() (dae.annotation.annotation_pipeline.ReannotationPipeline method) get_description() (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) get_description_etag() (in module datasets_api.views) (in module gpf_instance.views) get_direct_datasets_parents() (datasets_api.models.DatasetHierarchy class method) get_directly_allowed_genotype_data() (in module datasets_api.permissions) get_effect() (dae.effect_annotation.effect_checkers.coding.CodingEffectChecker method) (dae.effect_annotation.effect_checkers.effect_checker.EffectChecker method) (dae.effect_annotation.effect_checkers.frame_shift.FrameShiftEffectChecker method) (dae.effect_annotation.effect_checkers.intron.IntronicEffectChecker method) (dae.effect_annotation.effect_checkers.promoter.PromoterEffectChecker method) (dae.effect_annotation.effect_checkers.protein_change.ProteinChangeEffectChecker method) (dae.effect_annotation.effect_checkers.splice_site.SpliceSiteEffectChecker method) (dae.effect_annotation.effect_checkers.start_loss.StartLossEffectChecker method) (dae.effect_annotation.effect_checkers.stop_loss.StopLossEffectChecker method) (dae.effect_annotation.effect_checkers.utr.UTREffectChecker method) get_effect_for_transcript() (dae.effect_annotation.annotator.EffectAnnotator method) get_effect_types() (dae.effect_annotation.effect.EffectTypesMixin class method) (in module dae.effect_annotation.annotation_effects) get_effect_types_set() (in module dae.effect_annotation.annotation_effects) get_empty() (dae.common_reports.denovo_report.EffectRow method) get_enrichment_builder() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_enrichment_config() (dae.enrichment_tool.enrichment_helper.EnrichmentHelper static method) get_exon_number_for() (dae.genomic_resources.gene_models.gene_models.TranscriptModel method) (dae.genomic_resources.gene_models.TranscriptModel method)

get_exonic_distance() (dae.effect_annotation.annotation_request.BaseAnnotationRequest method) get_exonic_length() (dae.effect_annotation.annotation_request.BaseAnnotationRequest method) get_exonic_position() (dae.effect_annotation.annotation_request.BaseAnnotationRequest method) get_family_pedigree() (in module dae.common_reports.family_counter) get_family_pq_filepaths() (dae.variants_loaders.parquet.loader.ParquetLoader method) get_family_read_counts() (dae.variants_loaders.dae.loader.DaeTransmittedFamiliesGenotypes method) get_family_type() (in module dae.common_reports.family_counter) get_file_chromosomes() (dae.genomic_resources.genomic_position_table.BigWigTable method) (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table.GenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table_bigwig.BigWigTable method) (dae.genomic_resources.genomic_position_table.table_inmemory.InmemoryGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table_tabix.TabixGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table_vcf.VCFGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable method) get_file_content() (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) get_file_url() (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) get_files() (dae.genomic_resources.repository.Manifest method) get_final() (dae.genomic_resources.aggregators.Aggregator method) (dae.genomic_resources.aggregators.ConcatAggregator method) (dae.genomic_resources.aggregators.DictAggregator method) (dae.genomic_resources.aggregators.JoinAggregator method) (dae.genomic_resources.aggregators.ListAggregator method) (dae.genomic_resources.aggregators.MaxAggregator method) (dae.genomic_resources.aggregators.MeanAggregator method) (dae.genomic_resources.aggregators.MedianAggregator method) (dae.genomic_resources.aggregators.MinAggregator method) (dae.genomic_resources.aggregators.ModeAggregator method) get_frame() (dae.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) (dae.effect_annotation.annotation_request.PositiveStrandAnnotationRequest method) get_full_id() (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) get_gene_models() (dae.effect_annotation.cli.EffectAnnotatorBuilder method) (dae.genomic_resources.genomic_context.GenomicContext method) get_gene_score() (dae.gene_scores.gene_scores.GeneScoresDb method) (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_gene_score_desc() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_gene_score_ids() (dae.gene_scores.gene_scores.GeneScoresDb method) get_gene_scores() (dae.gene_scores.gene_scores.GeneScoresDb method) get_gene_set() (dae.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) (dae.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) (dae.gene_sets.gene_sets_db.BaseGeneSetCollection method) (dae.gene_sets.gene_sets_db.GeneSetCollection method) (dae.gene_sets.gene_sets_db.GeneSetsDb method) get_gene_set_collection_ids() (dae.gene_sets.gene_sets_db.GeneSetsDb method) get_gene_set_from_collections() (dae.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection class method) get_gene_set_ids() (dae.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) (dae.gene_sets.gene_sets_db.GeneSetsDb method) get_gene_sets_types_legend() (dae.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) get_gene_value() (dae.gene_scores.gene_scores.GeneScore method) get_gene_view_summary_variants() (studies.study_wrapper.StudyWrapper method) get_gene_view_summary_variants_download() (studies.study_wrapper.StudyWrapper method) get_genes() (dae.gene_scores.gene_scores.GeneScore method) get_genomic_context() (dae.effect_annotation.cli.EffectAnnotatorBuilder method) (in module dae.genomic_resources.genomic_context) get_genomic_resource() (in module dae.annotation.score_annotator) get_genomic_resource_id_version() (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) get_genomic_resources_repository() (dae.genomic_resources.genomic_context.GenomicContext method) get_genotype_data() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_genotype_data_config() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_genotype_data_ids() (dae.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_genotype_group() (dae.studies.variants_db.VariantsDb method) get_genotype_group_config() (dae.studies.variants_db.VariantsDb method) get_genotype_storage() (dae.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) (dae.import_tools.import_tools.ImportProject method) (dae.studies.dataset_helpers.DatasetHelpers method) get_genotype_storage_factory() (in module dae.genotype_storage) get_genotype_storage_types() (in module dae.genotype_storage) get_genotype_study() (dae.studies.variants_db.VariantsDb method) get_genotype_study_config() (dae.studies.variants_db.VariantsDb method) get_global_statistic_file() (dae.genomic_resources.implementations.reference_genome_impl.GenomeStatisticsMixin static method) get_gp() (dae.gene_profile.db.GeneProfileDB method) get_gp_configuration() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_gp_statistic() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_gpf_instance() (dae.import_tools.import_tools.ImportProject method) get_graph() (dae.pedigrees.pedigrees.FamilyConnections method) get_grr() (dae.effect_annotation.cli.EffectAnnotatorBuilder method) get_header() (dae.effect_annotation.cli.VariantColumnInputFile method) get_histogram_file() (dae.genomic_resources.histogram.HistogramStatisticMixin static method) get_histogram_filename() (dae.gene_scores.gene_scores.GeneScore method) (dae.genomic_resources.genomic_scores.GenomicScore method) get_histogram_image_file() (dae.genomic_resources.histogram.HistogramStatisticMixin static method) get_histogram_image_filename() (dae.gene_scores.gene_scores.GeneScore method) (dae.genomic_resources.genomic_scores.GenomicScore method) get_histogram_image_url() (dae.gene_scores.gene_scores.GeneScore method) (dae.genomic_resources.genomic_scores.GenomicScore method) get_id() (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) get_idx() (in module dae.genomic_resources.genomic_position_table.table) get_image() (dae.pheno.pheno_data.PhenotypeData method) get_import_storage() (dae.import_tools.import_tools.ImportProject method) get_import_storage_factory() (in module dae.import_tools.import_tools) get_import_storage_types() (in module dae.import_tools.import_tools) get_import_variants_buckets() (dae.import_tools.import_tools.ImportProject method) get_individual() (dae.pedigrees.pedigrees.FamilyConnections method) get_individuals() (dae.pedigrees.pedigrees.FamilyConnections method) get_individuals_with_rank() (dae.pedigrees.pedigrees.FamilyConnections method) get_info() (dae.annotation.annotation_pipeline.AnnotationPipeline method) (dae.annotation.annotation_pipeline.Annotator method) (dae.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation method) (dae.gene_scores.implementations.gene_scores_impl.GeneScoreImplementation method) (dae.gene_sets.gene_sets_db.GeneSetCollection method) (dae.genomic_resources.cnv_collection.CnvCollectionImplementation method) (dae.genomic_resources.implementations.annotation_pipeline_impl.AnnotationPipelineImplementation method) (dae.genomic_resources.implementations.gene_models_impl.GeneModelsImpl method) (dae.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation method) (dae.genomic_resources.implementations.liftover_chain_impl.LiftoverChainImplementation method) (dae.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeImplementation method) (dae.genomic_resources.resource_implementation.GenomicResourceImplementation method) (dae.genomic_resources.resource_implementation.InfoImplementationMixin method) get_input_filenames() (dae.import_tools.import_tools.ImportProject method) get_instance_timestamp_etag() (in module datasets_api.permissions) get_instrument_measures() (dae.pheno.pheno_data.PhenotypeData method) get_instruments() (dae.pheno.pheno_data.PhenotypeData method) get_interval() (dae.pedigrees.pedigrees.Realization method) get_interval_locus_ploidy() (in module dae.utils.variant_utils) get_labels() (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) get_last_login_for() (users_api.models.AuthenticationLog static method), [1] get_leaf_children() (dae.studies.study.GenotypeData method) get_line_iterator() (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table_tabix.TabixGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table_vcf.VCFGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable method) get_lines() (dae.effect_annotation.cli.VariantColumnInputFile method) get_locked_out_error() (users_api.models.AuthenticationLog static method), [1] get_locus_ploidy() (in module dae.utils.variant_utils) get_manifest() (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) get_mating_units() (dae.pedigrees.pedigrees.FamilyConnections method) get_max() (dae.gene_scores.gene_scores.GeneScore method) get_maximal_set() (dae.pedigrees.pedigrees.Realization method) get_measure() (dae.pheno.pheno_data.PhenotypeData method) get_measure_description() (dae.pheno.pheno_data.PhenotypeData method) get_measure_ids() (pheno_browser_api.views.PhenoMeasuresDownload method) get_measures() (dae.pheno.pheno_data.PhenotypeData method) get_measures_df() (dae.pheno.db.PhenoDb method) get_measures_info() (dae.pheno.pheno_data.PhenotypeData method) (dae.pheno.pheno_data.PhenotypeGroup method) (dae.pheno.pheno_data.PhenotypeStudy method) get_member() (dae.pedigrees.family.Family method) get_members_with_roles() (dae.pedigrees.family.Family method) get_members_with_statuses() (dae.pedigrees.family.Family method) get_memory_limit() (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) get_min() (dae.gene_scores.gene_scores.GeneScore method) get_min_max_file() (dae.genomic_resources.statistics.min_max.MinMaxValueStatisticMixin static method) get_next_by_created_at() (users_api.models.BaseVerificationCode method), [1] (users_api.models.ResetPasswordCode method), [1] (users_api.models.SetPasswordCode method), [1] get_next_by_time() (users_api.models.AuthenticationLog method), [1] get_normalize_measure_id() (dae.pheno_tool.tool.PhenoTool method) get_nucleotides_count_to_full_codon() (dae.effect_annotation.annotation_request.BaseAnnotationRequest static method) get_number_range() (dae.gene_scores.gene_scores.GeneScore method) (dae.genomic_resources.genomic_scores.GenomicScore method) get_or_create() (users_api.models.WdaeUserManager method), [1] get_or_create_resource() (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) get_out_attributes() (dae.effect_annotation.cli.AnnotationAttributes method) get_page_display() (query_state_save.models.QueryState method) get_paginated_response() (utils.pagination.WdaePageNumberPagination method) get_parents() (dae.person_sets.person_sets.PersonSet method) (dae.person_sets.PersonSet method) (datasets_api.models.DatasetHierarchy class method) get_parquet_dataset_dir() (dae.import_tools.import_tools.ImportProject method) get_parser() (in module dae.genomic_resources.gene_models.parsing) get_partition_descriptor() (dae.import_tools.import_tools.ImportProject method) get_pedigree() (dae.import_tools.import_tools.ImportProject method) get_pedigree_column_names() (in module dae.pedigrees.family) get_pedigree_filename() (dae.import_tools.import_tools.ImportProject method) get_pedigree_loader() (dae.import_tools.import_tools.ImportProject method) get_pedigree_params() (dae.import_tools.import_tools.ImportProject method) get_people_measure_values() (dae.pheno.db.PhenoDb method) (dae.pheno.pheno_data.PhenotypeData method) (dae.pheno.pheno_data.PhenotypeGroup method) (dae.pheno.pheno_data.PhenotypeStudy method) get_people_measure_values_df() (dae.pheno.db.PhenoDb method) (dae.pheno.pheno_data.PhenotypeData method) (dae.pheno.pheno_data.PhenotypeGroup method) (dae.pheno.pheno_data.PhenotypeStudy method) get_permissions_etag() (in module datasets_api.permissions) get_permitted_datasets() (query_base.query_base.QueryBaseView method) get_person_color() (dae.person_sets.person_sets.PersonSetCollection static method) (dae.person_sets.PersonSetCollection static method) get_person_set() (dae.person_sets.person_sets.PersonSetCollection method) (dae.person_sets.PersonSetCollection method) get_person_set_collection() (dae.studies.study.GenotypeData method) get_person_set_collection_legend() (dae.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) get_person_set_of_person() (dae.person_sets.person_sets.PersonSetCollection method) (dae.person_sets.PersonSetCollection method) get_pheno_browser_images_dir() (in module dae.pheno.pheno_data) get_pheno_db_dir() (in module dae.pheno.pheno_data) get_pheno_tool_adapter() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_phenotype_data() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) (dae.pheno.registry.PhenoRegistry method) get_phenotype_data_config() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) (dae.pheno.registry.PhenoRegistry method) get_phenotype_data_ids() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) (dae.pheno.registry.PhenoRegistry method) get_pipeline() (dae.annotation.context.CLIAnnotationContext static method) get_previous_by_created_at() (users_api.models.BaseVerificationCode method), [1] (users_api.models.ResetPasswordCode method), [1] (users_api.models.SetPasswordCode method), [1] get_previous_by_time() (users_api.models.AuthenticationLog method), [1] get_processing_parquet_dataset_dir() (dae.import_tools.import_tools.ImportProject method) get_protein_length() (dae.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) (dae.effect_annotation.annotation_request.PositiveStrandAnnotationRequest method) get_protein_position() (dae.effect_annotation.annotation_request.BaseAnnotationRequest method) (dae.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) (dae.effect_annotation.annotation_request.PositiveStrandAnnotationRequest method) get_protein_position_for_pos() (dae.effect_annotation.annotation_request.BaseAnnotationRequest method) get_queryset() (groups_api.views.GroupsViewSet method) get_records_in_region() (dae.genomic_resources.genomic_position_table.BigWigTable method) (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table.GenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table_bigwig.BigWigTable method) (dae.genomic_resources.genomic_position_table.table_inmemory.InmemoryGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table_tabix.TabixGenomicPositionTable method) get_reference_genome() (dae.genomic_resources.genomic_context.GenomicContext method) get_refernce_genome() (dae.effect_annotation.cli.EffectAnnotatorBuilder method) get_region_scores() (dae.genomic_resources.genomic_scores.PositionScore method) get_regression_ids() (dae.pheno.pheno_data.PhenotypeStudy method) get_regression_measures() (dae.pheno.prepare_data.PreparePhenoBrowserBase method) get_regressions() (dae.pheno.pheno_data.PhenotypeData method) (dae.pheno.pheno_data.PhenotypeGroup method) (dae.pheno.pheno_data.PhenotypeStudy method) get_remaining_lockout_time() (users_api.models.AuthenticationLog static method), [1] get_repo_url() (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) get_resource() (dae.genomic_resources.cached_repository.GenomicResourceCachedRepo method) (dae.genomic_resources.group_repository.GenomicResourceGroupRepo method) (dae.genomic_resources.repository.GenomicResourceProtocolRepo method) (dae.genomic_resources.repository.GenomicResourceRepo method) (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) get_resource_cached_files() (dae.genomic_resources.cached_repository.GenomicResourceCachedRepo method) get_resource_file_size() (dae.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) get_resource_file_timestamp() (dae.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) get_resource_file_url() (dae.genomic_resources.cached_repository.CachingProtocol method) (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) get_resource_ids() (dae.annotation.annotation_pipeline.AnnotationPipeline method) get_resource_implementation_builder() (in module dae.genomic_resources) get_resource_url() (dae.genomic_resources.cached_repository.CachingProtocol method) (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) get_result_by_sex() (dae.pheno_tool.pheno_tool_adapter.PhenoToolAdapter method) (pheno_tool_api.views.PhenoToolView static method) get_row_group_size() (dae.import_tools.import_tools.ImportProject method) get_schema() (dae.enrichment_tool.base_enrichment_background.BaseEnrichmentResourceBackground static method) (dae.enrichment_tool.samocha_background.SamochaEnrichmentBackground static method) (dae.gene_scores.gene_scores.GeneScore static method) (dae.gene_sets.gene_sets_db.GeneSetCollection static method) (dae.genomic_resources.gene_models.gene_models.GeneModels static method) (dae.genomic_resources.gene_models.GeneModels static method) (dae.genomic_resources.genomic_scores.AlleleScore static method) (dae.genomic_resources.genomic_scores.GenomicScore static method) (dae.genomic_resources.genomic_scores.NPScore static method) (dae.genomic_resources.genomic_scores.PositionScore static method) (dae.genomic_resources.liftover_chain.LiftoverChain static method) (dae.genomic_resources.reference_genome.ReferenceGenome static method) (dae.genomic_resources.resource_implementation.ResourceConfigValidationMixin static method) get_score() (dae.genomic_resources.genomic_scores.ScoreLine method) get_score_definition() (dae.genomic_resources.genomic_scores.GenomicScore method) get_score_desc() (dae.gene_scores.gene_scores.GeneScoresDb method) get_score_df() (dae.gene_scores.gene_scores.GeneScore method) get_score_histogram() (dae.gene_scores.gene_scores.GeneScore method) (dae.genomic_resources.genomic_scores.GenomicScore method) get_score_ids() (dae.gene_scores.gene_scores.GeneScoresDb method) get_scores() (dae.gene_scores.gene_scores.GeneScore method) (dae.gene_scores.gene_scores.GeneScoresDb method) (dae.genomic_scores.scores.GenomicScoresRegistry method) get_sequence() (dae.genomic_resources.reference_genome.ReferenceGenome method) get_serializer_class() (groups_api.views.GroupsViewSet method) (users_api.views.UserViewSet method), [1] get_sibship_units() (dae.pedigrees.pedigrees.FamilyConnections method) get_source() (dae.genomic_resources.genomic_context.GenomicContext method) (dae.genomic_resources.genomic_context.PriorityGenomicContext method) (dae.genomic_resources.genomic_context.SimpleGenomicContext method) (dae.gpf_instance_plugin.gpf_instance_context_plugin.GPFInstanceGenomicContext method) get_source_attributes() (dae.effect_annotation.cli.AnnotationAttributes method) get_statistics() (dae.genomic_resources.implementations.gene_models_impl.GeneModelsImpl method) (dae.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeImplementation method) (dae.genomic_resources.resource_implementation.GenomicResourceImplementation method) get_statistics_folder() (dae.genomic_resources.resource_implementation.ResourceStatistics static method) get_stats() (dae.person_sets.person_sets.PersonSetCollection method) (dae.person_sets.PersonSetCollection method) get_status_code() (users_api.forms.WdaeLoginForm method) get_storage_types() (dae.duckdb_storage.duckdb_genotype_storage.DuckDbParquetStorage class method) (dae.duckdb_storage.duckdb_genotype_storage.DuckDbS3ParquetStorage class method) (dae.duckdb_storage.duckdb_genotype_storage.DuckDbS3Storage class method) (dae.duckdb_storage.duckdb_genotype_storage.DuckDbStorage class method) (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage class method) (dae.genotype_storage.genotype_storage.GenotypeStorage class method) (dae.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage class method) (dae.parquet_storage.storage.ParquetGenotypeStorage class method) get_studies_ids() (dae.studies.study.GenotypeData method) (dae.studies.study.GenotypeDataGroup method) (dae.studies.study.GenotypeDataStudy method) (studies.study_wrapper.StudyWrapper method) get_study_config_tables() (in module dae.duckdb_storage.duckdb_storage_helpers) get_summary() (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) get_summary_pq_filepaths() (dae.variants_loaders.parquet.loader.ParquetLoader method) get_sym_2_fn() (in module dae.enrichment_tool.event_counters) get_template() (dae.gene_scores.implementations.gene_scores_impl.GeneScoreImplementation method) (dae.gene_sets.gene_sets_db.GeneSetCollection method) (dae.genomic_resources.implementations.annotation_pipeline_impl.AnnotationPipelineImplementation method) (dae.genomic_resources.implementations.gene_models_impl.GeneModelsImpl method) (dae.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation method) (dae.genomic_resources.implementations.liftover_chain_impl.LiftoverChainImplementation method) (dae.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeImplementation method) (dae.genomic_resources.resource_implementation.InfoImplementationMixin method) get_template_data() (dae.genomic_resources.resource_implementation.InfoImplementationMixin method) get_total_count() (dae.genomic_resources.aggregators.Aggregator method) get_transcript_models() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_type() (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) get_unused_keys() (dae.annotation.annotation_config.ParamsUsageMonitor method) get_url() (dae.genomic_resources.cached_repository.CachingProtocol method) (dae.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) get_used_count() (dae.genomic_resources.aggregators.Aggregator method) get_used_keys() (dae.annotation.annotation_config.ParamsUsageMonitor method) get_user_groups() (in module datasets_api.permissions) get_user_info() (in module users_api.views), [1] get_values() (dae.effect_annotation.cli.AnnotationAttributes method) (dae.gene_scores.gene_scores.GeneScore method) get_variant_loader() (dae.import_tools.import_tools.ImportProject method) get_variant_loader_chrom_lens() (dae.import_tools.import_tools.ImportProject method) get_variant_loader_chromosomes() (dae.import_tools.import_tools.ImportProject method) get_variant_loader_types() (dae.import_tools.import_tools.ImportProject method) get_variant_params() (dae.import_tools.import_tools.ImportProject method) get_variant_partitions() (dae.parquet.partition_descriptor.PartitionDescriptor method) get_version_str() (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) get_visible_groups() (users_api.management.commands.export_base.ExportUsersBase method) get_wdae_children() (in module datasets_api.permissions) get_wdae_dataset() (in module datasets_api.permissions) get_wdae_parents() (in module datasets_api.permissions) get_wgpf_instance() (in module gpf_instance.gpf_instance) get_work_dir() (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) get_x_scale() (dae.gene_scores.gene_scores.GeneScore method) get_y_scale() (dae.gene_scores.gene_scores.GeneScore method) getDims() (in module dae.tools.phase) glob() (in module dae.utils.fs_utils) glot_and() (in module dae.utils.sql_utils) gp_from_table_row() (dae.gene_profile.db.GeneProfileDB method) gp_from_table_row_single_view() (dae.gene_profile.db.GeneProfileDB method) gp_table_exists() (dae.gene_profile.db.GeneProfileDB method) gpf_instance module gpf_instance.apps module gpf_instance.gpf_instance module gpf_instance.urls module gpf_instance.views module gpf_instance_genomic_context_fixture() (in module dae.conftest) GPFConfigParser (class in dae.configuration.gpf_config_parser) GPFConfigValidator (class in dae.configuration.gpf_config_parser) GPFInstance (class in dae.gpf_instance) (class in dae.gpf_instance.gpf_instance) GPFInstanceGenomicContext (class in dae.gpf_instance_plugin.gpf_instance_context_plugin) GPFInstanceGenomicContextProvider (class in dae.gpf_instance_plugin.gpf_instance_context_plugin) gpfjs module gpfjs.views module GPFOAuth2Authentication (class in utils.authentication) GPStatistic (class in dae.gene_profile.statistic) GpUserState (class in users_api.models), [1] gpuserstate (users_api.models.WdaeUser attribute), [1] GpUserState.DoesNotExist, [1] GpUserState.MultipleObjectsReturned, [1] GraphColumn (class in dae.pheno.graphs) GreaterThanEqNode (class in dae.query_variants.attributes_query) GreaterThanNode (class in dae.query_variants.attributes_query) grey (wdae.default_settings.CustomFormatter attribute) group_post_delete() (in module users_api.models), [1] group_pre_delete() (in module users_api.models), [1] GroupCreateSerializer (class in groups_api.serializers) GroupCreateSerializer.Meta (class in groups_api.serializers) GroupRetrieveSerializer (class in groups_api.serializers) GroupRetrieveSerializer.Meta (class in groups_api.serializers) groups (datasets_api.models.Dataset attribute) (users_api.models.WdaeUser attribute), [1] groups_api module groups_api.migrations module groups_api.serializers module groups_api.urls module groups_api.views module GroupSerializer (class in groups_api.serializers) GroupSerializer.Meta (class in groups_api.serializers) GroupsViewSet (class in groups_api.views) grr (dae.gpf_instance.gpf_instance.GPFInstance property) (dae.gpf_instance.GPFInstance property) gt2str() (in module dae.utils.variant_utils) gt_flatten() (dae.variants.family_variant.FamilyAllele method) (dae.variants.family_variant.FamilyVariant method) gtf_canonical_index() (in module dae.genomic_resources.gene_models.serialization)

