Index

A

abspath() (in module dae.utils.fs_utils) abstract (users_api.models.BaseVerificationCode.Meta attribute) AbstractDuckDbImportStorage (class in dae.duckdb_storage.duckdb_import_storage) AbstractDuckDbStorage (class in dae.duckdb_storage.duckdb_genotype_storage) AbstractFormat (class in dae.annotation.format_handlers) AbstractLiftoverAnnotator (class in dae.annotation.liftover_annotator) AbstractRunner (class in dae.tools.gpf_validation_runner) AbstractTaskGraphExecutor (class in dae.task_graph.executor) acgt_genome_19() (in module dae.conftest) acgt_genome_38() (in module dae.conftest) 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.gpf_instance.adjustments.adjust_duckdb_storage.AdjustDuckDbStorageCommand static method) (dae.gpf_instance.adjustments.adjust_impala_storage.AdjustImpalaStorageCommand static method) (dae.task_graph.cli_tools.TaskGraphCli static method) (users_api.management.commands.user_set_name.Command method) (users_api.management.commands.user_setpasswd.Command method) (users_api.management.commands.users_remove.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_count() (dae.genomic_resources.statistics.min_max.MinMaxValue method) add_gene() (dae.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) 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_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.gene_sets.implementations.gene_sets_impl.GeneSetCollectionImpl 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.CnvCollectionImplementation 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_tasks_to_graph() (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) 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.gpf_instance.adjustments.gpf_instance_adjustments.EnableDisableStudies method) (dae.gpf_instance.adjustments.gpf_instance_adjustments.StudyConfigsAdjustmentCommand method) adjust_study() (dae.gpf_instance.adjustments.gpf_instance_adjustments.DefaultGenotypeStorage method) (dae.gpf_instance.adjustments.gpf_instance_adjustments.EnableDisableStudies method) (dae.gpf_instance.adjustments.gpf_instance_adjustments.StudyConfigsAdjustmentCommand method) adjust_zero_based_line() (in module dae.genomic_resources.genomic_position_table.table) AdjustDuckDbStorageCommand (class in dae.gpf_instance.adjustments.adjust_duckdb_storage) AdjustImpalaStorageCommand (class in dae.gpf_instance.adjustments.adjust_impala_storage) AdjustmentsCommand (class in dae.gpf_instance.adjustments.adjust_command) 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) affected_statues (dae.studies.study.PSCQueryAdjustments attribute) aggregate() (dae.genomic_resources.aggregators.Aggregator method) aggregate_gene_values() (dae.annotation.gene_score_annotator.GeneScoreAnnotator method) Aggregator (class in dae.genomic_resources.aggregators) aliases() (dae.variants.attributes.Sex static method) 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.attribute_queries.SyntaxSugarTransformer 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.genomic_resources.genomic_scores.AlleleScore.Mode attribute) alleles (dae.variants.family_variant.FamilyVariant property) (dae.variants.variant.SummaryVariant property) alleles_mode() (dae.genomic_resources.genomic_scores.AlleleScore method) AlleleScore (class in dae.genomic_resources.genomic_scores) AlleleScore.Mode (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) allow_only_whole_values_y (dae.genomic_resources.histogram.CategoricalHistogramConfig attribute) allowed_datasets (users_api.models.WdaeUser property) 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) and_() (dae.query_variants.attribute_queries.AttributeQueryTransformerFunction method) (dae.query_variants.attribute_queries.AttributeQueryTransformerSQL method) Annotatable (class in dae.annotation.annotatable) Annotatable.Type (class in dae.annotation.annotatable) annotate() (dae.annotation.annotate_utils.AnnotationTool 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.PositionScoreAnnotator 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_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.VariantsLoader property) (dae.variants_loaders.raw.loader.VariantsLoaderDecorator property) AnnotationAttributes (class in dae.effect_annotation.cli) AnnotationConfigParser (class in dae.annotation.annotation_config) AnnotationConfigurationError AnnotationDependencyGraph (dae.annotation.annotation_pipeline.ReannotationPipeline attribute) AnnotationEffect (class in dae.effect_annotation.effect) AnnotationPipeline (class in dae.annotation.annotation_pipeline) 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.attribute_queries.SyntaxSugarTransformer 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_mask() (dae.utils.variant_utils.BitmaskEnumTranslator 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) 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) AttributeInfo (class in dae.annotation.annotation_config) AttributeQueryTransformerFunction (class in dae.query_variants.attribute_queries) AttributeQueryTransformerSQL (class in dae.query_variants.attribute_queries) AttributeQueryTransformerSQLLegacy (class in dae.query_variants.attribute_queries) attributes (dae.annotation.annotation_config.AnnotatorInfo attribute) (dae.annotation.annotation_pipeline.Annotator property) (dae.genomic_resources.genomic_scores.CNV attribute) (dae.variants.family_variant.FamilyAllele property) (dae.variants.variant.SummaryAllele property) (dae.variants.variant.SummaryVariant property) auth_token (users_api.models.WdaeUser attribute) authentication_classes (users_api.views.FederationCredentials attribute) (users_api.views.UserViewSet attribute) AuthenticationLog (class in users_api.models) AuthenticationLog.DoesNotExist AuthenticationLog.MultipleObjectsReturned 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) BaseAnnotationRequest (class in dae.effect_annotation.annotation_request) 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) BasePasswordView (class in users_api.views) BaseQueryBuilder (class in dae.query_variants.sql.schema2.base_query_builder) BaseResourceSchema (class in dae.gene_sets.gene_sets_db) BaseVerificationCode (class in users_api.models) BaseVerificationCode.Meta (class in users_api.models) 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.