H

half_sibling (dae.variants.attributes.Role attribute) handle() (users_api.management.commands.dataset_groups.Command method) (users_api.management.commands.datasets_export.Command method) (users_api.management.commands.datasets_restore.Command method) (users_api.management.commands.datasets_show.Command method) (users_api.management.commands.groups_cleanup.Command method) (users_api.management.commands.unlock_user.Command method) (users_api.management.commands.user_create.Command method) (users_api.management.commands.user_set_name.Command method) (users_api.management.commands.user_setpasswd.Command method) (users_api.management.commands.users_add.Command method) (users_api.management.commands.users_export.Command method) (users_api.management.commands.users_group_add.Command method) (users_api.management.commands.users_group_remove.Command method) (users_api.management.commands.users_remove.Command method) (users_api.management.commands.users_restore.Command method) (users_api.management.commands.users_show.Command method) handle_dataset() (users_api.management.commands.datasets_restore.Command method) handle_partial_permissions() (in module datasets_api.permissions) handle_user() (users_api.management.commands.import_base.ImportUsersBase method) (users_api.management.commands.users_export.Command method) has_annotation_file() (dae.variants_loaders.raw.loader.AnnotationDecorator static method) has_attr() (dae.pedigrees.family.Person method) has_attribute() (dae.variants.family_variant.FamilyAllele method) (dae.variants.variant.SummaryAllele method) (dae.variants.variant.SummaryVariant method) has_both_parents() (dae.pedigrees.family.Person method) has_cnv (dae.studies.study.GenotypeData property) has_coding_bins() (dae.parquet.partition_descriptor.PartitionDescriptor method) has_complex (dae.studies.study.GenotypeData property) has_dad() (dae.pedigrees.family.Person method) has_denovo (dae.studies.study.GenotypeData property) has_denovo_variants() (dae.import_tools.import_tools.ImportProject method) has_descriptions (dae.pheno.db.PhenoDb property) has_enrichment_config() (dae.enrichment_tool.enrichment_helper.EnrichmentHelper static method) has_family_bins() (dae.parquet.partition_descriptor.PartitionDescriptor method) has_family_partitions() (dae.parquet.partition_descriptor.PartitionDescriptor method) has_frequency_bins() (dae.parquet.partition_descriptor.PartitionDescriptor method) has_gene_score() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) has_gene_set_collection() (dae.gene_sets.gene_sets_db.GeneSetsDb method) has_gene_sets() (dae.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) has_genotype_storage() (dae.import_tools.import_tools.ImportProject method) has_measure() (dae.pheno.pheno_data.PhenotypeData method) has_members() (dae.pedigrees.family.Family method) has_missing_parent() (dae.pedigrees.family.Person method) has_mom() (dae.pedigrees.family.Person method) has_no_parent() (dae.pedigrees.family.Person method) has_object_permission() (datasets_api.permissions.IsDatasetAllowed method) has_parent() (dae.pedigrees.family.Person method)

has_partitions() (dae.parquet.partition_descriptor.PartitionDescriptor method) has_permission() (datasets_api.permissions.IsDatasetAllowed method) has_pheno_data() (studies.study_wrapper.StudyWrapper method) (studies.study_wrapper.StudyWrapperBase method) has_phenotype_data() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) (dae.pheno.registry.PhenoRegistry method) has_region_bins() (dae.parquet.partition_descriptor.PartitionDescriptor method) has_summary_partitions() (dae.parquet.partition_descriptor.PartitionDescriptor method) has_tag() (dae.pedigrees.family.Person method) has_transmitted (dae.studies.study.GenotypeData property) has_unlimited_download (users_api.models.WdaeUser property), [1] has_utr3_region() (dae.effect_annotation.annotation_request.BaseAnnotationRequest method) (dae.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) has_utr5_region() (dae.effect_annotation.annotation_request.BaseAnnotationRequest method) (dae.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) has_variants() (dae.schema2_storage.schema2_layout.Schema2DatasetLayout method) has_view_range() (dae.genomic_resources.histogram.NumberHistogramConfig method) has_wildcard() (dae.annotation.annotation_config.AnnotationConfigParser static method) hashsum() (in module dae.utils.filehash) head() (pheno_browser_api.views.PhenoMeasuresDownload method) header (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) HelloWorldAnnotator (class in dae.annotation.debug_annotator) help (dae.gene_scores.gene_scores.ScoreDesc attribute) (dae.genomic_scores.scores.ScoreDesc attribute) (users_api.management.commands.dataset_groups.Command attribute) (users_api.management.commands.datasets_export.Command attribute) (users_api.management.commands.datasets_restore.Command attribute) (users_api.management.commands.datasets_show.Command attribute) (users_api.management.commands.groups_cleanup.Command attribute) (users_api.management.commands.unlock_user.Command attribute) (users_api.management.commands.user_create.Command attribute) (users_api.management.commands.user_set_name.Command attribute) (users_api.management.commands.user_setpasswd.Command attribute) (users_api.management.commands.users_add.Command attribute) (users_api.management.commands.users_export.Command attribute) (users_api.management.commands.users_group_add.Command attribute) (users_api.management.commands.users_group_remove.Command attribute) (users_api.management.commands.users_remove.Command attribute) (users_api.management.commands.users_restore.Command attribute) (users_api.management.commands.users_show.Command attribute) hist (dae.gene_scores.gene_scores.ScoreDesc attribute) (dae.genomic_scores.scores.ScoreDesc attribute) hist_conf (dae.gene_scores.gene_scores.ScoreDef attribute) (dae.genomic_resources.genomic_scores.ScoreDef attribute) HistogramError HistogramStatisticMixin (class in dae.genomic_resources.histogram) HistogramView (class in gene_scores.views) http_process_test_server() (in module dae.genomic_resources.testing) http_threaded_test_server() (in module dae.genomic_resources.testing)

I

id (dae.duckdb_storage.duckdb_storage_config.DuckDbBaseConf attribute) (dae.person_sets.person_sets.PersonSetCollectionConfig attribute) (dae.person_sets.person_sets.PersonSetConfig attribute) (dae.person_sets.PersonSetCollectionConfig attribute) (dae.person_sets.PersonSetConfig attribute) (datasets_api.models.Dataset attribute) (datasets_api.models.DatasetHierarchy attribute) (query_state_save.models.QueryState attribute) (user_queries.models.UserQuery attribute) (users_api.models.AuthenticationLog attribute), [1] (users_api.models.GpUserState attribute), [1] (users_api.models.ResetPasswordCode attribute), [1] (users_api.models.SetPasswordCode attribute), [1] (users_api.models.WdaeUser attribute), [1] id_to_position (dae.pedigrees.layout.Layout property) import_dataset() (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) (dae.parquet_storage.storage.ParquetGenotypeStorage method) import_pheno_data() (in module dae.pheno.pheno_import) ImportConfig (class in dae.pheno.common) ImportConfigNormalizer (class in dae.import_tools.import_tools) ImportProject (class in dae.import_tools.import_tools) ImportStorage (class in dae.import_tools.import_tools) ImportUsersBase (class in users_api.management.commands.import_base) in_start_codons() (dae.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) (dae.effect_annotation.annotation_request.PositiveStrandAnnotationRequest method) inc() (dae.utils.statistics.StatsCollection method) include_reference (dae.import_tools.import_tools.ImportProject property) increase_indent() (dae.configuration.study_config_builder.ConfigDumper method) indel (dae.variants.core.Allele.Type attribute) index (dae.import_tools.import_tools.Bucket attribute) index() (in module gpfjs.views) Individual (class in dae.pedigrees.pedigrees) individual_set() (dae.pedigrees.pedigrees.Individual method) (dae.pedigrees.pedigrees.IndividualGroup method) (dae.pedigrees.pedigrees.MatingUnit method) (dae.pedigrees.pedigrees.SibshipUnit method) IndividualGroup (class in dae.pedigrees.pedigrees) individuals_by_rank (dae.pedigrees.layout.Layout property) IndividualWithCoordinates (class in dae.pedigrees.layout) infer_gene_model_parser() (in module dae.genomic_resources.gene_models.parsing) InferenceConfig (class in dae.pheno.common) info_get() (in module dae.tools.vcfinfo_extractor) info_get_allele() (in module dae.tools.vcfinfo_extractor) info_get_allele_percent() (in module dae.tools.vcfinfo_extractor) InfoImplementationMixin (class in dae.genomic_resources.resource_implementation) Inheritance (class in dae.variants.attributes) inheritance() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) inheritance_converter() (in module dae.query_variants.attributes_query) inheritance_in_members (dae.variants.family_variant.FamilyAllele property) InheritanceTransformer (class in dae.query_variants.attributes_query_inheritance) init_gpf_instance_genomic_context_plugin() (in module dae.gpf_instance_plugin.gpf_instance_context_plugin) init_normalize_measures() (dae.pheno_tool.tool.PhenoTool method) init_test_gpf_instance_genomic_context_plugin() (in module dae.gpf_instance_plugin.gpf_instance_context_plugin) initial (datasets_api.migrations.0001_initial.Migration attribute) (user_queries.migrations.0001_initial.Migration attribute) (users_api.migrations.0001_initial.Migration attribute) InmemoryGenomicPositionTable (class in dae.genomic_resources.genomic_position_table.table_inmemory) InmemoryGenotypeStorage (class in dae.inmemory_storage.inmemory_genotype_storage) InmemoryImportStorage (class in dae.inmemory_storage.inmemory_import_storage) input_dir (dae.import_tools.import_tools.ImportProject property) input_files (dae.task_graph.graph.Task attribute) input_reference_genome (dae.annotation.annotation_config.AnnotationPreamble attribute) (dae.annotation.annotation_config.RawPreamble attribute) input_reference_genome_res (dae.annotation.annotation_config.AnnotationPreamble attribute) InputAnnotableAnnotatorDecorator (class in dae.annotation.annotation_pipeline) insert_gp() (dae.gene_profile.db.GeneProfileDB method) insert_gps() (dae.gene_profile.db.GeneProfileDB method) instance_id (datasets_api.models.DatasetHierarchy attribute) InstanceIdCommand (class in dae.tools.gpf_instance_adjustments) Instrument (class in dae.pheno.pheno_data) instruments (dae.pheno.pheno_data.PhenotypeData property) instruments_dir (dae.pheno.common.ImportConfig attribute) instruments_tab_separated (dae.pheno.common.ImportConfig attribute) int_type() (dae.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method) (dae.query_variants.sql.schema2.base_query_builder.Dialect static method) internal (dae.annotation.annotation_config.AttributeInfo attribute) intersection() (dae.pedigrees.pedigrees.Interval method) (dae.utils.regions.Region method) (in module dae.utils.regions) intersects() (dae.utils.regions.Region method) Interval (class in dae.pedigrees.pedigrees) IntervalForVertex (class in dae.pedigrees.pedigrees) IntronicEffectChecker (class in dae.effect_annotation.effect_checkers.intron) invalidate() (dae.genomic_resources.cached_repository.CachingProtocol method) (dae.genomic_resources.cached_repository.GenomicResourceCachedRepo method) (dae.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.group_repository.GenomicResourceGroupRepo method) (dae.genomic_resources.repository.GenomicResource method) (dae.genomic_resources.repository.GenomicResourceProtocolRepo method) (dae.genomic_resources.repository.GenomicResourceRepo method) (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method)

inverse_curve_p1() (dae.pedigrees.layout.Line method) inverse_curve_p2() (dae.pedigrees.layout.Line method) inverse_curve_y_at() (dae.pedigrees.layout.Line method) is_active (users_api.models.WdaeUser attribute), [1] is_active_vertex() (dae.pedigrees.pedigrees.Realization method) is_all_reference_genotype() (in module dae.utils.variant_utils) is_all_unknown_genotype() (in module dae.utils.variant_utils) is_child() (dae.pedigrees.family.Person method) is_closed() (dae.query_variants.query_runners.QueryRunner method) is_cnv() (dae.variants.core.Allele.Type class method) is_coding() (dae.genomic_resources.gene_models.gene_models.TranscriptModel method) (dae.genomic_resources.gene_models.TranscriptModel method) is_connected() (dae.pedigrees.pedigrees.FamilyConnections method) is_convertible_to_numeric() (in module dae.pheno.prepare.measure_classifier) is_done() (dae.query_variants.query_runners.QueryResult method) (dae.query_variants.query_runners.QueryRunner method) is_email_valid() (in module utils.email_regex) is_empty() (dae.common_reports.denovo_report.DenovoReport method) (dae.common_reports.denovo_report.DenovoReportTable method) (dae.common_reports.denovo_report.EffectCell method) (dae.common_reports.people_counter.PeopleCounter method) (dae.query_variants.sql.schema2.sql_query_builder.QueryHeuristics method) is_empty_field() (dae.common_reports.people_counter.PeopleCounter method) is_gr_id_token() (in module dae.genomic_resources.repository) is_group (dae.studies.study.GenotypeData property) (dae.studies.study.GenotypeDataGroup property) (dae.studies.study.GenotypeDataStudy property) (studies.study_wrapper.StudyWrapper property) is_in_interval_order() (dae.pedigrees.pedigrees.Realization method) is_individual() (dae.pedigrees.pedigrees.Individual method) (dae.pedigrees.pedigrees.IndividualGroup method) is_loaded() (dae.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground method) (dae.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground method) (dae.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground method) (dae.enrichment_tool.samocha_background.SamochaEnrichmentBackground method) (dae.genomic_resources.gene_models.gene_models.GeneModels method) (dae.genomic_resources.gene_models.GeneModels method) is_maximal() (dae.pedigrees.pedigrees.Realization method) is_nan() (in module dae.pheno.prepare.measure_classifier) is_numeric() (dae.pheno.common.MeasureType static method) is_open() (dae.annotation.annotation_pipeline.Annotator method) (dae.annotation.annotation_pipeline.AnnotatorDecorator method) (dae.annotation.score_annotator.GenomicScoreAnnotatorBase method) (dae.genomic_resources.cnv_collection.CnvCollection method) (dae.genomic_resources.genomic_scores.GenomicScore method) (dae.genomic_resources.liftover_chain.LiftoverChain method) (dae.genomic_resources.reference_genome.ReferenceGenome method) is_parent() (dae.pedigrees.family.Person method) is_password_valid() (in module utils.password_requirements) is_pedigree_only() (dae.person_sets.person_sets.PersonSetCollection method) (dae.person_sets.PersonSetCollection method) is_pseudoautosomal() (dae.genomic_resources.reference_genome.ReferenceGenome method) is_read_only() (dae.duckdb_storage.duckdb_genotype_storage.AbstractDuckDbStorage method) (dae.genotype_storage.genotype_storage.GenotypeStorage method) is_reference() (dae.variants.family_variant.FamilyVariant method) is_reference_allele (dae.variants.variant.SummaryAllele property) is_reference_genotype() (in module dae.utils.variant_utils) is_row_empty() (dae.common_reports.denovo_report.EffectRow method) is_s3url() (in module dae.utils.fs_utils) is_staff (users_api.models.WdaeUser attribute), [1] is_start_codon_affected() (dae.effect_annotation.annotation_request.BaseAnnotationRequest method) (dae.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) is_started() (dae.query_variants.query_runners.QueryRunner method) is_stop_codon_affected() (dae.effect_annotation.annotation_request.BaseAnnotationRequest method) (dae.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) is_study() (datasets_api.models.DatasetHierarchy class method) is_superuser (users_api.models.WdaeUser attribute), [1] is_text() (dae.pheno.common.MeasureType static method) is_tr() (dae.variants.core.Allele.Type class method) is_unknown() (dae.variants.family_variant.FamilyVariant method) is_unknown_genotype() (in module dae.utils.variant_utils) is_user_locked_out() (users_api.models.AuthenticationLog static method), [1] is_valid_family() (dae.pedigrees.pedigrees.FamilyConnections static method) is_version_constraint_satisfied() (in module dae.genomic_resources.repository) IsDatasetAllowed (class in datasets_api.permissions) isin() (dae.utils.regions.Region method) isnan() (in module dae.utils.helpers) items() (dae.pedigrees.families_data.FamiliesData method) iterator_to_json() (in module users_api.views), [1] (in module utils.streaming_response_util)

J

join() (in module dae.utils.fs_utils) join_base_url_and_parquet_scan() (in module dae.duckdb_storage.duckdb_storage_helpers) join_gene_models() (in module dae.genomic_resources.gene_models) (in module dae.genomic_resources.gene_models.gene_models) join_line() (in module dae.utils.dae_utils)

join_pheno_df_with_variants() (dae.pheno_tool.tool.PhenoTool static method) JoinAggregator (class in dae.genomic_resources.aggregators) JsonVariantsDataSerializer (class in dae.parquet.schema2.variant_serializers) jump_threshold (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute)

K

keys() (dae.pedigrees.families_data.FamiliesData method)

L

label (dae.pedigrees.family.FamilyTag property) (dae.pheno.graphs.GraphColumn property) LARGE_DELETION (dae.annotation.annotatable.Annotatable.Type attribute) large_deletion (dae.variants.core.Allele.Type attribute) LARGE_DPI (dae.pheno.prepare_data.PreparePhenoBrowserBase attribute) LARGE_DUPLICATION (dae.annotation.annotatable.Annotatable.Type attribute) large_duplication (dae.variants.core.Allele.Type attribute) large_values_desc (dae.gene_scores.gene_scores.ScoreDef attribute) (dae.gene_scores.gene_scores.ScoreDesc attribute) (dae.genomic_resources.genomic_scores.ScoreDef attribute) (dae.genomic_scores.scores.ScoreDesc attribute) last_login (users_api.models.WdaeUser attribute), [1] Layout (class in dae.pedigrees.layout) layout (dae.pedigrees.family.Person property) Layout.BBox (class in dae.pedigrees.layout) layout_parser() (in module dae.pedigrees.layout) LeafNode (class in dae.query_variants.attributes_query) legend_json() (dae.person_sets.person_sets.PersonSetCollection method) (dae.person_sets.PersonSetCollection method) LessThanEqNode (class in dae.query_variants.attributes_query) LessThanNode (class in dae.query_variants.attributes_query) liftover_allele() (dae.annotation.liftover_annotator.AbstractLiftoverAnnotator method) liftover_cnv() (dae.annotation.liftover_annotator.AbstractLiftoverAnnotator method) liftover_grr_fixture() (in module dae.conftest) liftover_header() (in module dae.tools.vcf_liftover) liftover_position() (dae.annotation.liftover_annotator.AbstractLiftoverAnnotator method) liftover_region() (dae.annotation.liftover_annotator.AbstractLiftoverAnnotator method) LiftoverChain (class in dae.genomic_resources.liftover_chain) LiftoverChainImplementation (class in dae.genomic_resources.implementations.liftover_chain_impl) Line (class in dae.genomic_resources.genomic_position_table) (class in dae.genomic_resources.genomic_position_table.line) (class in dae.pedigrees.layout) line_iterator (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) LinearRegression (class in dae.pheno.utils.lin_regress) LineBase (class in dae.genomic_resources.genomic_position_table.line) LineBuffer (class in dae.genomic_resources.genomic_position_table) (class in dae.genomic_resources.genomic_position_table.line) list() (users_api.views.UserViewSet method), [1] list_gp_gene_symbols() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) list_symbols() (dae.gene_profile.db.GeneProfileDB method) ListAggregator (class in dae.genomic_resources.aggregators) ListAllDetailsView (class in family_api.views) ListFamiliesView (class in family_api.views) ListMembersView (class in family_api.views) load() (dae.common_reports.common_report.CommonReport static method) (dae.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground method) (dae.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground method) (dae.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground method) (dae.enrichment_tool.samocha_background.SamochaEnrichmentBackground method) (dae.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) (dae.genomic_resources.gene_models.gene_models.GeneModels method) (dae.genomic_resources.gene_models.GeneModels method) (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) (dae.pedigrees.loader.FamiliesLoader method) (dae.task_graph.cache.FileTaskCache method) (dae.task_graph.cache.NoTaskCache method) (dae.task_graph.cache.TaskCache method)

load_collection() (dae.gene_sets.denovo_gene_set_helpers.DenovoGeneSetHelpers class method) load_config() (dae.configuration.gpf_config_parser.GPFConfigParser class method) load_config_raw() (dae.configuration.gpf_config_parser.GPFConfigParser class method) load_definition_file() (in module dae.genomic_resources.repository_factory) load_descriptions() (in module dae.pheno.pheno_import) load_directory_configs() (dae.configuration.gpf_config_parser.GPFConfigParser class method) load_extensions() (gpf_instance.apps.WDAEConfig static method) load_from_dir() (dae.variants_loaders.parquet.loader.ParquetLoader static method) load_gene_mapping() (in module dae.genomic_resources.gene_models.parsing) load_gene_models() (in module dae.genomic_resources.gene_models.parsing) load_gene_sets() (dae.gene_sets.gene_sets_db.GeneSetCollection method) load_gene_terms() (in module dae.gene_sets.gene_term) load_histogram() (in module dae.genomic_resources.histogram) load_inference_configs() (in module dae.pheno.pheno_import) load_manifest() (dae.genomic_resources.cached_repository.CachingProtocol method) (dae.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) load_measure() (dae.pheno.prepare_data.PreparePhenoBrowserBase method) load_meta() (dae.schema2_storage.schema2_import_storage.Schema2ImportStorage static method) load_ncbi_gene_info() (in module dae.gene_sets.gene_term) load_pedigree_file() (dae.pedigrees.loader.FamiliesLoader static method) load_pheno_data() (dae.pheno.registry.PhenoRegistry class method) load_pheno_groups() (dae.pheno.registry.PhenoRegistry class method) load_pipeline_from_file() (in module dae.annotation.annotation_factory) load_pipeline_from_yaml() (in module dae.annotation.annotation_factory) load_resource_file_state() (dae.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) load_schema2_dataset_layout() (in module dae.schema2_storage.schema2_layout) load_simple_families_file() (dae.pedigrees.loader.FamiliesLoader static method) load_study_config() (in module dae.tools.gpf_convert_study_config) load_yaml() (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) location (dae.variants.variant.SummaryVariant property) location_variant_to_vcf_transformer() (in module dae.variants_loaders.raw.flexible_variant_loader) log_authentication_attempt() (users_api.models.AuthenticationLog static method), [1] log_filter() (in module utils.logger) log_line() (dae.pheno.prepare.measure_classifier.ClassifierReport method) logical_and() (dae.query_variants.attributes_query.BitwiseTreeTransformer method) (dae.query_variants.attributes_query.StringQueryToTreeTransformer method) (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) logical_or() (dae.query_variants.attributes_query.BitwiseTreeTransformer method) (dae.query_variants.attributes_query.StringQueryToTreeTransformer method) (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) logout() (in module users_api.views), [1] lookup_field (groups_api.views.GroupsViewSet attribute)

M

M (dae.variants.attributes.Sex attribute) main() (dae.tools.gpf_validation_runner.MainRunner method) (in module dae.common_reports.generate_common_report) (in module dae.gene_profile.generate_gene_profile) (in module dae.gene_sets.generate_denovo_gene_sets) (in module dae.genomic_resources.draw_score_histograms) (in module dae.import_tools.cli) (in module dae.pedigrees.generate_families_cache) (in module dae.pheno.pheno_import) (in module dae.task_graph.demo_graphs_cli) (in module dae.tools.cnv_liftover) (in module dae.tools.dae_liftover) (in module dae.tools.denovo_liftover) (in module dae.tools.draw_pedigree) (in module dae.tools.gpf_convert_study_config) (in module dae.tools.gpf_validation_runner) (in module dae.tools.ped2ped) (in module dae.tools.simple_family2pedigree) (in module dae.tools.simple_study_import) (in module dae.tools.stats_liftover) (in module dae.tools.to_gpf_gene_models_format) (in module dae.tools.vcf_liftover) (in module dae.tools.vcfinfo_extractor) MainRunner (class in dae.tools.gpf_validation_runner) make_all_region_bins() (dae.parquet.partition_descriptor.PartitionDescriptor method) make_coding_bin() (dae.parquet.partition_descriptor.PartitionDescriptor method) make_enrichment_builder() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) make_family_bin() (dae.parquet.partition_descriptor.PartitionDescriptor method) make_frequency_bin() (dae.parquet.partition_descriptor.PartitionDescriptor method) make_pedigree_filter() (in module dae.person_filters) (in module dae.person_filters.person_filters) make_pheno_filter() (in module dae.person_filters) (in module dae.person_filters.person_filters) make_pheno_tool_adapter() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) make_region_bin() (dae.parquet.partition_descriptor.PartitionDescriptor method) make_region_bins_regions() (dae.parquet.partition_descriptor.PartitionDescriptor method) make_validation_runner() (dae.tools.gpf_validation_runner.MainRunner method) male (dae.enrichment_tool.event_counters.EnrichmentResult attribute) (dae.enrichment_tool.event_counters.EventCountersResult attribute) (dae.enrichment_tool.event_counters.EventsResult attribute) (dae.enrichment_tool.event_counters.VariantEventsResult attribute) (dae.person_sets.ChildrenBySex attribute) (dae.person_sets.ChildrenStats attribute) (dae.person_sets.person_sets.ChildrenBySex attribute) (dae.person_sets.person_sets.ChildrenStats attribute) (dae.variants.attributes.Sex attribute) male_female_colors() (in module dae.pheno.graphs) male_female_legend() (in module dae.pheno.graphs) MALE_PRB (dae.pedigrees.family.FamilyTag attribute) males_count() (dae.pheno.graphs.GraphColumn method) Manifest (class in dae.genomic_resources.repository) manifest (dae.genomic_resources.repository.ManifestUpdate attribute) ManifestEntry (class in dae.genomic_resources.repository) ManifestUpdate (class in dae.genomic_resources.repository) map_chromosome() (dae.genomic_resources.genomic_position_table.table.GenomicPositionTable method) (dae.genomic_resources.liftover_chain.LiftoverChain static method) MarkdownFileView (class in gpf_instance.views) mat2str() (in module dae.utils.variant_utils) match() (dae.query_variants.attributes_query.Matcher method) match_labels_query() (dae.annotation.annotation_config.AnnotationConfigParser static method) matched_alleles (dae.variants.variant.SummaryVariant property) matched_alleles_indexes (dae.variants.variant.SummaryVariant property) matched_gene_effects (dae.variants.variant.SummaryVariant property) Matcher (class in dae.query_variants.attributes_query) maternal_aunt (dae.variants.attributes.Role attribute) maternal_cousin (dae.variants.attributes.Role attribute) maternal_grandfather (dae.variants.attributes.Role attribute) maternal_grandmother (dae.variants.attributes.Role attribute) maternal_half_sibling (dae.variants.attributes.Role attribute) maternal_uncle (dae.variants.attributes.Role attribute) Mating (class in dae.pedigrees.family_role_builder) MatingUnit (class in dae.pedigrees.pedigrees) MAX_CHARS (dae.pheno.prepare.measure_classifier.ClassifierReport attribute) MAX_CHILD_NUMBER (dae.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute) max_rank (dae.pheno.common.RankRange attribute) max_rank() (dae.pedigrees.pedigrees.FamilyConnections method) MAX_SHOWN_VARIANTS (genotype_browser.views.GenotypeBrowserQueryView attribute), [1] max_x (dae.pedigrees.layout.Layout.BBox attribute) max_y (dae.pedigrees.layout.Layout.BBox attribute) MaxAggregator (class in dae.genomic_resources.aggregators) maximally_extend_variant() (in module dae.genomic_resources.variant_utils) md5 (dae.genomic_resources.repository.ManifestEntry attribute) (dae.genomic_resources.repository.ResourceFileState attribute) md5sum() (in module dae.utils.filehash) MeanAggregator (class in dae.genomic_resources.aggregators) Measure (class in dae.pheno.pheno_data) measure_to_json() (pheno_tool_api.views.PhenoToolInstruments method) measure_type (dae.pheno.common.InferenceConfig attribute) MeasureClassifier (class in dae.pheno.prepare.measure_classifier) measures (dae.pheno.pheno_data.PhenotypeData property) measures_api module measures_api.urls module measures_api.views module MeasureType (class in dae.pheno.common) media (users_api.forms.WdaeLoginForm property) (users_api.forms.WdaePasswordForgottenForm property) (users_api.forms.WdaeRegisterPasswordForm property) (users_api.forms.WdaeResetPasswordForm property) media_type (sentry.views.PlainTextParser attribute) MedianAggregator (class in dae.genomic_resources.aggregators) member_index (dae.pedigrees.family.Person property) MemberDetailsView (class in family_api.views) members (dae.pedigrees.pedigrees.FamilyConnections property) members_fpids (dae.variants.family_variant.FamilyDelegate property) members_ids (dae.pedigrees.family.Family property) (dae.variants.family_variant.FamilyDelegate property) members_in_order (dae.pedigrees.family.Family property) (dae.variants.family_variant.FamilyDelegate property) members_in_order_get_family_structure() (in module studies.response_transformer) members_index() (dae.pedigrees.family.Family method) memory_limit (dae.duckdb_storage.duckdb_storage_config.DuckDbBaseConf attribute) mendelian (dae.variants.attributes.Inheritance attribute) mendelian() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) merge() (dae.genomic_resources.histogram.CategoricalHistogram method) (dae.genomic_resources.histogram.NullHistogram method) (dae.genomic_resources.histogram.NumberHistogram method) (dae.genomic_resources.implementations.reference_genome_impl.ChromosomeStatistic method) (dae.genomic_resources.implementations.reference_genome_impl.GenomeStatistic method) (dae.genomic_resources.statistics.base_statistic.Statistic method) (dae.genomic_resources.statistics.min_max.MinMaxValue method) merge_config() (dae.configuration.gpf_config_parser.GPFConfigParser static method) merge_configs() (dae.person_sets.person_sets.PersonSetCollection static method) (dae.person_sets.PersonSetCollection static method) merge_families() (in module dae.pedigrees.families_data) merge_inference_configs() (in module dae.pheno.pheno_import) merge_non_partitioned() (in module dae.annotation.parquet) merge_parquets() (in module dae.parquet.helpers) merge_partitioned() (in module dae.annotation.parquet) merge_variants_parquets() (in module dae.parquet.parquet_writer) meta (dae.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute) (dae.schema2_storage.schema2_layout.Schema2DatasetLayout attribute) metadata (dae.annotation.annotation_config.AnnotationPreamble attribute) (dae.annotation.annotation_config.RawPreamble attribute) Migration (class in datasets_api.migrations.0001_initial) (class in datasets_api.migrations.0002_dataset_groups) (class in datasets_api.migrations.0003_alter_dataset_options) (class in datasets_api.migrations.0004_dataset_broken) (class in datasets_api.migrations.0005_dataset_dataset_name) (class in datasets_api.migrations.0006_datasethierarchy) (class in datasets_api.migrations.0007_datasethierarchy_direct) (class in datasets_api.migrations.0008_datasethierarchy_instance_id) (class in query_state_save.migrations.0001_initial) (class in query_state_save.migrations.0002_auto_20190205_0736) (class in user_queries.migrations.0001_initial) (class in users_api.migrations.0001_initial) (class in users_api.migrations.0002_auto_20190424_0751) (class in users_api.migrations.0003_authenticationlog) (class in users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more) (class in users_api.migrations.0005_gpuserstate) min_individuals (dae.pheno.common.InferenceConfig attribute) MIN_QUEUE_SIZE (dae.task_graph.executor.DaskExecutor attribute) min_rank (dae.pheno.common.RankRange attribute) min_x (dae.pedigrees.layout.Layout.BBox attribute) min_y (dae.pedigrees.layout.Layout.BBox attribute) MinAggregator (class in dae.genomic_resources.aggregators) MinMaxValue (class in dae.genomic_resources.statistics.min_max) MinMaxValueStatisticMixin (class in dae.genomic_resources.statistics.min_max) missing (dae.pedigrees.family.Person property) (dae.variants.attributes.Inheritance attribute) missing() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) MISSING_DAD (dae.pedigrees.family.FamilyTag attribute) MISSING_MOM (dae.pedigrees.family.FamilyTag attribute) Mode (class in dae.genomic_resources.repository) mode() (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) ModeAggregator (class in dae.genomic_resources.aggregators) model (groups_api.serializers.GroupCreateSerializer.Meta attribute) (groups_api.serializers.GroupRetrieveSerializer.Meta attribute) (groups_api.serializers.GroupSerializer.Meta attribute) (query_state_save.serializers.QueryStateSerializer.Meta attribute) (users_api.serializers.UserSerializer.Meta attribute), [1] (users_api.serializers.UserWithoutEmailSerializer.Meta attribute), [1] model_computed_fields (dae.duckdb_storage.duckdb_storage_config.DuckDbBaseConf attribute) (dae.duckdb_storage.duckdb_storage_config.DuckDbConf attribute) (dae.duckdb_storage.duckdb_storage_config.DuckDbParquetConf attribute) (dae.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (dae.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute) (dae.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) (dae.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (dae.gene_sets.denovo_gene_sets_config.DGSSpec attribute) (dae.gene_sets.denovo_gene_sets_config.EffectsCriteria attribute) (dae.gene_sets.denovo_gene_sets_config.RecurrencyCriteriaBase attribute) (dae.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute) (dae.gene_sets.denovo_gene_sets_config.SexesCriteria attribute) (dae.gene_sets.denovo_gene_sets_config.SingleCriteria attribute) (dae.gene_sets.denovo_gene_sets_config.TripleCriteria attribute) (dae.person_sets.person_sets.PersonSetCollectionConfig attribute) (dae.person_sets.person_sets.PersonSetConfig attribute) (dae.person_sets.person_sets.SourceConfig attribute) (dae.person_sets.PersonSetCollectionConfig attribute) (dae.person_sets.PersonSetConfig attribute) (dae.person_sets.SourceConfig attribute) (dae.pheno.common.ImportConfig attribute) (dae.pheno.common.InferenceConfig attribute) (dae.pheno.common.RankRange attribute) model_config (dae.duckdb_storage.duckdb_storage_config.DuckDbBaseConf attribute) (dae.duckdb_storage.duckdb_storage_config.DuckDbConf attribute) (dae.duckdb_storage.duckdb_storage_config.DuckDbParquetConf attribute) (dae.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (dae.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute) (dae.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) (dae.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (dae.gene_sets.denovo_gene_sets_config.DGSSpec attribute) (dae.gene_sets.denovo_gene_sets_config.EffectsCriteria attribute) (dae.gene_sets.denovo_gene_sets_config.RecurrencyCriteriaBase attribute) (dae.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute) (dae.gene_sets.denovo_gene_sets_config.SexesCriteria attribute) (dae.gene_sets.denovo_gene_sets_config.SingleCriteria attribute) (dae.gene_sets.denovo_gene_sets_config.TripleCriteria attribute) (dae.person_sets.person_sets.PersonSetCollectionConfig attribute) (dae.person_sets.person_sets.PersonSetConfig attribute) (dae.person_sets.person_sets.SourceConfig attribute) (dae.person_sets.PersonSetCollectionConfig attribute) (dae.person_sets.PersonSetConfig attribute) (dae.person_sets.SourceConfig attribute) (dae.pheno.common.ImportConfig attribute) (dae.pheno.common.InferenceConfig attribute) (dae.pheno.common.RankRange attribute) model_fields (dae.duckdb_storage.duckdb_storage_config.DuckDbBaseConf attribute) (dae.duckdb_storage.duckdb_storage_config.DuckDbConf attribute) (dae.duckdb_storage.duckdb_storage_config.DuckDbParquetConf attribute) (dae.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (dae.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute) (dae.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) (dae.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (dae.gene_sets.denovo_gene_sets_config.DGSSpec attribute) (dae.gene_sets.denovo_gene_sets_config.EffectsCriteria attribute) (dae.gene_sets.denovo_gene_sets_config.RecurrencyCriteriaBase attribute) (dae.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute) (dae.gene_sets.denovo_gene_sets_config.SexesCriteria attribute) (dae.gene_sets.denovo_gene_sets_config.SingleCriteria attribute) (dae.gene_sets.denovo_gene_sets_config.TripleCriteria attribute) (dae.person_sets.person_sets.PersonSetCollectionConfig attribute) (dae.person_sets.person_sets.PersonSetConfig attribute) (dae.person_sets.person_sets.SourceConfig attribute) (dae.person_sets.PersonSetCollectionConfig attribute) (dae.person_sets.PersonSetConfig attribute) (dae.person_sets.SourceConfig attribute) (dae.pheno.common.ImportConfig attribute) (dae.pheno.common.InferenceConfig attribute) (dae.pheno.common.RankRange attribute) modified() (in module dae.utils.fs_utils) modify_tuple() (dae.configuration.gpf_config_parser.GPFConfigParser class method) module common_reports_api common_reports_api.urls common_reports_api.views dae dae.annotation dae.annotation.annotatable dae.annotation.annotate_columns dae.annotation.annotate_doc dae.annotation.annotate_schema2_parquet dae.annotation.annotate_utils dae.annotation.annotate_vcf dae.annotation.annotation_config dae.annotation.annotation_factory dae.annotation.annotation_pipeline dae.annotation.annotator_base dae.annotation.cnv_collection_annotator dae.annotation.context dae.annotation.debug_annotator dae.annotation.effect_annotator dae.annotation.gene_score_annotator dae.annotation.gene_set_annotator dae.annotation.liftover_annotator dae.annotation.normalize_allele_annotator dae.annotation.parquet dae.annotation.reannotate_instance dae.annotation.record_to_annotatable dae.annotation.score_annotator dae.annotation.simple_effect_annotator dae.common_reports dae.common_reports.common_report dae.common_reports.denovo_report dae.common_reports.family_counter dae.common_reports.family_report dae.common_reports.generate_common_report dae.common_reports.people_counter dae.configuration dae.configuration.gpf_config_parser dae.configuration.schemas dae.configuration.schemas.dae_conf dae.configuration.schemas.gene_profile dae.configuration.schemas.gene_weights_db dae.configuration.schemas.import_config dae.configuration.schemas.person_sets dae.configuration.schemas.phenotype_data dae.configuration.schemas.study_config dae.configuration.study_config_builder dae.configuration.utils dae.conftest dae.dask dae.dask.config dae.dask.named_cluster dae.duckdb_storage dae.duckdb_storage.duckdb2_variants dae.duckdb_storage.duckdb_connection_factory dae.duckdb_storage.duckdb_genotype_storage dae.duckdb_storage.duckdb_import_storage dae.duckdb_storage.duckdb_legacy_genotype_storage dae.duckdb_storage.duckdb_storage_config dae.duckdb_storage.duckdb_storage_helpers dae.duckdb_storage.duckdb_variants dae.effect_annotation dae.effect_annotation.annotation_effects dae.effect_annotation.annotation_request dae.effect_annotation.annotator dae.effect_annotation.cli dae.effect_annotation.effect dae.effect_annotation.effect_checkers dae.effect_annotation.effect_checkers.coding dae.effect_annotation.effect_checkers.effect_checker dae.effect_annotation.effect_checkers.frame_shift dae.effect_annotation.effect_checkers.intron dae.effect_annotation.effect_checkers.promoter dae.effect_annotation.effect_checkers.protein_change dae.effect_annotation.effect_checkers.splice_site dae.effect_annotation.effect_checkers.start_loss dae.effect_annotation.effect_checkers.stop_loss dae.effect_annotation.effect_checkers.utr dae.effect_annotation.gene_codes dae.effect_annotation.variant dae.enrichment_tool dae.enrichment_tool.base_enrichment_background dae.enrichment_tool.build_coding_length_enrichment_background dae.enrichment_tool.build_ur_synonymous_enrichment_background dae.enrichment_tool.enrichment_builder dae.enrichment_tool.enrichment_cache_builder dae.enrichment_tool.enrichment_helper dae.enrichment_tool.enrichment_serializer dae.enrichment_tool.event_counters dae.enrichment_tool.gene_weights_background dae.enrichment_tool.genotype_helper dae.enrichment_tool.resource_implementations dae.enrichment_tool.resource_implementations.enrichment_resource_impl dae.enrichment_tool.samocha_background dae.gene_profile dae.gene_profile.db dae.gene_profile.exporter dae.gene_profile.generate_gene_profile dae.gene_profile.statistic dae.gene_scores dae.gene_scores.gene_scores dae.gene_scores.implementations dae.gene_scores.implementations.gene_scores_impl dae.gene_sets dae.gene_sets.denovo_gene_set_collection dae.gene_sets.denovo_gene_set_helpers dae.gene_sets.denovo_gene_sets_config dae.gene_sets.denovo_gene_sets_db dae.gene_sets.gene_sets_db dae.gene_sets.gene_term dae.gene_sets.generate_denovo_gene_sets dae.genomic_resources dae.genomic_resources.aggregators dae.genomic_resources.cached_repository dae.genomic_resources.cli dae.genomic_resources.cnv_collection dae.genomic_resources.draw_score_histograms dae.genomic_resources.fsspec_protocol dae.genomic_resources.gene_models dae.genomic_resources.gene_models.gene_models dae.genomic_resources.gene_models.parsing dae.genomic_resources.gene_models.serialization dae.genomic_resources.genomic_context dae.genomic_resources.genomic_position_table dae.genomic_resources.genomic_position_table.line dae.genomic_resources.genomic_position_table.table dae.genomic_resources.genomic_position_table.table_bigwig dae.genomic_resources.genomic_position_table.table_inmemory dae.genomic_resources.genomic_position_table.table_tabix dae.genomic_resources.genomic_position_table.table_vcf dae.genomic_resources.genomic_position_table.utils dae.genomic_resources.genomic_scores dae.genomic_resources.group_repository dae.genomic_resources.histogram dae.genomic_resources.implementations dae.genomic_resources.implementations.annotation_pipeline_impl dae.genomic_resources.implementations.gene_models_impl dae.genomic_resources.implementations.genomic_scores_impl dae.genomic_resources.implementations.liftover_chain_impl dae.genomic_resources.implementations.reference_genome_impl dae.genomic_resources.liftover_chain dae.genomic_resources.reference_genome dae.genomic_resources.repository dae.genomic_resources.repository_factory dae.genomic_resources.resource_implementation dae.genomic_resources.statistics dae.genomic_resources.statistics.base_statistic dae.genomic_resources.statistics.min_max dae.genomic_resources.testing dae.genomic_resources.variant_utils dae.genomic_scores dae.genomic_scores.scores dae.genotype_storage dae.genotype_storage.genotype_storage dae.genotype_storage.genotype_storage_registry dae.gpf_instance dae.gpf_instance.gpf_instance dae.gpf_instance_plugin dae.gpf_instance_plugin.gpf_instance_context_plugin dae.import_tools dae.import_tools.cli dae.import_tools.import_tools dae.inmemory_storage dae.inmemory_storage.inmemory_genotype_storage dae.inmemory_storage.inmemory_import_storage dae.inmemory_storage.raw_variants dae.parquet dae.parquet.helpers dae.parquet.parquet_writer dae.parquet.partition_descriptor dae.parquet.schema2 dae.parquet.schema2.parquet_io dae.parquet.schema2.serializers dae.parquet.schema2.variant_serializers dae.parquet_storage dae.parquet_storage.storage dae.pedigrees dae.pedigrees.drawing dae.pedigrees.families_data dae.pedigrees.family dae.pedigrees.family_role_builder dae.pedigrees.family_tag_builder dae.pedigrees.generate_families_cache dae.pedigrees.layout dae.pedigrees.loader dae.pedigrees.pedigrees dae.pedigrees.testing dae.person_filters dae.person_filters.person_filters dae.person_sets dae.person_sets.person_sets dae.pheno dae.pheno.common dae.pheno.db dae.pheno.graphs dae.pheno.pheno_data dae.pheno.pheno_import dae.pheno.prepare dae.pheno.prepare.measure_classifier dae.pheno.prepare_data dae.pheno.registry dae.pheno.utils dae.pheno.utils.commons dae.pheno.utils.lin_regress dae.pheno_tool dae.pheno_tool.pheno_tool_adapter dae.pheno_tool.tool dae.query_variants dae.query_variants.attributes_query dae.query_variants.attributes_query_inheritance dae.query_variants.base_query_variants dae.query_variants.query_runners dae.query_variants.sql dae.query_variants.sql.schema2 dae.query_variants.sql.schema2.base_query_builder dae.query_variants.sql.schema2.base_variants dae.query_variants.sql.schema2.family_builder dae.query_variants.sql.schema2.sql_query_builder dae.query_variants.sql.schema2.summary_builder dae.schema2_storage dae.schema2_storage.schema2_import_storage dae.schema2_storage.schema2_layout dae.studies dae.studies.dataset_helpers dae.studies.study dae.studies.variants_db dae.task_graph dae.task_graph.cache dae.task_graph.cli_tools dae.task_graph.demo_graphs_cli dae.task_graph.executor dae.task_graph.graph dae.task_graph.logging dae.testing dae.testing.acgt_import dae.testing.alla_import dae.testing.foobar_import dae.testing.import_helpers dae.testing.setup_helpers dae.testing.t4c8_import dae.tools dae.tools.annotate_variants dae.tools.cnv_liftover dae.tools.cshl2vcf dae.tools.dae_liftover dae.tools.denovo_liftover dae.tools.draw_pedigree dae.tools.gpf_convert_study_config dae.tools.gpf_instance_adjustments dae.tools.gpf_validation_runner dae.tools.grr_cache_repo dae.tools.ped2ped dae.tools.phase dae.tools.simple_family2pedigree dae.tools.simple_study_import dae.tools.stats_liftover dae.tools.to_gpf_gene_models_format dae.tools.vcf_liftover dae.tools.vcfinfo_extractor dae.utils dae.utils.cnv_utils dae.utils.dae_utils dae.utils.debug_closing dae.utils.dict_utils dae.utils.filehash dae.utils.fixtures dae.utils.fs_utils dae.utils.helpers dae.utils.progress dae.utils.regions dae.utils.sql_utils dae.utils.statistics dae.utils.variant_utils dae.utils.verbosity_configuration dae.variants dae.variants.attributes dae.variants.core dae.variants.family_variant dae.variants.variant dae.variants_loaders dae.variants_loaders.cnv dae.variants_loaders.cnv.flexible_cnv_loader dae.variants_loaders.cnv.loader dae.variants_loaders.dae dae.variants_loaders.dae.loader dae.variants_loaders.parquet dae.variants_loaders.parquet.loader dae.variants_loaders.raw dae.variants_loaders.raw.flexible_variant_loader dae.variants_loaders.raw.loader dae.variants_loaders.vcf dae.variants_loaders.vcf.loader datasets_api datasets_api.migrations datasets_api.migrations.0001_initial datasets_api.migrations.0002_dataset_groups datasets_api.migrations.0003_alter_dataset_options datasets_api.migrations.0004_dataset_broken datasets_api.migrations.0005_dataset_dataset_name datasets_api.migrations.0006_datasethierarchy datasets_api.migrations.0007_datasethierarchy_direct datasets_api.migrations.0008_datasethierarchy_instance_id datasets_api.models datasets_api.permissions datasets_api.urls datasets_api.views enrichment_api enrichment_api.urls enrichment_api.views family_api family_api.urls family_api.views gene_profiles_api gene_profiles_api.table_views gene_profiles_api.urls gene_profiles_api.views gene_scores gene_scores.urls gene_scores.views gene_sets gene_sets.urls gene_sets.views gene_view gene_view.urls gene_view.views genomes_api genomes_api.urls genomes_api.views genomic_scores_api genomic_scores_api.urls genomic_scores_api.views genotype_browser, [1] genotype_browser.urls, [1] genotype_browser.views, [1] gpf_instance gpf_instance.apps gpf_instance.gpf_instance gpf_instance.urls gpf_instance.views gpfjs gpfjs.views groups_api groups_api.migrations groups_api.serializers groups_api.urls groups_api.views measures_api measures_api.urls measures_api.views person_sets_api person_sets_api.urls person_sets_api.views pheno_browser_api pheno_browser_api.urls pheno_browser_api.views pheno_tool_api pheno_tool_api.urls pheno_tool_api.views query_base query_base.query_base query_state_save query_state_save.migrations query_state_save.migrations.0001_initial query_state_save.migrations.0002_auto_20190205_0736 query_state_save.models query_state_save.serializers query_state_save.urls query_state_save.views sentry sentry.urls sentry.views studies studies.query_transformer studies.response_transformer studies.study_wrapper user_queries user_queries.admin user_queries.migrations user_queries.migrations.0001_initial user_queries.models user_queries.urls user_queries.views users_api, [1] users_api.forms users_api.management users_api.management.commands users_api.management.commands.dataset_groups users_api.management.commands.dataset_mixin users_api.management.commands.datasets_export users_api.management.commands.datasets_restore users_api.management.commands.datasets_show users_api.management.commands.export_base users_api.management.commands.groups_cleanup users_api.management.commands.import_base users_api.management.commands.unlock_user users_api.management.commands.user_create users_api.management.commands.user_set_name users_api.management.commands.user_setpasswd users_api.management.commands.users_add users_api.management.commands.users_export users_api.management.commands.users_group_add users_api.management.commands.users_group_remove users_api.management.commands.users_remove users_api.management.commands.users_restore users_api.management.commands.users_show users_api.migrations users_api.migrations.0001_initial users_api.migrations.0002_auto_20190424_0751 users_api.migrations.0003_authenticationlog users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more users_api.migrations.0005_gpuserstate users_api.models, [1] users_api.serializers, [1] users_api.urls, [1] users_api.validators, [1] users_api.views, [1] utils utils.authentication utils.datasets utils.email_regex utils.expand_gene_set utils.gene_sets utils.logger utils.pagination utils.password_requirements utils.query_params utils.streaming_response_util utils.testing wdae wdae.default_settings wdae.eager_settings wdae.gpfjs_settings wdae.remote_settings wdae.settings wdae.silk_settings wdae.test_settings wdae.urls wdae.wgpf wdaemanage