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.schema2_storage.schema2_import_storage.Schema2ImportStorage attribute) (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) BitmaskEnumTranslator (class in dae.utils.variant_utils) broken_families (dae.pedigrees.families_data.FamiliesData property) browsable_figure_path() (dae.pheno.prepare_data.PreparePhenoBrowserBase class method) browser (dae.pheno.pheno_data.PhenotypeData property) 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.DaeAlleleRecordToAnnotatable 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.pheno.pheno_data.PhenotypeData method) (dae.studies.study.GenotypeData method) build_annotation_filename() (in module dae.inmemory_storage.annotation_serialization) 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_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.GeneProfileDBWriter 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.QueryVariants 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_set_collection_implementation_from_resource() (in module dae.gene_sets.implementations.gene_sets_impl) 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_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_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.build_pheno_browser) build_phenotype_study() (dae.pheno.storage.PhenotypeStorage method) build_pipeline_genomic_context() (dae.annotation.annotation_pipeline.AnnotationPipeline method) 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.pheno.pheno_data.PhenotypeData method) (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_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.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_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.QueryVariants 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_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.gene_sets.implementations.gene_sets_impl.GeneSetCollectionImpl 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.CnvCollectionImplementation 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_regression() (dae.pheno.utils.lin_regress.LinearRegression 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.gene_sets.implementations.gene_sets_impl.GeneSetCollectionImpl 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.CnvCollectionImplementation 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) calc_zygosity_status_value() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static 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) categorical_attr() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) categorical_config (dae.pheno.common.MeasureHistogramConfigs attribute) CategoricalHistogram (class in dae.genomic_resources.histogram) CategoricalHistogramConfig (class in dae.genomic_resources.histogram) CategoricalHistogramSchema (class in dae.gene_sets.gene_sets_db) 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) change_environment() (in module dae.utils.fixtures) change_password() (in module users_api.views) (users_api.models.WdaeUser static method) 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_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_statuses_query_value() (dae.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) 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) 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) children_zygosity (dae.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute) 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.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.CNV attribute) (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) clear() (dae.genomic_resources.aggregators.Aggregator method) (dae.genomic_resources.genomic_position_table.line.LineBuffer method) (dae.genomic_resources.genomic_position_table.LineBuffer 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.gpf_instance.adjustments.gpf_instance_adjustments) (in module dae.tools.annotate_variants) (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.format_handlers.AbstractFormat method) (dae.annotation.format_handlers.ColumnsFormat method) (dae.annotation.format_handlers.ParquetFormat method) (dae.annotation.format_handlers.VCFFormat 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.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.gpf_instance.adjustments.adjust_command.AdjustmentsCommand method) (dae.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) (dae.parquet.schema2.parquet_io.VariantsParquetWriter method) (dae.pheno.pheno_data.PhenotypeData 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.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.VariantsLoader method) (dae.variants_loaders.raw.loader.VariantsLoaderDecorator method) (dae.variants_loaders.vcf.loader.SingleVcfLoader method) (dae.variants_loaders.vcf.loader.VcfLoader method) (dae.variants_loaders.vcf.serializer.VcfSerializer method)