mom (dae.variants.attributes.Role attribute) MULTIPLEX (dae.pedigrees.family.FamilyTag attribute) MultiReader (class in dae.variants_loaders.parquet.loader) mutation_type() (dae.effect_annotation.effect_checkers.protein_change.ProteinChangeEffectChecker method)

N

name (dae.annotation.annotation_config.AttributeInfo attribute) (dae.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground property) (dae.enrichment_tool.base_enrichment_background.BaseEnrichmentResourceBackground property) (dae.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property) (dae.enrichment_tool.samocha_background.SamochaEnrichmentBackground property) (dae.gene_scores.gene_scores.ScoreDef attribute) (dae.gene_scores.gene_scores.ScoreDesc attribute) (dae.gene_sets.denovo_gene_sets_config.EffectsCriteria attribute) (dae.gene_sets.denovo_gene_sets_config.RecurrencyCriteriaBase attribute) (dae.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute) (dae.gene_sets.denovo_gene_sets_config.SexesCriteria attribute) (dae.gene_sets.denovo_gene_sets_config.SingleCriteria attribute) (dae.gene_sets.denovo_gene_sets_config.TripleCriteria attribute) (dae.gene_sets.gene_sets_db.GeneSet attribute) (dae.genomic_resources.repository.ManifestEntry attribute) (dae.genomic_scores.scores.ScoreDesc attribute) (dae.person_sets.person_sets.PersonSetCollectionConfig attribute) (dae.person_sets.person_sets.PersonSetConfig attribute) (dae.person_sets.PersonSetCollectionConfig attribute) (dae.person_sets.PersonSetConfig attribute) (dae.studies.study.GenotypeData property) (gpf_instance.apps.WDAEConfig attribute) (groups_api.views.GroupsViewSet attribute) (user_queries.models.UserQuery attribute) (users_api.models.WdaeUser attribute), [1] (users_api.views.UserViewSet attribute), [1] names() (dae.genomic_resources.repository.Manifest method) (in module dae.pheno.graphs) nan (dae.pheno.prepare.measure_classifier.Convertible attribute) NCBIGeneInfo (class in dae.gene_sets.gene_term) NEEDS_COMPUTE (dae.task_graph.cache.CacheRecordType attribute) negation() (dae.query_variants.attributes_query.BitwiseTreeTransformer method) (dae.query_variants.attributes_query.StringQueryToTreeTransformer method) negative_primitive() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) NegativeStrandAnnotationRequest (class in dae.effect_annotation.annotation_request)

NegPrimitive (class in dae.query_variants.attributes_query_inheritance) NO_RANK (dae.pedigrees.pedigrees.Individual attribute) non_numeric (dae.pheno.prepare.measure_classifier.Convertible attribute) non_numeric_cutoff (dae.pheno.common.InferenceConfig attribute) noncoding_regions() (dae.annotation.simple_effect_annotator.SimpleEffectAnnotator method) normalization_rules (dae.configuration.gpf_config_parser.GPFConfigValidator attribute) normalize() (dae.import_tools.import_tools.ImportConfigNormalizer method) normalize_allele() (in module dae.annotation.normalize_allele_annotator) normalize_variant() (in module dae.genomic_resources.variant_utils) NormalizeAlleleAnnotator (class in dae.annotation.normalize_allele_annotator) not_role() (dae.variants.attributes.Role static method) not_sequenced (dae.pedigrees.family.Person property) NoTaskCache (class in dae.task_graph.cache) NotNode (class in dae.query_variants.attributes_query) NotNode() (dae.query_variants.attributes_query.QueryTreeToLambdaTransformer method) (dae.query_variants.attributes_query.QueryTreeToSQLBitwiseTransformer static method) NOTSET (dae.tools.gpf_validation_runner.TestStatus attribute) NPScore (class in dae.genomic_resources.genomic_scores) NPScoreAggr (class in dae.genomic_resources.genomic_scores) NPScoreAnnotator (class in dae.annotation.score_annotator) NPScoreBase (class in dae.genomic_resources.genomic_scores) NPScoreQuery (class in dae.genomic_resources.genomic_scores) ns_tokens (dae.gene_sets.gene_term.NCBIGeneInfo attribute) nuc_aggregator (dae.genomic_resources.genomic_scores.ScoreDef attribute) NUCLEAR (dae.pedigrees.family.FamilyTag attribute) NuclearCode (class in dae.effect_annotation.gene_codes) nucleotide_aggregator (dae.genomic_resources.genomic_scores.NPScoreAggr attribute) (dae.genomic_resources.genomic_scores.NPScoreQuery attribute) NullHistogram (class in dae.genomic_resources.histogram) NullHistogramConfig (class in dae.genomic_resources.histogram) number_of_bins (dae.genomic_resources.histogram.NumberHistogramConfig attribute) number_of_children_with_event (dae.common_reports.denovo_report.EffectCell property) number_of_observed_events (dae.common_reports.denovo_report.EffectCell property) NumberHistogram (class in dae.genomic_resources.histogram) NumberHistogramConfig (class in dae.genomic_resources.histogram) numeric (dae.pheno.prepare.measure_classifier.Convertible attribute)

O

oauth2_provider_accesstoken (users_api.models.WdaeUser attribute), [1] oauth2_provider_application (users_api.models.WdaeUser attribute), [1] oauth2_provider_grant (users_api.models.WdaeUser attribute), [1] oauth2_provider_idtoken (users_api.models.WdaeUser attribute), [1] oauth2_provider_refreshtoken (users_api.models.WdaeUser attribute), [1] oauth_cookie_to_header() (in module utils.authentication) objects (datasets_api.models.Dataset attribute) (datasets_api.models.DatasetHierarchy attribute) (query_state_save.models.QueryState attribute) (user_queries.models.UserQuery attribute) (users_api.models.AuthenticationLog attribute), [1] (users_api.models.GpUserState attribute), [1] (users_api.models.ResetPasswordCode attribute), [1] (users_api.models.SetPasswordCode attribute), [1] (users_api.models.WdaeUser attribute), [1] observed_rate_per_child (dae.common_reports.denovo_report.EffectCell property) obtain_resource_file_lock() (dae.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) OffsetLayoutDrawer (class in dae.pedigrees.drawing) omission (dae.variants.attributes.Inheritance attribute) omission() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) open() (dae.annotation.annotation_pipeline.AnnotationPipeline method) (dae.annotation.annotation_pipeline.Annotator method) (dae.annotation.annotation_pipeline.AnnotatorDecorator method) (dae.annotation.cnv_collection_annotator.CnvCollectionAnnotator method) (dae.annotation.effect_annotator.EffectAnnotatorAdapter method) (dae.annotation.liftover_annotator.AbstractLiftoverAnnotator method) (dae.annotation.normalize_allele_annotator.NormalizeAlleleAnnotator method) (dae.annotation.score_annotator.GenomicScoreAnnotatorBase method) (dae.annotation.simple_effect_annotator.SimpleEffectAnnotator method) (dae.genomic_resources.cnv_collection.CnvCollection method) (dae.genomic_resources.genomic_position_table.BigWigTable method) (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table.GenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table_bigwig.BigWigTable method) (dae.genomic_resources.genomic_position_table.table_inmemory.InmemoryGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table_tabix.TabixGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.table_vcf.VCFGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable method) (dae.genomic_resources.genomic_scores.AlleleScore method) (dae.genomic_resources.genomic_scores.GenomicScore method) (dae.genomic_resources.genomic_scores.NPScore method) (dae.genomic_resources.genomic_scores.PositionScore method) (dae.genomic_resources.liftover_chain.LiftoverChain method) (dae.genomic_resources.reference_genome.ReferenceGenome method) open_bigwig_file() (dae.genomic_resources.cached_repository.CachingProtocol method) (dae.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method)

open_raw_file() (dae.genomic_resources.cached_repository.CachingProtocol method) (dae.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) open_tabix_file() (dae.genomic_resources.cached_repository.CachingProtocol method) (dae.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) open_vcf_file() (dae.genomic_resources.cached_repository.CachingProtocol method) (dae.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) operations (datasets_api.migrations.0001_initial.Migration attribute) (datasets_api.migrations.0002_dataset_groups.Migration attribute) (datasets_api.migrations.0003_alter_dataset_options.Migration attribute) (datasets_api.migrations.0004_dataset_broken.Migration attribute) (datasets_api.migrations.0005_dataset_dataset_name.Migration attribute) (datasets_api.migrations.0006_datasethierarchy.Migration attribute) (datasets_api.migrations.0007_datasethierarchy_direct.Migration attribute) (datasets_api.migrations.0008_datasethierarchy_instance_id.Migration attribute) (query_state_save.migrations.0001_initial.Migration attribute) (query_state_save.migrations.0002_auto_20190205_0736.Migration attribute) (user_queries.migrations.0001_initial.Migration attribute) (users_api.migrations.0001_initial.Migration attribute) (users_api.migrations.0002_auto_20190424_0751.Migration attribute) (users_api.migrations.0003_authenticationlog.Migration attribute) (users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more.Migration attribute) (users_api.migrations.0005_gpuserstate.Migration attribute) OPTION (dae.variants_loaders.raw.loader.ArgumentType attribute) ordinal (dae.pheno.common.InferenceConfig attribute) (dae.pheno.common.MeasureType attribute) OrNode (class in dae.query_variants.attributes_query) OrNode() (dae.query_variants.attributes_query.QueryTreeToBitwiseLambdaTransformer method) (dae.query_variants.attributes_query.QueryTreeToLambdaTransformer method) (dae.query_variants.attributes_query.QueryTreeToSQLBitwiseTransformer static method) other (dae.pheno.common.MeasureType attribute) (dae.variants.attributes.Inheritance attribute) other() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) other_parent() (dae.pedigrees.pedigrees.MatingUnit method) output (dae.pheno.common.ImportConfig attribute) overlap_enrichment_result_dict() (in module dae.enrichment_tool.event_counters) overlap_event_counts() (in module dae.enrichment_tool.event_counters)

P

page (query_state_save.models.QueryState attribute) PAGE_SIZE (dae.gene_profile.db.GeneProfileDB attribute) (dae.pheno.db.PhenoDb attribute) page_size (datasets_api.views.DatasetPermissionsSingleView attribute) (datasets_api.views.DatasetPermissionsView attribute) paginate_queryset() (utils.pagination.WdaePageNumberPagination method) parameters (dae.annotation.annotation_config.AnnotatorInfo attribute) (dae.annotation.annotation_config.AttributeInfo attribute) ParamsUsageMonitor (class in dae.annotation.annotation_config) parent (dae.variants.attributes.Role attribute) parents (dae.person_sets.ChildrenStats attribute) (dae.person_sets.person_sets.ChildrenStats attribute) (dae.studies.study.GenotypeData property) parents_id() (dae.pedigrees.family_role_builder.Mating static method) ParquetGenotypeStorage (class in dae.parquet_storage.storage) ParquetImportStorage (class in dae.parquet_storage.storage) ParquetLoader (class in dae.variants_loaders.parquet.loader) ParquetLoaderException ParquetLoaderVariants (class in dae.parquet_storage.storage) parse() (dae.parquet.partition_descriptor.PartitionDescriptor static method) (sentry.views.PlainTextParser method) parse_and_interpolate() (dae.configuration.gpf_config_parser.GPFConfigParser static method) parse_and_interpolate_file() (dae.configuration.gpf_config_parser.GPFConfigParser class method) parse_ccds_gene_models_format() (in module dae.genomic_resources.gene_models.parsing) parse_cli_argument() (dae.variants_loaders.raw.loader.CLIArgument method) parse_cli_arguments() (dae.pedigrees.loader.FamiliesLoader class method) (dae.variants_loaders.cnv.loader.CNVLoader class method) (dae.variants_loaders.dae.loader.DaeTransmittedLoader class method) (dae.variants_loaders.dae.loader.DenovoLoader class method) (dae.variants_loaders.raw.loader.CLILoader class method) (dae.variants_loaders.vcf.loader.VcfLoader class method) (in module dae.genomic_resources.draw_score_histograms) (in module dae.tools.cnv_liftover) (in module dae.tools.dae_liftover) (in module dae.tools.denovo_liftover) (in module dae.tools.simple_family2pedigree) (in module dae.tools.stats_liftover) (in module dae.tools.vcf_liftover) parse_cli_genome_options() (in module dae.tools.annotate_variants) parse_cli_variants_options() (in module dae.tools.annotate_variants) parse_complete() (dae.annotation.annotation_config.AnnotationConfigParser static method) parse_default_gene_models_format() (in module dae.genomic_resources.gene_models.parsing) parse_denovo_gene_sets_config() (in module dae.gene_sets.denovo_gene_sets_config) parse_denovo_gene_sets_study_config() (in module dae.gene_sets.denovo_gene_sets_config) parse_dgsc_query() (in module dae.gene_sets.denovo_gene_sets_config) parse_dict() (dae.parquet.partition_descriptor.PartitionDescriptor static method) parse_duckdb_config() (in module dae.duckdb_storage.duckdb_storage_config) parse_gr_id_version_token() (in module dae.genomic_resources.repository) parse_gtf_gene_models_format() (in module dae.genomic_resources.gene_models.parsing) parse_known_gene_models_format() (in module dae.genomic_resources.gene_models.parsing) parse_minimal() (dae.annotation.annotation_config.AnnotationConfigParser static method) parse_person_set_collection_config() (in module dae.person_sets) (in module dae.person_sets.person_sets) parse_person_set_collections_study_config() (in module dae.person_sets) (in module dae.person_sets.person_sets) parse_person_set_config() (in module dae.person_sets) (in module dae.person_sets.person_sets) parse_phenotype_data_config() (in module dae.pheno.pheno_import) parse_query_params() (in module utils.query_params) parse_raw() (dae.annotation.annotation_config.AnnotationConfigParser static method) (in module dae.genomic_resources.gene_models.parsing) parse_raw_attribute_config() (dae.annotation.annotation_config.AnnotationConfigParser static method) parse_raw_attributes() (dae.annotation.annotation_config.AnnotationConfigParser static method) parse_recurrency_criteria() (in module dae.gene_sets.denovo_gene_sets_config) parse_ref_flat_gene_models_format() (in module dae.genomic_resources.gene_models.parsing) parse_ref_seq_gene_models_format() (in module dae.genomic_resources.gene_models.parsing) parse_resource_id_version() (in module dae.genomic_resources.repository) parse_short() (dae.annotation.annotation_config.AnnotationConfigParser static method) parse_str() (dae.annotation.annotation_config.AnnotationConfigParser static method) parse_string() (dae.parquet.partition_descriptor.PartitionDescriptor static method) parse_ucscgenepred_models_format() (in module dae.genomic_resources.gene_models.parsing) partial_update() (users_api.views.UserViewSet method), [1] partition_directory() (dae.parquet.partition_descriptor.PartitionDescriptor static method) partition_filename() (dae.parquet.partition_descriptor.PartitionDescriptor static method) PartitionDescriptor (class in dae.parquet.partition_descriptor) PASSED (dae.tools.gpf_validation_runner.TestStatus attribute) passed_case_count (dae.tools.gpf_validation_runner.AbstractRunner property) (dae.tools.gpf_validation_runner.MainRunner property) password (users_api.models.WdaeUser attribute), [1] password_reset() (users_api.views.UserViewSet method), [1] paternal_aunt (dae.variants.attributes.Role attribute) paternal_cousin (dae.variants.attributes.Role attribute) paternal_grandfather (dae.variants.attributes.Role attribute) paternal_grandmother (dae.variants.attributes.Role attribute) paternal_half_sibling (dae.variants.attributes.Role attribute) paternal_uncle (dae.variants.attributes.Role attribute) path (users_api.models.BaseVerificationCode attribute), [1] (users_api.models.ResetPasswordCode attribute), [1] (users_api.models.SetPasswordCode attribute), [1] path_to_fixtures() (in module dae.utils.fixtures) path_to_partitions() (dae.parquet.partition_descriptor.PartitionDescriptor static method) PDFLayoutDrawer (class in dae.pedigrees.drawing) ped_df (dae.pedigrees.families_data.FamiliesData property) pedigree (dae.pheno.common.ImportConfig attribute) (dae.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute) (dae.schema2_storage.schema2_layout.Schema2DatasetLayout attribute) (dae.testing.import_helpers.StudyInputLayout attribute) (dae.testing.StudyInputLayout attribute) pedigree_import() (in module dae.testing.import_helpers) pedigree_parquet_schema() (in module dae.parquet.parquet_writer) pedigree_samples() (dae.pedigrees.families_data.FamiliesData method) peek_first() (dae.genomic_resources.genomic_position_table.line.LineBuffer method) (dae.genomic_resources.genomic_position_table.LineBuffer method) peek_last() (dae.genomic_resources.genomic_position_table.line.LineBuffer method) (dae.genomic_resources.genomic_position_table.LineBuffer method) PeopleCounter (class in dae.common_reports.people_counter) PeopleCounters (class in dae.common_reports.people_counter) PeopleReport (class in dae.common_reports.people_counter) percent_of_children_with_events (dae.common_reports.denovo_report.EffectCell property) peripheral_regions() (dae.annotation.simple_effect_annotator.SimpleEffectAnnotator method) permission_classes (groups_api.views.GroupsViewSet attribute) (query_base.query_base.DatasetAccessRightsView attribute) (users_api.views.UserViewSet attribute), [1] permitted_datasets() (datasets_api.permissions.IsDatasetAllowed static method) Person (class in dae.pedigrees.family) person_column (dae.pheno.common.ImportConfig attribute) person_ids() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) person_set_collections (dae.studies.study.GenotypeData property) (studies.study_wrapper.StudyWrapper property) person_sets_api module person_sets_api.urls module person_sets_api.views module PersonFilter (class in dae.person_filters) (class in dae.person_filters.person_filters) PersonFilterRange (class in dae.person_filters) (class in dae.person_filters.person_filters) PersonFilterSet (class in dae.person_filters) (class in dae.person_filters.person_filters) persons (dae.enrichment_tool.genotype_helper.AlleleEvent attribute) persons_with_parents() (dae.pedigrees.families_data.FamiliesData method) persons_with_roles() (dae.pedigrees.families_data.FamiliesData method) persons_without_parents() (dae.pedigrees.families_data.FamiliesData method) PersonSet (class in dae.person_sets) (class in dae.person_sets.person_sets) PersonSetCollection (class in dae.person_sets) (class in dae.person_sets.person_sets) PersonSetCollectionConfig (class in dae.person_sets) (class in dae.person_sets.person_sets) PersonSetConfig (class in dae.person_sets) (class in dae.person_sets.person_sets) phase() (in module dae.tools.phase) pheno_browser_api module pheno_browser_api.urls module pheno_browser_api.views module pheno_cli_parser() (in module dae.pheno.pheno_import) pheno_id (dae.pheno.pheno_data.PhenotypeData property) pheno_tool_api module pheno_tool_api.urls module pheno_tool_api.views module PhenoConfigView (class in pheno_browser_api.views) PhenoDb (class in dae.pheno.db) PhenoFilter (class in dae.person_filters) (class in dae.person_filters.person_filters) PhenoFilterRange (class in dae.person_filters) (class in dae.person_filters.person_filters)

PhenoFilterSet (class in dae.person_filters) (class in dae.person_filters.person_filters) PhenoImagesView (class in pheno_browser_api.views) PhenoInstrumentsView (class in pheno_browser_api.views) PhenoMeasureDescriptionView (class in pheno_browser_api.views) PhenoMeasureHistogramView (class in measures_api.views) PhenoMeasurePartitionsView (class in measures_api.views) PhenoMeasureRegressionsView (class in measures_api.views) PhenoMeasuresCount (class in pheno_browser_api.views) PhenoMeasuresDownload (class in pheno_browser_api.views) PhenoMeasuresInfoView (class in pheno_browser_api.views) PhenoMeasuresView (class in measures_api.views) (class in pheno_browser_api.views) PhenoMeasureValues (class in pheno_browser_api.views) PhenoRegistry (class in dae.pheno.registry) PhenoResult (class in dae.pheno_tool.tool) PhenoTool (class in dae.pheno_tool.tool) PhenoToolAdapter (class in dae.pheno_tool.pheno_tool_adapter) PhenoToolAdapterBase (class in dae.pheno_tool.pheno_tool_adapter) PhenoToolDownload (class in pheno_tool_api.views) PhenoToolHelper (class in dae.pheno_tool.tool) PhenoToolInstruments (class in pheno_tool_api.views) PhenoToolMeasure (class in pheno_tool_api.views) PhenoToolMeasures (class in pheno_tool_api.views) PhenoToolPeopleValues (class in pheno_tool_api.views) PhenoToolView (class in pheno_tool_api.views) phenotype (dae.studies.study.GenotypeData property) PHENOTYPE_ATTRS (studies.response_transformer.ResponseTransformer attribute) PhenotypeData (class in dae.pheno.pheno_data) PhenotypeGroup (class in dae.pheno.pheno_data) PhenotypeStudy (class in dae.pheno.pheno_data) PlainTextParser (class in sentry.views) plot() (dae.genomic_resources.histogram.CategoricalHistogram method) (dae.genomic_resources.histogram.NullHistogram method) (dae.genomic_resources.histogram.NumberHistogram method) plot_function (dae.genomic_resources.histogram.CategoricalHistogramConfig attribute) (dae.genomic_resources.histogram.NumberHistogramConfig attribute) plot_histogram() (in module dae.genomic_resources.histogram) Point (class in dae.pedigrees.layout) poisson_test() (in module dae.enrichment_tool.samocha_background) pop_first() (dae.genomic_resources.genomic_position_table.line.LineBuffer method) (dae.genomic_resources.genomic_position_table.LineBuffer method) pos (dae.annotation.annotatable.Annotatable property) pos_aggregator (dae.genomic_resources.genomic_scores.ScoreDef attribute) pos_begin (dae.genomic_resources.cnv_collection.CNV attribute) (dae.genomic_resources.genomic_position_table.Line attribute) (dae.genomic_resources.genomic_position_table.line.Line attribute) (dae.genomic_resources.genomic_position_table.line.LineBase attribute) POS_BEGIN (dae.genomic_resources.genomic_position_table.table.GenomicPositionTable attribute) (dae.genomic_resources.genomic_position_table.table_vcf.VCFGenomicPositionTable attribute) (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) pos_begin (dae.genomic_resources.genomic_scores.ScoreLine property) pos_begin_key (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) pos_end (dae.annotation.annotatable.Annotatable property) (dae.genomic_resources.cnv_collection.CNV attribute) (dae.genomic_resources.genomic_position_table.Line attribute) (dae.genomic_resources.genomic_position_table.line.Line attribute) (dae.genomic_resources.genomic_position_table.line.LineBase attribute) POS_END (dae.genomic_resources.genomic_position_table.table.GenomicPositionTable attribute) (dae.genomic_resources.genomic_position_table.table_vcf.VCFGenomicPositionTable attribute) (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) pos_end (dae.genomic_resources.genomic_scores.ScoreLine property) pos_end_key (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) Position (class in dae.annotation.annotatable) position (dae.annotation.annotatable.Annotatable property) POSITION (dae.annotation.annotatable.Annotatable.Type attribute) position (dae.variants.core.Allele property) (dae.variants.core.Allele.Type attribute) (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) (dae.variants.variant.SummaryVariant property) position_aggregator (dae.genomic_resources.genomic_scores.AlleleScoreAggr attribute) (dae.genomic_resources.genomic_scores.AlleleScoreQuery attribute) (dae.genomic_resources.genomic_scores.NPScoreAggr attribute) (dae.genomic_resources.genomic_scores.NPScoreQuery attribute) (dae.genomic_resources.genomic_scores.PositionScoreAggr attribute) (dae.genomic_resources.genomic_scores.PositionScoreQuery attribute) PositionScore (class in dae.genomic_resources.genomic_scores) PositionScoreAggr (class in dae.genomic_resources.genomic_scores) PositionScoreAnnotator (class in dae.annotation.score_annotator) PositionScoreAnnotatorBase (class in dae.annotation.score_annotator) PositionScoreQuery (class in dae.genomic_resources.genomic_scores) PositiveStrandAnnotationRequest (class in dae.effect_annotation.annotation_request) possible_denovo (dae.variants.attributes.Inheritance attribute) possible_denovo() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) possible_omission (dae.variants.attributes.Inheritance attribute) possible_omission() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) possiblePersonPhasing() (in module dae.tools.phase) possiblePersonPhasingR() (in module dae.tools.phase) post() (common_reports_api.views.FamiliesDataDownloadView method) (common_reports_api.views.FamilyCounterDownloadView method) (common_reports_api.views.FamilyCounterListView method) (datasets_api.views.DatasetDescriptionView method) (enrichment_api.views.EnrichmentTestView method) (gene_scores.views.GeneScoresPartitionsView method) (gene_sets.views.GeneSetDownloadView method) (gene_sets.views.GeneSetsView method) (gene_view.views.DownloadSummaryVariantsView method) (gene_view.views.QueryVariantsView method) (genotype_browser.views.GenotypeBrowserQueryView method), [1] (gpf_instance.views.MarkdownFileView method) (measures_api.views.PhenoMeasureHistogramView method) (measures_api.views.PhenoMeasurePartitionsView method) (pheno_browser_api.views.PhenoMeasureValues method) (pheno_tool_api.views.PhenoToolDownload method) (pheno_tool_api.views.PhenoToolPeopleValues method) (pheno_tool_api.views.PhenoToolView method) (query_state_save.views.QueryStateDeleteView method) (query_state_save.views.QueryStateLoadView method) (query_state_save.views.QueryStateSaveView method) (user_queries.views.UserQuerySaveView method) (users_api.views.BasePasswordView method), [1] (users_api.views.FederationCredentials method), [1] (users_api.views.ForgotPassword method), [1] (users_api.views.RESTLoginView method), [1] (users_api.views.UserGpStateView method), [1] (users_api.views.WdaeLoginView method), [1] prb (dae.variants.attributes.Role attribute) preamble (dae.annotation.annotation_config.RawFullConfig attribute) prepare_allowed_datasets_query() (datasets_api.permissions.IsDatasetAllowed static method) PreparePhenoBrowserBase (class in dae.pheno.prepare_data) Primitive (class in dae.query_variants.attributes_query_inheritance) primitive() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) print_meta() (dae.annotation.annotate_schema2_parquet.AnnotateSchema2ParquetTool method) PriorityGenomicContext (class in dae.genomic_resources.genomic_context) probe_columns() (in module dae.genomic_resources.gene_models.parsing) probe_header() (in module dae.genomic_resources.gene_models.parsing) process_config() (dae.configuration.gpf_config_parser.GPFConfigParser static method) process_graph() (dae.task_graph.cli_tools.TaskGraphCli static method) produce_annotation_pipeline() (dae.annotation.annotate_utils.AnnotationTool static method) produce_genotype() (dae.variants_loaders.dae.loader.DenovoLoader static method) produce_partfile_paths() (in module dae.annotation.annotate_utils) produce_regions() (in module dae.annotation.annotate_utils) (in module dae.annotation.parquet) produce_schema2_annotation_tasks() (in module dae.annotation.parquet) produce_schema2_merging_tasks() (in module dae.annotation.parquet) produce_tabix_index() (in module dae.annotation.annotate_columns) produce_tree() (datasets_api.views.DatasetHierarchyView method) ProfileView (class in gene_profiles_api.views) progress() (in module dae.utils.progress) progress_nl() (in module dae.utils.progress) PromoterEffectChecker (class in dae.effect_annotation.effect_checkers.promoter) protein_coding_gene_number (dae.genomic_resources.implementations.gene_models_impl.StatisticsData attribute) protein_coding_transcript_number (dae.genomic_resources.implementations.gene_models_impl.StatisticsData attribute) ProteinChangeEffectChecker (class in dae.effect_annotation.effect_checkers.protein_change) proto_builder() (in module dae.genomic_resources.testing) prune() (dae.genomic_resources.genomic_position_table.line.LineBuffer method) (dae.genomic_resources.genomic_position_table.LineBuffer method) (dae.task_graph.graph.TaskGraph method) psc_id (dae.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (dae.person_sets.person_sets.PSCQuery attribute) (dae.person_sets.PSCQuery attribute) PSCQuery (class in dae.person_sets) (class in dae.person_sets.person_sets) pseudo_autosomal (dae.variants.attributes.GeneticModel attribute) pub_med (dae.studies.study.GenotypeData property) put() (users_api.views.FederationCredentials method), [1] put_value_in_result_queue() (dae.query_variants.query_runners.QueryRunner method) pvalues (dae.pheno.utils.lin_regress.LinearRegression property) pysam_file (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute)