closing (class in dae.utils.debug_closing) CNV (class in dae.genomic_resources.genomic_scores) 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.genomic_scores) CnvCollectionAnnotator (class in dae.annotation.cnv_collection_annotator) CnvCollectionImplementation (class in dae.genomic_resources.implementations.genomic_scores_impl) 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) (users_api.views.ResetPassword attribute) (users_api.views.SetPassword attribute) 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_child_configs() (dae.pheno.prepare_data.PreparePhenoBrowserBase method) 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_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) collections_descriptions (dae.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb property) (dae.gene_sets.gene_sets_db.GeneSetsDb property) 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) ColumnsFormat (class in dae.annotation.format_handlers) 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.user_set_name) (class in users_api.management.commands.user_setpasswd) (class in users_api.management.commands.users_remove) (class in users_api.management.commands.users_show) common_report (dae.pheno.common.StudyConfig attribute) common_reports_api module CommonReport (class in dae.common_reports.common_report) CommonStudyMixin (class in dae.studies.study) 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) configure_argument_parser() (in module dae.annotation.annotate_doc) configure_task_logging() (in module dae.task_graph.logging) 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) 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_float() (in module dae.pheno.prepare.measure_classifier) convert_to_int() (in module dae.pheno.prepare.measure_classifier) 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_measures() (dae.pheno.browser.PhenoBrowser method) (dae.pheno.pheno_data.PhenotypeData method) (dae.pheno.pheno_data.PhenotypeGroup method) (dae.pheno.pheno_data.PhenotypeStudy method) count_total (dae.pheno.prepare.measure_classifier.InferenceReport attribute) count_unique_values (dae.pheno.prepare.measure_classifier.InferenceReport attribute) count_variant() (dae.common_reports.denovo_report.EffectCell method) (dae.common_reports.denovo_report.EffectRow method) (in module dae.gene_profile.generate_gene_profile) count_with_values (dae.pheno.prepare.measure_classifier.InferenceReport attribute) count_without_values (dae.pheno.prepare.measure_classifier.InferenceReport attribute) CountAggregator (class in dae.genomic_resources.aggregators) counter() (dae.tools.gpf_validation_runner.AbstractRunner method) (dae.tools.gpf_validation_runner.MainRunner method) CounterBase (class in dae.enrichment_tool.event_counters) CreatableSlugRelatedField (class in users_api.serializers) create() (dae.task_graph.cache.TaskCache static method) (users_api.models.BaseVerificationCode class method) (users_api.models.WdaeUserManager method) (users_api.serializers.DatasetSerializer method) (users_api.serializers.UserSerializer method) (users_api.views.UserViewSet method) create_aggregator() (in module dae.genomic_resources.aggregators) create_aggregator_definition() (in module dae.genomic_resources.aggregators) create_and_node() (in module dae.query_variants.attribute_queries) create_annotation_request() (dae.effect_annotation.annotator.AnnotationRequestFactory static method) create_background() (dae.enrichment_tool.enrichment_helper.EnrichmentHelper method) create_browser() (dae.pheno.pheno_data.PhenotypeData static method) create_browser_tables() (dae.pheno.browser.PhenoBrowser static 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_or_node() (in module dae.query_variants.attribute_queries) 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) create_table() (dae.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) (dae.pheno.common.ImportManifest static 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) create_utr_effect() (dae.effect_annotation.effect_checkers.utr.UTREffectChecker method) created_at (users_api.models.BaseVerificationCode attribute) (users_api.models.ResetPasswordCode attribute) (users_api.models.SetPasswordCode attribute) 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) 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)

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.docker_annotator module dae.annotation.effect_annotator module dae.annotation.format_handlers 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.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.convert_gene_profile_to_duckdb 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.implementations module dae.gene_sets.implementations.gene_sets_impl module dae.genomic_resources module dae.genomic_resources.aggregators module dae.genomic_resources.cached_repository module dae.genomic_resources.cli 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.adjustments module dae.gpf_instance.adjustments.adjust_command module dae.gpf_instance.adjustments.adjust_duckdb_storage module dae.gpf_instance.adjustments.adjust_impala_storage module dae.gpf_instance.adjustments.gpf_instance_adjustments 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.annotation_serialization 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.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.browser module dae.pheno.build_pheno_browser module dae.pheno.common module dae.pheno.db module dae.pheno.graphs module dae.pheno.import_tools 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.storage module dae.pheno.update_pheno_descriptions 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.attribute_queries 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.dae2vcf module dae.tools.dae_liftover module dae.tools.denovo2vcf module dae.tools.denovo_liftover module dae.tools.draw_pedigree module dae.tools.generate_common_report module dae.tools.generate_denovo_gene_sets module dae.tools.gpf_convert_study_config 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.vcf2tsv 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.stats_collection 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 dae.variants_loaders.vcf.serializer 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) DaeAlleleRecordToAnnotatable (class in dae.annotation.record_to_annotatable) 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 (users_api.models.GpUserState attribute) data_dictionary (dae.pheno.common.PhenoImportConfig attribute) data_reset() (dae.