Q

QUAD (dae.pedigrees.family.FamilyTag attribute) query (user_queries.models.UserQuery attribute) query_base module query_base.query_base module query_fpids() (dae.person_sets.person_sets.PersonSetCollection method) (dae.person_sets.PersonSetCollection method) query_gp_statistics() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) query_gps() (dae.gene_profile.db.GeneProfileDB method) query_id (user_queries.models.UserQuery attribute) query_person_ids() (dae.person_sets.person_sets.PersonSetCollection method) (dae.person_sets.PersonSetCollection method) query_resources() (dae.annotation.annotation_config.AnnotationConfigParser static method) query_result_summary_variants() (dae.studies.study.GenotypeData method) query_result_variants() (dae.studies.study.GenotypeData method) query_state_save module query_state_save.migrations module query_state_save.migrations.0001_initial module query_state_save.migrations.0002_auto_20190205_0736 module query_state_save.models module query_state_save.serializers module query_state_save.urls module query_state_save.views module query_str() (dae.query_variants.attributes_query.Matcher method) query_summary_variants() (dae.duckdb_storage.duckdb2_variants.DuckDb2Variants method) (dae.inmemory_storage.raw_variants.RawFamilyVariants method) (dae.query_variants.base_query_variants.QueryVariantsBase method) (dae.query_variants.sql.schema2.base_variants.SqlSchema2Variants method) (dae.studies.study.GenotypeData method)

query_variants() (dae.duckdb_storage.duckdb2_variants.DuckDb2Variants method) (dae.inmemory_storage.raw_variants.RawFamilyVariants method) (dae.query_variants.base_query_variants.QueryVariantsBase method) (dae.query_variants.sql.schema2.base_variants.SqlSchema2Variants method) (dae.studies.study.GenotypeData method) query_variants_wdae() (studies.study_wrapper.StudyWrapperBase method) query_variants_wdae_streaming() (studies.study_wrapper.StudyWrapper method) (studies.study_wrapper.StudyWrapperBase method) QueryBaseView (class in query_base.query_base) QueryBuilderBase (class in dae.query_variants.sql.schema2.sql_query_builder) QueryHeuristics (class in dae.query_variants.sql.schema2.sql_query_builder) QueryResult (class in dae.query_variants.query_runners) QueryRunner (class in dae.query_variants.query_runners) queryset (users_api.views.UserViewSet attribute), [1] QueryState (class in query_state_save.models) QueryState.DoesNotExist QueryState.MultipleObjectsReturned QueryStateDeleteView (class in query_state_save.views) QueryStateLoadView (class in query_state_save.views) QueryStateSaveView (class in query_state_save.views) QueryStateSerializer (class in query_state_save.serializers) QueryStateSerializer.Meta (class in query_state_save.serializers) QueryTransformer (class in studies.query_transformer) QueryTransformerMatcher (class in dae.query_variants.attributes_query) QueryTreeToBitwiseLambdaTransformer (class in dae.query_variants.attributes_query) QueryTreeToLambdaTransformer (class in dae.query_variants.attributes_query) QueryTreeToSQLBitwiseTransformer (class in dae.query_variants.attributes_query) QueryTreeToSQLTransformer (class in dae.query_variants.attributes_query) QueryVariantsBase (class in dae.query_variants.base_query_variants) QueryVariantsView (class in gene_view.views) QUOTE (dae.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute)

R

RankRange (class in dae.pheno.common) raw (dae.pheno.common.MeasureType attribute) raw_values (dae.genomic_resources.histogram.CategoricalHistogram property) RawFamilyVariants (class in dae.inmemory_storage.raw_variants) RawFullConfig (class in dae.annotation.annotation_config) RawMemoryVariants (class in dae.inmemory_storage.raw_variants) RawPreamble (class in dae.annotation.annotation_config) RawVariantsQueryRunner (class in dae.inmemory_storage.raw_variants) read_and_classify_measure() (in module dae.pheno.pheno_import) read_ewa_set_file() (in module dae.gene_sets.gene_term) read_gmt_file() (in module dae.gene_sets.gene_term) read_input() (in module dae.annotation.annotate_columns) read_instrument_measure_names() (in module dae.pheno.pheno_import) read_mapping_file() (in module dae.gene_sets.gene_term) read_only (dae.duckdb_storage.duckdb_storage_config.DuckDbConf attribute) (dae.genotype_storage.genotype_storage.GenotypeStorage property) read_pedigree() (in module dae.pheno.pheno_import) Reader (class in dae.variants_loaders.parquet.loader) READONLY (dae.genomic_resources.repository.Mode attribute) ReadOnlyRepositoryProtocol (class in dae.genomic_resources.repository) READWRITE (dae.genomic_resources.repository.Mode attribute) ReadWriteRepositoryProtocol (class in dae.genomic_resources.repository) ready() (gpf_instance.apps.WDAEConfig method) real_attr() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) real_persons (dae.pedigrees.families_data.FamiliesData property) Realization (class in dae.pedigrees.pedigrees) ReannotateInstanceTool (class in dae.annotation.reannotate_instance) ReannotationPipeline (class in dae.annotation.annotation_pipeline) reason (dae.genomic_resources.histogram.NullHistogramConfig attribute) rebuild_families() (dae.studies.study.GenotypeDataGroup method) rec (dae.enrichment_tool.event_counters.EnrichmentResult attribute) (dae.enrichment_tool.event_counters.EventCountersResult attribute) (dae.enrichment_tool.event_counters.EventsResult attribute) (dae.enrichment_tool.event_counters.VariantEventsResult attribute) rec_genes (dae.enrichment_tool.event_counters.EnrichmentResult attribute) (dae.enrichment_tool.event_counters.EventCountersResult attribute) reconfigure() (in module dae.dask.config) RecordToAnnotable (class in dae.annotation.record_to_annotatable) RecordToCNVAllele (class in dae.annotation.record_to_annotatable) RecordToPosition (class in dae.annotation.record_to_annotatable) RecordToRegion (class in dae.annotation.record_to_annotatable) RecordToVcfAllele (class in dae.annotation.record_to_annotatable) recreate_dataset_perm() (datasets_api.models.Dataset class method) recurrency (dae.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) (dae.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) RecurrencyCriteriaBase (class in dae.gene_sets.denovo_gene_sets_config) RecurrentCriteria (class in dae.gene_sets.denovo_gene_sets_config) recursive_dict_update() (in module dae.utils.dict_utils) recursive_dict_update_inplace() (in module dae.utils.dict_utils) red (wdae.default_settings.CustomFormatter attribute) red_print() (in module dae.utils.progress) redefine() (dae.pedigrees.families_data.FamiliesData method) (dae.pedigrees.family.Family method) (dae.pedigrees.family.Person method) ref (dae.annotation.annotatable.VCFAllele property) (dae.genomic_resources.genomic_position_table.Line attribute) (dae.genomic_resources.genomic_position_table.line.Line attribute) (dae.genomic_resources.genomic_position_table.line.LineBase attribute) REF (dae.genomic_resources.genomic_position_table.table.GenomicPositionTable attribute) ref (dae.genomic_resources.genomic_scores.ScoreLine property) ref_allele (dae.variants.variant.SummaryVariant property) ref_key (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) reference (dae.annotation.annotatable.VCFAllele property) (dae.variants.attributes.Inheritance attribute) (dae.variants.core.Allele property) (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) (dae.variants.variant.SummaryVariant property) reference() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) reference_genome (dae.gpf_instance.gpf_instance.GPFInstance property) (dae.gpf_instance.GPFInstance property) reference_genotype() (in module dae.utils.variant_utils) ReferenceGenome (class in dae.genomic_resources.reference_genome) ReferenceGenomeImplementation (class in dae.genomic_resources.implementations.reference_genome_impl) ReferenceGenomeStatistics (class in dae.genomic_resources.implementations.reference_genome_impl) refresh_cached_resource() (dae.genomic_resources.cached_repository.CachingProtocol method) refresh_cached_resource_file() (dae.genomic_resources.cached_repository.CachingProtocol method) Region (class in dae.annotation.annotatable) (class in dae.utils.regions) REGION (dae.annotation.annotatable.Annotatable.Type attribute) region() (dae.genomic_resources.genomic_position_table.line.LineBuffer method) (dae.genomic_resources.genomic_position_table.LineBuffer method) region_bin (dae.import_tools.import_tools.Bucket attribute) region_bins (dae.query_variants.sql.schema2.sql_query_builder.QueryHeuristics attribute) region_bins() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) region_bins_count() (dae.parquet.partition_descriptor.PartitionDescriptor method) REGION_BINS_HEURISTIC_CUTOFF (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase attribute) region_to_dict() (genomes_api.views.GeneModels method) region_to_region_bins() (dae.parquet.partition_descriptor.PartitionDescriptor method) regions (dae.import_tools.import_tools.Bucket attribute) regions() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) regions2bedfile() (in module dae.utils.regions) register() (dae.annotation.context.CLIAnnotationContext static method) (dae.genomic_resources.genomic_context.CLIGenomicContext static method) (dae.genomic_resources.genomic_context.DefaultRepositoryContextProvider static method) (in module users_api.views), [1] register_annotator_factory() (in module dae.annotation.annotation_factory) register_context() (in module dae.genomic_resources.genomic_context) register_context_provider() (in module dae.genomic_resources.genomic_context) register_default_storage() (dae.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) register_enrichment_builder() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) register_genotype_data() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) (dae.studies.variants_db.VariantsDb method) register_genotype_storage() (dae.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method)

register_genotype_storage_factory() (in module dae.genotype_storage) register_import_storage_factory() (in module dae.import_tools.import_tools) register_pheno_tool_adapter() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) register_phenotype_data() (dae.pheno.registry.PhenoRegistry method) register_preexisting_user() (users_api.models.WdaeUser method), [1] register_storage_config() (dae.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) register_storages_configs() (dae.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) regression_display_names (dae.pheno.db.PhenoDb property) regression_display_names_with_ids (dae.pheno.db.PhenoDb property) regression_ids (dae.pheno.db.PhenoDb property) relabel_chromosomes() (dae.genomic_resources.gene_models.gene_models.GeneModels method) (dae.genomic_resources.gene_models.GeneModels method) reload() (dae.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) (dae.studies.variants_db.VariantsDb method) reload_statistics() (dae.genomic_resources.resource_implementation.GenomicResourceImplementation method) remove_annoying_characters() (in module dae.pheno.utils.commons) remove_elements() (dae.common_reports.denovo_report.EffectRow method) remove_empty_person_sets() (dae.person_sets.person_sets.PersonSetCollection static method) (dae.person_sets.PersonSetCollection static method) remove_study_config() (dae.studies.dataset_helpers.DatasetHelpers method) remove_wdae_dataset_and_groups() (users_api.management.commands.dataset_mixin.DatasetBaseMixin method) rename_gene_terms() (in module dae.gene_sets.gene_term) rename_genes() (dae.gene_sets.gene_term.GeneTerms method) rename_study_config() (dae.studies.dataset_helpers.DatasetHelpers method) rename_wdae_dataset_and_groups() (users_api.management.commands.dataset_mixin.DatasetBaseMixin method) replace_tables() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) repo_id (dae.genomic_resources.repository.GenomicResourceRepo property) report_alleles() (in module dae.tools.vcf_liftover) report_only (dae.pheno.common.ImportConfig attribute) report_variant() (in module dae.tools.vcf_liftover) report_vcf_variant() (in module dae.tools.vcf_liftover) request_logging() (in module utils.logger) request_logging_function_view() (in module utils.logger) REQUIRED_FIELDS (users_api.models.WdaeUser attribute), [1] reset (wdae.default_settings.CustomFormatter attribute) reset() (dae.genomic_resources.gene_models.gene_models.GeneModels method) (dae.genomic_resources.gene_models.GeneModels method) reset_password() (users_api.models.WdaeUser method), [1] reset_regions() (dae.variants_loaders.cnv.loader.CNVLoader method) (dae.variants_loaders.dae.loader.DenovoLoader method) (dae.variants_loaders.raw.loader.VariantsGenotypesLoader method) (dae.variants_loaders.raw.loader.VariantsLoader method) (dae.variants_loaders.vcf.loader.VcfLoader method) ResetPassword (class in users_api.views), [1] ResetPasswordCode (class in users_api.models), [1] resetpasswordcode (users_api.models.WdaeUser attribute), [1] ResetPasswordCode.DoesNotExist, [1] ResetPasswordCode.MultipleObjectsReturned, [1] resolve_repeated_attributes() (in module dae.annotation.annotation_factory) resource (dae.genomic_resources.resource_implementation.InfoImplementationMixin attribute) resource_builder() (in module dae.genomic_resources.testing) resource_id (dae.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground property) (dae.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property) (dae.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation property) (dae.gene_scores.gene_scores.ScoreDesc attribute) (dae.genomic_resources.gene_models.gene_models.GeneModels property) (dae.genomic_resources.gene_models.GeneModels property) (dae.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation property) (dae.genomic_resources.reference_genome.ReferenceGenome property) (dae.genomic_resources.resource_implementation.GenomicResourceImplementation property) (dae.genomic_scores.scores.ScoreDesc attribute) resource_ids (dae.annotation.annotation_pipeline.Annotator property) ResourceConfigValidationMixin (class in dae.genomic_resources.resource_implementation) ResourceFileState (class in dae.genomic_resources.repository) resources (dae.annotation.annotation_config.AnnotatorInfo attribute) (dae.annotation.annotation_pipeline.Annotator property) ResourceStatistics (class in dae.genomic_resources.resource_implementation) RESPONSE_LIMIT (genomes_api.views.GeneSymbolsSearch attribute) ResponseTransformer (class in studies.response_transformer) RESTLoginView (class in users_api.views), [1] result (dae.task_graph.cache.CacheRecord property) result_or_error (dae.task_graph.cache.CacheRecord attribute) result_queue (dae.query_variants.query_runners.QueryRunner property) retrieve() (users_api.views.UserViewSet method), [1] rev_chrom_map (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) reverse_complement() (in module dae.utils.variant_utils) rm_file() (in module dae.utils.fs_utils) Role (class in dae.variants.attributes) role (dae.pedigrees.family.Person property) role_labels() (in module dae.pheno.graphs) roles() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) roles_converter() (in module dae.query_variants.attributes_query) row() (dae.genomic_resources.genomic_position_table.BigWigLine method) (dae.genomic_resources.genomic_position_table.Line method) (dae.genomic_resources.genomic_position_table.line.BigWigLine method) (dae.genomic_resources.genomic_position_table.line.Line method) (dae.genomic_resources.genomic_position_table.line.LineBase method) (dae.genomic_resources.genomic_position_table.line.VCFLine method) (dae.genomic_resources.genomic_position_table.VCFLine method) rules (dae.configuration.gpf_config_parser.GPFConfigValidator attribute) run() (dae.annotation.annotate_utils.AnnotationTool method) (dae.duckdb_storage.duckdb2_variants.DuckDb2Runner method) (dae.duckdb_storage.duckdb_variants.DuckDbRunner method) (dae.inmemory_storage.raw_variants.RawVariantsQueryRunner method) (dae.pheno.prepare_data.PreparePhenoBrowserBase method) (dae.query_variants.query_runners.QueryRunner method) (dae.tools.gpf_validation_runner.GenotypeBrowserRunner method) run_annotate() (dae.annotation.simple_effect_annotator.SimpleEffectAnnotator method) run_validation() (users_api.serializers.UserSerializer method), [1] run_with_project() (in module dae.import_tools.cli) RUNNER_CLASS (dae.duckdb_storage.duckdb_variants.DuckDbVariants attribute) (dae.query_variants.base_query_variants.QueryVariantsBase attribute) (dae.query_variants.sql.schema2.base_variants.SqlSchema2Variants attribute)

S

s3_test_protocol() (in module dae.genomic_resources.testing) s3_test_server_endpoint() (in module dae.genomic_resources.testing) safe_db_name() (in module dae.pheno.db) safe_task_id() (in module dae.task_graph.logging) SamochaEnrichmentBackground (class in dae.enrichment_tool.samocha_background) sample_index (dae.pedigrees.family.Person property) samples_index (dae.pedigrees.family.Family property) SandwichInstance (class in dae.pedigrees.pedigrees) SandwichSolver (class in dae.pedigrees.pedigrees) save() (dae.common_reports.common_report.CommonReport method) (dae.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) (dae.gene_sets.gene_term.GeneTerms method) (dae.pheno.db.PhenoDb method) (dae.utils.statistics.StatsCollection method) save_annotation_file() (dae.variants_loaders.raw.loader.AnnotationDecorator static method) save_as_default_gene_models() (in module dae.genomic_resources.gene_models) (in module dae.genomic_resources.gene_models.serialization) save_as_tabix_table() (in module dae.genomic_resources.genomic_position_table.utils) save_families() (dae.pedigrees.loader.FamiliesLoader static method) save_fig() (dae.pheno.prepare_data.PreparePhenoBrowserBase class method) save_histogram() (in module dae.genomic_resources.histogram) save_index() (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) save_liftover_stats() (in module dae.tools.stats_liftover) save_manifest() (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) save_ped_df_to_parquet() (in module dae.parquet.parquet_writer) save_pedigree() (dae.pedigrees.loader.FamiliesLoader static method) save_regression() (dae.pheno.db.PhenoDb method) save_regression_values() (dae.pheno.db.PhenoDb method) save_resource_file_state() (dae.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) save_study_config() (in module dae.import_tools.import_tools) scale() (dae.pedigrees.layout.Layout method) schema1_partition() (dae.parquet.partition_descriptor.PartitionDescriptor method) schema2_project_dataset_layout() (in module dae.schema2_storage.schema2_import_storage) Schema2DatasetLayout (class in dae.schema2_storage.schema2_layout) Schema2ImportStorage (class in dae.schema2_storage.schema2_import_storage) schema_family (dae.parquet.schema2.serializers.AlleleParquetSerializer property) schema_summary (dae.parquet.schema2.serializers.AlleleParquetSerializer property) score (dae.genomic_resources.genomic_scores.AlleleScoreAggr attribute) (dae.genomic_resources.genomic_scores.AlleleScoreQuery attribute) (dae.genomic_resources.genomic_scores.NPScoreAggr attribute) (dae.genomic_resources.genomic_scores.NPScoreQuery attribute) (dae.genomic_resources.genomic_scores.PositionScoreAggr attribute) (dae.genomic_resources.genomic_scores.PositionScoreQuery attribute) score_id (dae.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property) (dae.gene_scores.gene_scores.ScoreDef attribute) (dae.gene_scores.gene_scores.ScoreDesc attribute) (dae.genomic_resources.genomic_scores.ScoreDef attribute) ScoreDef (class in dae.gene_scores.gene_scores) (class in dae.genomic_resources.genomic_scores) ScoreDesc (class in dae.gene_scores.gene_scores) (class in dae.genomic_scores.scores) ScoreLine (class in dae.genomic_resources.genomic_scores) search_fields (groups_api.views.GroupsViewSet attribute) (users_api.views.UserViewSet attribute), [1] search_measures() (dae.pheno.db.PhenoDb method) (dae.pheno.pheno_data.PhenotypeData method) (dae.pheno.pheno_data.PhenotypeGroup method) (dae.pheno.pheno_data.PhenotypeStudy method) search_measures_df() (dae.pheno.db.PhenoDb method) select_events_in_person_set() (dae.enrichment_tool.event_counters.CounterBase method) selected_person_set_collections (dae.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) selected_person_sets (dae.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (dae.person_sets.person_sets.PSCQuery attribute) (dae.person_sets.PSCQuery attribute) send_already_existing_email() (in module users_api.models), [1] send_reset_email() (in module users_api.models), [1] send_reset_inactive_acc_email() (in module users_api.models), [1] send_verif_email() (in module users_api.models), [1] sentry module sentry() (in module sentry.views) sentry.urls module sentry.views module SEP1 (dae.variants_loaders.raw.loader.AnnotationDecorator attribute) SEP2 (dae.variants_loaders.raw.loader.AnnotationDecorator attribute) SEP3 (dae.variants_loaders.raw.loader.AnnotationDecorator attribute) SequentialExecutor (class in dae.task_graph.executor) serialize() (dae.enrichment_tool.enrichment_serializer.EnrichmentSerializer method) (dae.genomic_resources.histogram.CategoricalHistogram method) (dae.genomic_resources.histogram.NullHistogram method) (dae.genomic_resources.histogram.NumberHistogram method) (dae.genomic_resources.implementations.gene_models_impl.GeneModelsStatistics method) (dae.genomic_resources.implementations.reference_genome_impl.ChromosomeStatistic method) (dae.genomic_resources.implementations.reference_genome_impl.GenomeStatistic method) (dae.genomic_resources.statistics.base_statistic.Statistic method) (dae.genomic_resources.statistics.min_max.MinMaxValue method) (dae.parquet.partition_descriptor.PartitionDescriptor method) serialize_all() (dae.enrichment_tool.enrichment_serializer.EnrichmentSerializer method) serialize_common_filter() (dae.enrichment_tool.enrichment_serializer.EnrichmentSerializer method) serialize_enrichment_result() (dae.enrichment_tool.enrichment_serializer.EnrichmentSerializer method) serialize_family() (dae.parquet.schema2.variant_serializers.JsonVariantsDataSerializer method) (dae.parquet.schema2.variant_serializers.VariantsDataSerializer method) serialize_female() (dae.enrichment_tool.enrichment_serializer.EnrichmentSerializer method) serialize_male() (dae.enrichment_tool.enrichment_serializer.EnrichmentSerializer method) serialize_overlap_filter() (dae.enrichment_tool.enrichment_serializer.EnrichmentSerializer method) serialize_people_groups() (dae.enrichment_tool.enrichment_serializer.EnrichmentSerializer method) serialize_rec() (dae.enrichment_tool.enrichment_serializer.EnrichmentSerializer method) serialize_rec_filter() (dae.enrichment_tool.enrichment_serializer.EnrichmentSerializer method) serialize_summary() (dae.parquet.schema2.variant_serializers.JsonVariantsDataSerializer method) (dae.parquet.schema2.variant_serializers.VariantsDataSerializer method) serialize_summary_schema() (in module dae.parquet.parquet_writer) serializer_class (groups_api.views.GroupsViewSet attribute) (users_api.views.UserViewSet attribute), [1] SessionAuthenticationWithoutCSRF (class in utils.authentication) SessionAuthenticationWithUnauthenticatedCSRF (class in utils.authentication) set() (dae.utils.verbosity_configuration.VerbosityConfiguration static method) set_argument() (dae.effect_annotation.cli.AnnotationAttributes static method) (dae.effect_annotation.cli.VariantColumnInputFile static method) (dae.effect_annotation.cli.VariantColumnOutputFile static method) set_arguments() (dae.effect_annotation.cli.EffectAnnotatorBuilder static method) (dae.utils.verbosity_configuration.VerbosityConfiguration static method) set_attr() (dae.pedigrees.family.Person method) (in module dae.pedigrees.family_tag_builder) set_attribute() (dae.variants_loaders.raw.loader.VariantsLoader method) set_broken() (datasets_api.models.Dataset class method) set_context() (users_api.validators.SomeSuperuserLeftValidator method), [1] set_figure_size() (in module dae.pheno.graphs) set_fit_request() (dae.pheno.utils.lin_regress.LinearRegression method) set_matched_alleles() (dae.variants.variant.SummaryVariant method) set_measure() (dae.pheno.prepare.measure_classifier.ClassifierReport method) set_negative_stats() (dae.pheno_tool.tool.PhenoResult method) set_password() (users_api.models.WdaeUser method), [1] set_position() (dae.effect_annotation.variant.Variant method) set_positive_stats() (dae.pheno_tool.tool.PhenoResult method) set_ref_alt() (dae.effect_annotation.variant.Variant method) set_ref_alt_from_variant() (dae.effect_annotation.variant.Variant method) set_result_queue() (dae.query_variants.query_runners.QueryRunner method) set_score_request() (dae.pheno.utils.lin_regress.LinearRegression method) set_study_id() (dae.query_variants.query_runners.QueryRunner method) set_tag() (dae.pedigrees.family.Family method) (dae.pedigrees.family.Person method) (in module dae.pedigrees.family_tag_builder) set_unusable_password() (users_api.models.WdaeUser method), [1] set_up_kubernetes_cluster() (in module dae.dask.named_cluster) set_up_local_cluster() (in module dae.dask.named_cluster) set_up_sge_cluster() (in module dae.dask.named_cluster) set_up_slurm_cluster() (in module dae.dask.named_cluster) set_verbosity() (dae.utils.verbosity_configuration.VerbosityConfiguration static method) SetPassword (class in users_api.views), [1] SetPasswordCode (class in users_api.models), [1] setpasswordcode (users_api.models.WdaeUser attribute), [1] SetPasswordCode.DoesNotExist, [1] SetPasswordCode.MultipleObjectsReturned, [1] setup_bigwig() (in module dae.genomic_resources.testing) setup_client() (in module dae.dask.named_cluster) setup_client_from_config() (in module dae.dask.named_cluster) setup_dae_transmitted() (in module dae.genomic_resources.testing) (in module dae.testing) setup_dataset() (in module dae.testing) (in module dae.testing.import_helpers) setup_dataset_config() (in module dae.testing.import_helpers) setup_denovo() (in module dae.genomic_resources.testing) (in module dae.testing) setup_directories() (in module dae.genomic_resources.testing) (in module dae.testing) setup_empty_gene_models() (in module dae.genomic_resources.testing) (in module dae.testing) setup_gene_models() (in module dae.genomic_resources.testing) (in module dae.testing) setup_genome() (in module dae.genomic_resources.testing) (in module dae.testing) setup_gpf_instance() (in module dae.testing) (in module dae.testing.setup_helpers) setup_gzip() (in module dae.genomic_resources.testing) setup_import_project() (in module dae.testing) (in module dae.testing.import_helpers) setup_import_project_config() (in module dae.testing.import_helpers) setup_pedigree() (in module dae.genomic_resources.testing) (in module dae.testing) setup_t4c8_grr() (in module dae.conftest) (in module utils.testing) setup_t4c8_instance() (in module dae.conftest) (in module utils.testing) setup_tabix() (in module dae.genomic_resources.testing) setup_vcf() (in module dae.genomic_resources.testing) (in module dae.testing) setup_wgpf_instance() (in module utils.testing) setup_work_dir() (dae.annotation.annotate_utils.AnnotationTool method) SEVERITY (dae.effect_annotation.effect.AnnotationEffect attribute)

Sex (class in dae.variants.attributes) sex (dae.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (dae.pedigrees.family.Person property) sex_converter() (in module dae.query_variants.attributes_query) sexes (dae.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) (dae.gene_sets.denovo_gene_sets_config.SexesCriteria attribute) sexes() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) SexesCriteria (class in dae.gene_sets.denovo_gene_sets_config) sha256sum() (in module dae.utils.filehash) short() (dae.variants.attributes.Sex method) (dae.variants.attributes.Status method) short_attributes() (dae.pheno.prepare.measure_classifier.ClassifierReport static method) shutdown() (dae.duckdb_storage.duckdb_genotype_storage.AbstractDuckDbStorage method) (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) (dae.genotype_storage.genotype_storage.GenotypeStorage method) (dae.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) (dae.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage method) (dae.parquet_storage.storage.ParquetGenotypeStorage method) sib (dae.variants.attributes.Role attribute) SibshipUnit (class in dae.pedigrees.pedigrees) sign() (in module dae.utils.fs_utils) simple_arg() (dae.query_variants.attributes_query.BitwiseTreeTransformer method) (dae.query_variants.attributes_query.StringQueryToTreeTransformer method) SimpleEffectAnnotator (class in dae.annotation.simple_effect_annotator) SimpleGenomicContext (class in dae.genomic_resources.genomic_context) SimpleGenomicContextProvider (class in dae.genomic_resources.genomic_context) SIMPLEX (dae.pedigrees.family.FamilyTag attribute) simplify_effects() (dae.effect_annotation.effect.AnnotationEffect class method) single_annotate() (dae.annotation.annotate_columns.AnnotateColumnsTool static method) SingleCriteria (class in dae.gene_sets.denovo_gene_sets_config) SingleVcfLoader (class in dae.variants_loaders.vcf.loader) size (dae.genomic_resources.cnv_collection.CNV property) (dae.genomic_resources.repository.ManifestEntry attribute) (dae.genomic_resources.repository.ResourceFileState attribute) SIZE (dae.pedigrees.layout.IndividualWithCoordinates attribute) size() (dae.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) skip (dae.pheno.common.InferenceConfig attribute) skipped (dae.pheno.common.MeasureType attribute) SMALL_DELETION (dae.annotation.annotatable.Annotatable.Type attribute) small_deletion (dae.variants.core.Allele.Type attribute) SMALL_DPI (dae.pheno.prepare_data.PreparePhenoBrowserBase attribute) SMALL_INSERTION (dae.annotation.annotatable.Annotatable.Type attribute) small_insertion (dae.variants.core.Allele.Type attribute) small_values_desc (dae.gene_scores.gene_scores.ScoreDef attribute) (dae.gene_scores.gene_scores.ScoreDesc attribute) (dae.genomic_resources.genomic_scores.ScoreDef attribute) (dae.genomic_scores.scores.ScoreDesc attribute) solve() (dae.pedigrees.pedigrees.SandwichSolver static method) SomeSuperuserLeftValidator (class in users_api.validators), [1] sort_effects() (dae.effect_annotation.effect.AnnotationEffect class method) source (dae.annotation.annotation_config.AttributeInfo attribute) (dae.genomic_scores.scores.ScoreDesc attribute) (dae.person_sets.person_sets.SourceConfig attribute) (dae.person_sets.SourceConfig attribute) SourceConfig (class in dae.person_sets) (class in dae.person_sets.person_sets) sources (dae.person_sets.person_sets.PersonSetCollectionConfig attribute) (dae.person_sets.PersonSetCollectionConfig attribute) SPECIAL_ATTRS (studies.response_transformer.ResponseTransformer attribute) SpliceSiteEffectChecker (class in dae.effect_annotation.effect_checkers.splice_site) split_events() (dae.enrichment_tool.event_counters.CounterBase method) split_into_regions() (dae.genomic_resources.reference_genome.ReferenceGenome method) (in module dae.utils.regions) split_iterable() (in module dae.utils.dae_utils) split_location() (dae.variants_loaders.dae.loader.DenovoLoader static method) spouse (dae.variants.attributes.Role attribute) SqlQueryBuilder (class in dae.query_variants.sql.schema2.sql_query_builder) SqlSchema2Variants (class in dae.query_variants.sql.schema2.base_variants) staff_update() (in module users_api.models), [1] start (dae.gene_sets.denovo_gene_sets_config.RecurrencyCriteriaBase attribute) (dae.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute) (dae.gene_sets.denovo_gene_sets_config.SingleCriteria attribute) (dae.gene_sets.denovo_gene_sets_config.TripleCriteria attribute) (dae.utils.regions.BedRegion property) (dae.utils.regions.Region property) start() (dae.duckdb_storage.duckdb_genotype_storage.DuckDbParquetStorage method) (dae.duckdb_storage.duckdb_genotype_storage.DuckDbS3ParquetStorage method) (dae.duckdb_storage.duckdb_genotype_storage.DuckDbS3Storage method) (dae.duckdb_storage.duckdb_genotype_storage.DuckDbStorage method) (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) (dae.genotype_storage.genotype_storage.GenotypeStorage method) (dae.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage method) (dae.parquet_storage.storage.ParquetGenotypeStorage method) (dae.query_variants.attributes_query.StringQueryToTreeTransformer method) (dae.query_variants.query_runners.QueryResult method) (dae.query_variants.query_runners.QueryRunner method) startCodons (dae.effect_annotation.gene_codes.NuclearCode attribute) StartLossEffectChecker (class in dae.effect_annotation.effect_checkers.start_loss) Statistic (class in dae.genomic_resources.statistics.base_statistic) statistic_id (dae.genomic_resources.statistics.base_statistic.Statistic attribute) StatisticsData (class in dae.genomic_resources.implementations.gene_models_impl) stats (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) StatsCollection (class in dae.utils.statistics) Status (class in dae.variants.attributes) status (dae.pedigrees.family.Person property) step_dad (dae.variants.attributes.Role attribute) step_mom (dae.variants.attributes.Role attribute) stop (dae.utils.regions.BedRegion property) (dae.utils.regions.Region property) stopCodons (dae.effect_annotation.gene_codes.NuclearCode attribute) StopLossEffectChecker (class in dae.effect_annotation.effect_checkers.stop_loss) storage_type (dae.duckdb_storage.duckdb_storage_config.DuckDbConf attribute) (dae.duckdb_storage.duckdb_storage_config.DuckDbParquetConf attribute) (dae.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (dae.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute) store_junit_results() (dae.tools.gpf_validation_runner.MainRunner static method) store_results() (dae.tools.gpf_validation_runner.GenotypeBrowserRunner method) (dae.tools.gpf_validation_runner.MainRunner method) StoredAnnotationDecorator (class in dae.variants_loaders.raw.loader) str2bool() (in module dae.utils.helpers) str2fgt() (in module dae.utils.variant_utils) str2gt() (in module dae.utils.variant_utils) str2lists() (in module dae.utils.variant_utils) str2mat() (in module dae.utils.variant_utils) str2mat_adjust_colsep() (in module dae.utils.variant_utils) STREAMING_CHUNK_SIZE (studies.response_transformer.ResponseTransformer attribute) streaming_search() (users_api.views.UserViewSet method), [1] stringify() (in module dae.annotation.annotate_utils) StringQueryToTreeTransformer (class in dae.query_variants.attributes_query) studies module studies.query_transformer module studies.response_transformer module studies.study_wrapper module StudiesView (class in datasets_api.views) study (dae.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute) (dae.schema2_storage.schema2_layout.Schema2DatasetLayout attribute) study_id (dae.import_tools.import_tools.ImportProject property) (dae.studies.study.GenotypeData property) (dae.testing.import_helpers.StudyInputLayout attribute) (dae.testing.StudyInputLayout attribute) (studies.study_wrapper.StudyWrapperBase property) study_id_from_path() (in module dae.utils.helpers) study_phenotype (dae.studies.study.GenotypeDataStudy property) study_type (dae.studies.study.GenotypeData property) study_update() (in module dae.testing) (in module dae.testing.import_helpers) StudyConfigBuilder (class in dae.configuration.study_config_builder) StudyConfigsAdjustmentCommand (class in dae.tools.gpf_instance_adjustments) StudyInputLayout (class in dae.testing) (class in dae.testing.import_helpers) StudyWrapper (class in studies.study_wrapper) StudyWrapperBase (class in studies.study_wrapper) SUBSTITUTION (dae.annotation.annotatable.Annotatable.Type attribute) substitution (dae.variants.core.Allele.Type attribute) suffix (groups_api.views.GroupsViewSet attribute) (users_api.views.UserViewSet attribute), [1] summary (dae.annotation.annotation_config.AnnotationPreamble attribute) (dae.annotation.annotation_config.RawPreamble attribute) (dae.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute) (dae.schema2_storage.schema2_layout.Schema2DatasetLayout attribute) summary() (dae.tools.gpf_validation_runner.MainRunner method) summary_allele (dae.variants.family_variant.FamilyAllele attribute) SUMMARY_ALLELE_BASE_SCHEMA (dae.parquet.schema2.serializers.AlleleParquetSerializer attribute) summary_allele_from_record() (dae.variants.variant.SummaryVariantFactory static method) summary_attributes (dae.variants.family_variant.FamilyAllele property) summary_base() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) SUMMARY_COLUMNS (dae.variants_loaders.parquet.loader.ParquetLoader attribute) summary_index (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) (dae.variants.variant.SummaryAllele property) (dae.variants.variant.SummaryVariant property) summary_partition() (dae.parquet.partition_descriptor.PartitionDescriptor method) summary_query() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) summary_variant_filter_duplicate_function() (dae.inmemory_storage.raw_variants.RawFamilyVariants class method) summary_variant_filter_function() (dae.inmemory_storage.raw_variants.RawFamilyVariants class method) summary_variant_from_records() (dae.variants.variant.SummaryVariantFactory static method) summary_variant_from_vcf() (dae.variants.variant.SummaryVariantFactory static method) summary_variants() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) summary_variants_iterator() (dae.inmemory_storage.raw_variants.RawFamilyVariants method) SummaryAllele (class in dae.variants.variant) SummaryQueryBuilder (class in dae.query_variants.sql.schema2.summary_builder) SummaryVariant (class in dae.variants.variant) SummaryVariantFactory (class in dae.variants.variant) SUPERUSER_GROUP (users_api.models.WdaeUser attribute), [1] svuid (dae.variants.variant.SummaryVariant property) symlink_pedigree_and_family_variants() (in module dae.annotation.parquet) syms (dae.gene_sets.gene_sets_db.GeneSet attribute) synonyms (dae.gene_sets.gene_term.GeneInfo attribute)

T

t4c8_dataset() (in module dae.conftest) t4c8_genes() (in module dae.testing.t4c8_import) t4c8_genome() (in module dae.testing.t4c8_import) t4c8_gpf() (in module dae.testing) (in module dae.testing.t4c8_import) t4c8_instance() (in module dae.conftest) t4c8_study_1() (in module dae.conftest) t4c8_study_2() (in module dae.conftest) t4c8_study_4() (in module dae.conftest) tabix_index_filename() (in module dae.utils.fs_utils) TabixGenomicPositionTable (class in dae.genomic_resources.genomic_position_table) (class in dae.genomic_resources.genomic_position_table.table_tabix) TableConfigurationView (class in gene_profiles_api.table_views) TableRowsView (class in gene_profiles_api.table_views) tag_affected_dad_family() (in module dae.pedigrees.family_tag_builder) tag_affected_mom_family() (in module dae.pedigrees.family_tag_builder) tag_affected_prb_family() (in module dae.pedigrees.family_tag_builder) tag_affected_sib_family() (in module dae.pedigrees.family_tag_builder) tag_control_family() (in module dae.pedigrees.family_tag_builder) tag_families_data() (in module dae.pedigrees.families_data) tag_family() (dae.pedigrees.family_tag_builder.FamilyTagsBuilder method) tag_family_type() (dae.pedigrees.family_tag_builder.FamilyTagsBuilder method) tag_female_prb_family() (in module dae.pedigrees.family_tag_builder) tag_labels (dae.pedigrees.family.Family property) tag_male_prb_family() (in module dae.pedigrees.family_tag_builder) tag_missing_dad_family() (in module dae.pedigrees.family_tag_builder) tag_missing_mom_family() (in module dae.pedigrees.family_tag_builder) tag_multiplex_family() (in module dae.pedigrees.family_tag_builder) tag_nuclear_family() (in module dae.pedigrees.family_tag_builder) tag_quad_family() (in module dae.pedigrees.family_tag_builder) tag_simplex_family() (in module dae.pedigrees.family_tag_builder) tag_trio_family() (in module dae.pedigrees.family_tag_builder) tag_unaffected_dad_family() (in module dae.pedigrees.family_tag_builder) tag_unaffected_mom_family() (in module dae.pedigrees.family_tag_builder) tag_unaffected_prb_family() (in module dae.pedigrees.family_tag_builder) tag_unaffected_sib_family() (in module dae.pedigrees.family_tag_builder) tags (dae.pedigrees.family.Family property) (dae.pedigrees.family.Person property) TAGS (dae.pedigrees.family_tag_builder.FamilyTagsBuilder attribute) TagsView (class in family_api.views) tandem_repeat (dae.variants.core.Allele.Type attribute) tandem_repeat() (in module dae.variants.variant) tandem_repeat_del (dae.variants.core.Allele.Type attribute) tandem_repeat_ins (dae.variants.core.Allele.Type attribute) Task (class in dae.task_graph.graph) task_graph_all_done() (in module dae.task_graph.executor) task_graph_run() (in module dae.task_graph.executor) task_graph_run_with_results() (in module dae.task_graph.executor) task_graph_status() (in module dae.task_graph.executor) task_id (dae.task_graph.graph.Task attribute) TaskCache (class in dae.task_graph.cache) TaskGraph (class in dae.task_graph.graph) TaskGraphCli (class in dae.task_graph.cli_tools) TaskGraphExecutor (class in dae.task_graph.executor) template (users_api.views.BasePasswordView attribute), [1] (users_api.views.ResetPassword attribute), [1] (users_api.views.SetPassword attribute), [1] test_frames() (dae.genomic_resources.gene_models.gene_models.TranscriptModel method) (dae.genomic_resources.gene_models.TranscriptModel method) TestResult (class in dae.tools.gpf_validation_runner) TestStatus (class in dae.tools.gpf_validation_runner) TestSuite (class in dae.tools.gpf_validation_runner) text (dae.pheno.common.MeasureType attribute) time (users_api.models.AuthenticationLog attribute), [1] time_fmt (wdae.default_settings.CustomFormatter attribute) timestamp (dae.genomic_resources.repository.ResourceFileState attribute) to_cshl_full() (dae.variants.variant.VariantDesc method) to_cshl_short() (dae.variants.variant.VariantDesc method) to_dict() (dae.common_reports.common_report.CommonReport method) (dae.common_reports.denovo_report.DenovoReport method) (dae.common_reports.denovo_report.DenovoReportTable method) (dae.common_reports.denovo_report.EffectCell method) (dae.common_reports.denovo_report.EffectRow method) (dae.common_reports.family_counter.FamiliesGroupCounters method) (dae.common_reports.family_counter.FamilyCounter method) (dae.common_reports.family_report.FamiliesReport method) (dae.common_reports.people_counter.PeopleCounter method) (dae.common_reports.people_counter.PeopleCounters method) (dae.common_reports.people_counter.PeopleReport method) (dae.genomic_resources.histogram.CategoricalHistogram method) (dae.genomic_resources.histogram.CategoricalHistogramConfig method) (dae.genomic_resources.histogram.NullHistogram method) (dae.genomic_resources.histogram.NullHistogramConfig method) (dae.genomic_resources.histogram.NumberHistogram method) (dae.genomic_resources.histogram.NumberHistogramConfig method) (dae.parquet.partition_descriptor.PartitionDescriptor method)

to_duckdb_transpile() (in module dae.utils.sql_utils) to_internal_value() (users_api.serializers.CreatableSlugRelatedField method), [1] (users_api.serializers.DatasetSerializer method), [1] to_json() (dae.gene_profile.statistic.GPStatistic method) (dae.genomic_scores.scores.ScoreDesc method) (dae.pedigrees.family.Family method) (dae.pedigrees.family.Person method) (dae.person_sets.person_sets.PersonSet method) (dae.person_sets.PersonSet method) (dae.pheno.pheno_data.Measure method) to_manifest_entries() (dae.genomic_resources.repository.Manifest method) to_name() (dae.variants.attributes.Role static method) (dae.variants.attributes.Sex static method) (dae.variants.attributes.Status static method) to_record() (dae.variants.family_variant.FamilyVariant method) (dae.variants.variant.SummaryAllele method) (dae.variants.variant.SummaryVariant method) to_representation() (groups_api.serializers.GroupRetrieveSerializer method) (users_api.serializers.DatasetSerializer method), [1] (users_api.serializers.UserSerializer method), [1] to_response_json() (in module dae.utils.helpers) to_tsv() (dae.gene_scores.gene_scores.GeneScore method) (dae.pedigrees.loader.FamiliesLoader static method) to_value() (dae.variants.attributes.Role static method) (dae.variants.attributes.Sex static method) (dae.variants.attributes.Status static method) to_xml_element() (dae.tools.gpf_validation_runner.TestResult method) (dae.tools.gpf_validation_runner.TestSuite method) token_converter() (dae.query_variants.attributes_query.QueryTreeToSQLTransformer static method) tokenize() (dae.annotation.annotatable.Annotatable static method) TOMLDict (class in dae.configuration.study_config_builder) TOMLList (class in dae.configuration.study_config_builder) total (dae.person_sets.ChildrenStats property) (dae.person_sets.person_sets.ChildrenStats property) total_len() (dae.genomic_resources.gene_models.gene_models.TranscriptModel method) (dae.genomic_resources.gene_models.TranscriptModel method) total_length() (in module dae.utils.regions) transcript_effects() (dae.effect_annotation.effect.AnnotationEffect class method) transcript_number (dae.genomic_resources.implementations.gene_models_impl.StatisticsData attribute) transcript_to_dict() (genomes_api.views.GeneModels method) transcript_to_gtf() (in module dae.genomic_resources.gene_models.serialization) TranscriptModel (class in dae.genomic_resources.gene_models) (class in dae.genomic_resources.gene_models.gene_models) transform() (dae.query_variants.attributes_query.BaseTreeTransformer method) transform_gene_view_summary_variant() (studies.response_transformer.ResponseTransformer static method) transform_gene_view_summary_variant_download() (studies.response_transformer.ResponseTransformer method) transform_kwargs() (studies.query_transformer.QueryTransformer method) transform_query_string_to_tree() (dae.query_variants.attributes_query.BaseQueryTransformerMatcher method) transform_request() (studies.study_wrapper.StudyWrapper method) transform_summary_variants() (studies.response_transformer.ResponseTransformer method) transform_tree_to_matcher() (dae.query_variants.attributes_query.QueryTransformerMatcher method) translate() (dae.pedigrees.layout.Layout method) transmission_type (dae.variants.family_variant.FamilyAllele property) (dae.variants.variant.SummaryAllele property) (dae.variants.variant.SummaryVariant property) TransmissionType (class in dae.variants.attributes) transmitted (dae.variants.attributes.TransmissionType attribute) TreeNode (class in dae.query_variants.attributes_query) trim_equal_ref_alt_parts() (dae.effect_annotation.variant.Variant method) trim_parsimonious() (in module dae.utils.variant_utils) trim_str_left() (in module dae.utils.variant_utils) trim_str_left_right() (in module dae.utils.variant_utils) trim_str_right() (in module dae.utils.variant_utils) trim_str_right_left() (in module dae.utils.variant_utils) TRIO (dae.pedigrees.family.FamilyTag attribute) trios (dae.pedigrees.family.Family property) TripleCriteria (class in dae.gene_sets.denovo_gene_sets_config) try_solve() (dae.pedigrees.pedigrees.SandwichSolver static method) tvalues (dae.pheno.utils.lin_regress.LinearRegression property) type (dae.annotation.annotation_config.AnnotatorInfo attribute) (dae.annotation.annotation_config.AttributeInfo attribute) (dae.genomic_resources.histogram.CategoricalHistogram attribute) (dae.genomic_resources.histogram.NullHistogram attribute) (dae.genomic_resources.histogram.NumberHistogram attribute) (dae.import_tools.import_tools.Bucket attribute) (dae.task_graph.cache.CacheRecord attribute) TYPE_DISPLAY_NAME (dae.variants.core.Allele attribute) types (dae.effect_annotation.effect.AlleleEffects property)

U

U (dae.variants.attributes.Sex attribute) ultra_rare() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) UMLIMITED_DOWNLOAD_GROUP (users_api.models.WdaeUser attribute), [1] unaffected (dae.variants.attributes.Status attribute) UNAFFECTED_DAD (dae.pedigrees.family.FamilyTag attribute) UNAFFECTED_MOM (dae.pedigrees.family.FamilyTag attribute) UNAFFECTED_PRB (dae.pedigrees.family.FamilyTag attribute) UNAFFECTED_SIB (dae.pedigrees.family.FamilyTag attribute) union() (in module dae.utils.regions) unique_regions() (in module dae.utils.regions) UNIQUE_VALUES_LIMIT (dae.genomic_resources.histogram.CategoricalHistogram attribute) unknown (dae.variants.attributes.Inheritance attribute) (dae.variants.attributes.Role attribute) (dae.variants.attributes.TransmissionType attribute) unknown() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) unmap_chromosome() (dae.genomic_resources.genomic_position_table.table.GenomicPositionTable method) unregister_genotype_data() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) (dae.studies.variants_db.VariantsDb method) unset_tag() (dae.pedigrees.family.Family method) (dae.pedigrees.family.Person method) (in module dae.pedigrees.family_tag_builder) unspecified (dae.enrichment_tool.event_counters.EnrichmentResult attribute) (dae.enrichment_tool.event_counters.EventCountersResult attribute) (dae.enrichment_tool.event_counters.EventsResult attribute) (dae.enrichment_tool.event_counters.VariantEventsResult attribute) (dae.person_sets.ChildrenBySex attribute) (dae.person_sets.ChildrenStats attribute) (dae.person_sets.person_sets.ChildrenBySex attribute) (dae.person_sets.person_sets.ChildrenStats attribute) (dae.variants.attributes.Sex attribute) (dae.variants.attributes.Status attribute) update() (dae.genomic_resources.repository.Manifest method) (users_api.serializers.DatasetSerializer method), [1] (users_api.serializers.UserSerializer method), [1] (users_api.views.UserViewSet method), [1] update_attributes() (dae.variants.family_variant.FamilyAllele method) (dae.variants.variant.SummaryAllele method) (dae.variants.variant.SummaryVariant method) update_frames() (dae.genomic_resources.gene_models.gene_models.TranscriptModel method) (dae.genomic_resources.gene_models.TranscriptModel method) update_gps_with_values() (dae.gene_profile.db.GeneProfileDB method) update_header() (in module dae.annotation.annotate_vcf) update_indexes() (dae.genomic_resources.gene_models.gene_models.GeneModels method) (dae.genomic_resources.gene_models.GeneModels method) update_manifest() (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) update_name() (datasets_api.models.Dataset class method) update_resource() (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) update_resource_file() (dae.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) update_study_config() (in module dae.testing) (in module dae.testing.import_helpers) url_to_pyarrow_fs() (in module dae.parquet.helpers) use_bit_and_function() (dae.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method) (dae.query_variants.sql.schema2.base_query_builder.Dialect static method) used_context_attributes (dae.annotation.annotation_pipeline.Annotator property) (dae.annotation.annotation_pipeline.InputAnnotableAnnotatorDecorator property) (dae.annotation.gene_score_annotator.GeneScoreAnnotator property) (dae.annotation.gene_set_annotator.GeneSetAnnotator property) user (user_queries.models.UserQuery attribute) (users_api.models.BaseVerificationCode attribute), [1] (users_api.models.GpUserState attribute), [1] (users_api.models.ResetPasswordCode attribute), [1] (users_api.models.SetPasswordCode attribute), [1] user_has_permission() (in module datasets_api.permissions) user_id (user_queries.models.UserQuery attribute) (users_api.models.BaseVerificationCode attribute), [1] (users_api.models.GpUserState attribute), [1] (users_api.models.ResetPasswordCode attribute), [1] (users_api.models.SetPasswordCode attribute), [1] user_permissions (users_api.models.WdaeUser attribute), [1] user_queries module user_queries.admin module user_queries.migrations module user_queries.migrations.0001_initial module user_queries.models module user_queries.urls module user_queries.views module UserGpStateView (class in users_api.views), [1] USERNAME_FIELD (users_api.models.WdaeUser attribute), [1] UserQuery (class in user_queries.models) UserQuery.DoesNotExist UserQuery.MultipleObjectsReturned userquery_set (query_state_save.models.QueryState attribute) (users_api.models.WdaeUser attribute), [1] UserQueryCollectView (class in user_queries.views) UserQuerySaveView (class in user_queries.views) users_api module, [1] users_api.forms module users_api.management module users_api.management.commands module

users_api.management.commands.dataset_groups module users_api.management.commands.dataset_mixin module users_api.management.commands.datasets_export module users_api.management.commands.datasets_restore module users_api.management.commands.datasets_show module users_api.management.commands.export_base module users_api.management.commands.groups_cleanup module users_api.management.commands.import_base module users_api.management.commands.unlock_user module users_api.management.commands.user_create module users_api.management.commands.user_set_name module users_api.management.commands.user_setpasswd module users_api.management.commands.users_add module users_api.management.commands.users_export module users_api.management.commands.users_group_add module users_api.management.commands.users_group_remove module users_api.management.commands.users_remove module users_api.management.commands.users_restore module users_api.management.commands.users_show module users_api.migrations module users_api.migrations.0001_initial module users_api.migrations.0002_auto_20190424_0751 module users_api.migrations.0003_authenticationlog module users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more module users_api.migrations.0005_gpuserstate module users_api.models module, [1] users_api.serializers module, [1] users_api.urls module, [1] users_api.validators module, [1] users_api.views module, [1] UserSerializer (class in users_api.serializers), [1] UserSerializer.Meta (class in users_api.serializers), [1] UserViewSet (class in users_api.views), [1] UserWithoutEmailSerializer (class in users_api.serializers), [1] UserWithoutEmailSerializer.Meta (class in users_api.serializers), [1] utils module utils.authentication module utils.datasets module utils.email_regex module utils.expand_gene_set module utils.gene_sets module utils.logger module utils.pagination module utils.password_requirements module utils.query_params module utils.streaming_response_util module utils.testing module utr3_len() (dae.genomic_resources.gene_models.gene_models.TranscriptModel method) (dae.genomic_resources.gene_models.TranscriptModel method) utr3_regions() (dae.genomic_resources.gene_models.gene_models.TranscriptModel method) (dae.genomic_resources.gene_models.TranscriptModel method) utr5_len() (dae.genomic_resources.gene_models.gene_models.TranscriptModel method) (dae.genomic_resources.gene_models.TranscriptModel method) utr5_regions() (dae.genomic_resources.gene_models.gene_models.TranscriptModel method) (dae.genomic_resources.gene_models.TranscriptModel method) utr_regions() (dae.annotation.simple_effect_annotator.SimpleEffectAnnotator method) UTREffectChecker (class in dae.effect_annotation.effect_checkers.utr) uuid (query_state_save.models.QueryState attribute)

V

validate() (users_api.models.BaseVerificationCode method), [1] (users_api.models.ResetPasswordCode method), [1] (users_api.models.SetPasswordCode method), [1] (users_api.serializers.UserSerializer method), [1] validate_aggregator() (in module dae.genomic_resources.aggregators) validate_and_normalize_config() (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage class method) (dae.genotype_storage.genotype_storage.GenotypeStorage class method) (dae.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage class method) (dae.parquet_storage.storage.ParquetGenotypeStorage class method) validate_and_normalize_schema() (dae.genomic_resources.resource_implementation.ResourceConfigValidationMixin class method) validate_config() (dae.configuration.gpf_config_parser.GPFConfigParser static method) validate_existing_path() (in module dae.configuration.utils) validate_path() (in module dae.configuration.utils) validation_rules (dae.configuration.gpf_config_parser.GPFConfigValidator attribute) VALIDATION_SCHEMA (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage attribute) (dae.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage attribute) (dae.parquet_storage.storage.ParquetGenotypeStorage attribute) value_max_len (dae.pheno.common.InferenceConfig attribute) value_order (dae.genomic_resources.histogram.CategoricalHistogramConfig attribute) value_type (dae.genomic_resources.genomic_scores.ScoreDef attribute) values (dae.person_sets.person_sets.PersonSetConfig attribute) (dae.person_sets.PersonSetConfig attribute) values() (dae.pedigrees.families_data.FamiliesData method) values_domain() (dae.genomic_resources.histogram.CategoricalHistogram method) (dae.genomic_resources.histogram.NullHistogram method) (dae.genomic_resources.histogram.NumberHistogram method) ValueTransformAnnotatorDecorator (class in dae.annotation.annotation_pipeline) Variant (class in dae.effect_annotation.variant) variant_columns (dae.effect_annotation.cli.VariantColumnInputFile attribute) variant_in_members (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) variant_in_members_fpid (dae.variants.family_variant.FamilyAllele property) variant_in_members_objects (dae.variants.family_variant.FamilyAllele property) variant_in_roles (dae.variants.family_variant.FamilyAllele property) variant_in_sexes (dae.variants.family_variant.FamilyAllele property) variant_in_statuses (dae.variants.family_variant.FamilyAllele property) variant_to_variant_type() (in module dae.variants_loaders.raw.flexible_variant_loader) variant_transformer() (studies.response_transformer.ResponseTransformer method) variant_type (dae.variants.variant.SummaryAllele property) variant_type_converter() (in module dae.query_variants.attributes_query) variant_types (dae.variants.variant.SummaryVariant property) VariantColumnInputFile (class in dae.effect_annotation.cli) VariantColumnOutputFile (class in dae.effect_annotation.cli) VariantDesc (class in dae.variants.variant)

VariantDetails (class in dae.variants.variant) VariantEvent (class in dae.enrichment_tool.genotype_helper) VariantEventsResult (class in dae.enrichment_tool.event_counters) VariantReportsFullView (class in common_reports_api.views) VariantReportsView (class in common_reports_api.views) variants_filenames (dae.variants_loaders.dae.loader.DaeTransmittedLoader property) (dae.variants_loaders.raw.loader.VariantsLoader property) (dae.variants_loaders.vcf.loader.VcfLoader property) VariantsDataSerializer (class in dae.parquet.schema2.variant_serializers) VariantsDb (class in dae.studies.variants_db) VariantsGenotypesLoader (class in dae.variants_loaders.raw.loader) VariantsLoader (class in dae.variants_loaders.raw.loader) VariantsLoaderDecorator (class in dae.variants_loaders.raw.loader) VariantsParquetWriter (class in dae.parquet.schema2.parquet_io) vcf (dae.testing.import_helpers.StudyInputLayout attribute) (dae.testing.StudyInputLayout attribute) vcf2cshl() (in module dae.variants.variant) vcf_import() (in module dae.testing) (in module dae.testing.import_helpers) vcf_study() (in module dae.testing) (in module dae.testing.import_helpers) VCFAllele (class in dae.annotation.annotatable) VcfFamiliesGenotypes (class in dae.variants_loaders.vcf.loader) VCFGenomicPositionTable (class in dae.genomic_resources.genomic_position_table) (class in dae.genomic_resources.genomic_position_table.table_vcf) VcfLikeRecordToVcfAllele (class in dae.annotation.record_to_annotatable) VCFLine (class in dae.genomic_resources.genomic_position_table) (class in dae.genomic_resources.genomic_position_table.line) VcfLoader (class in dae.variants_loaders.vcf.loader) verbose (dae.pheno.common.ImportConfig attribute) VerbosityConfiguration (class in dae.utils.verbosity_configuration) verification_code_model (users_api.views.BasePasswordView attribute), [1] (users_api.views.ResetPassword attribute), [1] (users_api.views.SetPassword attribute), [1] verify_pheno_folder() (dae.pheno.db.PhenoDb static method) verify_phenotype_data_name() (in module dae.pheno.pheno_import) version() (in module gpf_instance.views) version_string_to_suffix() (in module dae.genomic_resources.repository) version_tuple_to_string() (in module dae.genomic_resources.repository) version_tuple_to_suffix() (in module dae.genomic_resources.repository) view_max() (dae.genomic_resources.histogram.NumberHistogram method) view_min() (dae.genomic_resources.histogram.NumberHistogram method) view_range (dae.genomic_resources.histogram.NumberHistogramConfig attribute) VisibleDatasetsView (class in datasets_api.views)

W

wdae module wdae.default_settings module wdae.eager_settings module wdae.gpfjs_settings module wdae.remote_settings module wdae.settings module wdae.silk_settings module wdae.test_settings module wdae.urls module wdae.wgpf module WDAEConfig (class in gpf_instance.apps) WdaeLoginForm (class in users_api.forms) WdaeLoginView (class in users_api.views), [1] wdaemanage module

WdaePageNumberPagination (class in utils.pagination) WdaePasswordForgottenForm (class in users_api.forms) WdaeRegisterPasswordForm (class in users_api.forms) WdaeResetPasswordForm (class in users_api.forms) WdaeUser (class in users_api.models), [1] WdaeUser.DoesNotExist, [1] WdaeUser.MultipleObjectsReturned, [1] WdaeUserManager (class in users_api.models), [1] WHERE (dae.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute) work() (dae.annotation.annotate_columns.AnnotateColumnsTool method) (dae.annotation.annotate_schema2_parquet.AnnotateSchema2ParquetTool method) (dae.annotation.annotate_utils.AnnotationTool method) (dae.annotation.annotate_vcf.AnnotateVCFTool method) (dae.annotation.reannotate_instance.ReannotateInstanceTool method) work_dir (dae.import_tools.import_tools.ImportProject property) worst (dae.effect_annotation.effect.AlleleEffects property) worst_effect (dae.variants.variant.SummaryAllele property) worst_effect() (dae.effect_annotation.effect.AnnotationEffect class method) write_columns() (dae.effect_annotation.cli.VariantColumnOutputFile method) write_dataset() (dae.parquet.schema2.parquet_io.VariantsParquetWriter method) write_new_meta() (in module dae.annotation.parquet) write_results() (in module dae.pheno.pheno_import) write_summary_variant() (dae.parquet.schema2.parquet_io.VariantsParquetWriter method)

X

x (dae.pedigrees.layout.Point attribute) X (dae.variants.attributes.GeneticModel attribute) X_broken (dae.variants.attributes.GeneticModel attribute)

x_center (dae.pedigrees.layout.IndividualWithCoordinates property) x_log_scale (dae.genomic_resources.histogram.NumberHistogramConfig attribute) x_min_log (dae.genomic_resources.histogram.NumberHistogramConfig attribute)

Y

y (dae.pedigrees.layout.Point attribute) y_center (dae.pedigrees.layout.IndividualWithCoordinates property) y_log_scale (dae.genomic_resources.histogram.CategoricalHistogramConfig attribute) (dae.genomic_resources.histogram.NumberHistogramConfig attribute)

year (dae.studies.study.GenotypeData property) yellow (wdae.default_settings.CustomFormatter attribute)

Z

zero_based_adjust() (in module dae.genomic_resources.genomic_position_table.table)