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) DataDictionaryConfig (class in dae.pheno.common) dataset_family_partition() (dae.parquet.partition_descriptor.PartitionDescriptor method) dataset_summary_partition() (dae.parquet.partition_descriptor.PartitionDescriptor method) DatasetHelpers (class in dae.studies.dataset_helpers) 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 DatasetSerializer (class in users_api.serializers) date_joined (users_api.models.WdaeUser attribute) 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_name (dae.pheno.pheno_import.MeasureReport attribute) dd() (in module dae.gene_sets.gene_term) deauthenticate() (users_api.models.WdaeUser method) decorate() (dae.annotation.annotation_pipeline.InputAnnotableAnnotatorDecorator static method) (dae.annotation.annotation_pipeline.ValueTransformAnnotatorDecorator 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) default_setters (dae.configuration.gpf_config_parser.GPFConfigValidator attribute) DefaultBox (class in dae.configuration.gpf_config_parser) DefaultGenotypeStorage (class in dae.gpf_instance.adjustments.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) delete_resource_file() (dae.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) delimiter (dae.pheno.common.DataDictionaryConfig attribute) (dae.pheno.common.InstrumentConfig attribute) (dae.pheno.common.InstrumentDictionaryConfig attribute) (dae.pheno.common.PhenoImportConfig attribute) (dae.pheno.pheno_import.ImportInstrument attribute) denovo (dae.testing.import_helpers.StudyInputLayout attribute) (dae.testing.StudyInputLayout attribute) (dae.variants.attributes.Inheritance attribute) (dae.variants.attributes.TransmissionType attribute) 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) 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) (query_state_save.migrations.0003_querystate_origin_querystate_timestamp.Migration attribute) (users_api.migrations.0002_auto_20190424_0751.Migration attribute) (users_api.migrations.0003_authenticationlog.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) 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_sets_db.MetaSchema 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.CommonStudyMixin property) (studies.study_wrapper.WDAEStudy property) description_column (dae.pheno.common.DataDictionaryConfig attribute) (dae.pheno.common.InstrumentDictionaryConfig attribute) deselected_family_tags (dae.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute) 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) destination (dae.pheno.common.PhenoImportConfig attribute) DestinationConfig (class in dae.pheno.common) destroy() (users_api.views.UserViewSet method) details (dae.variants.family_variant.FamilyAllele property) (dae.variants.variant.SummaryAllele property) (dae.variants.variant.SummaryVariant property) determine_destination() (in module dae.pheno.pheno_import) determine_histogram_type() (in module dae.pheno.prepare.measure_classifier) 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) dictionary (dae.pheno.common.InstrumentDescriptionsConfig attribute) (dae.pheno.common.MeasureDescriptionsConfig attribute) diff() (dae.pedigrees.family.Person method) difference() (in module dae.utils.regions) directory (dae.gene_sets.gene_sets_db.GeneSetResourceSchema attribute) disable_study_config() (dae.studies.dataset_helpers.DatasetHelpers method) display_name (dae.pheno.common.RegressionMeasure attribute) (dae.variants.attributes.Role property) DISPLAY_NAME_TYPE (dae.variants.core.Allele attribute) display_values (dae.genomic_resources.histogram.CategoricalHistogram property) displayed_values_count (dae.gene_sets.gene_sets_db.CategoricalHistogramSchema attribute) (dae.gene_sets.gene_sets_db.NumericHistogramSchema attribute) (dae.genomic_resources.histogram.CategoricalHistogramConfig attribute) displayed_values_percent (dae.gene_sets.gene_sets_db.CategoricalHistogramSchema attribute) (dae.genomic_resources.histogram.CategoricalHistogramConfig 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) DockerAnnotator (class in dae.annotation.docker_annotator) 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) draw() (dae.pedigrees.drawing.OffsetLayoutDrawer method) draw_categorical_violin_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.GeneProfileDBWriter method) dry_run() (dae.annotation.annotate_schema2_parquet.AnnotateSchema2ParquetTool 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)

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) 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) email (users_api.models.AuthenticationLog attribute) (users_api.models.WdaeUser attribute) email_user() (users_api.models.WdaeUser method) enabled (dae.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) EnableDisableStudies (class in dae.gpf_instance.adjustments.gpf_instance_adjustments) end (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_type (dae.gene_sets.gene_sets_db.CategoricalHistogramSchema attribute) (dae.genomic_resources.histogram.CategoricalHistogramConfig attribute) enrichment_api module 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) EnrichmentResult (class in dae.enrichment_tool.event_counters) EnrichmentSerializer (class in dae.enrichment_tool.enrichment_serializer) EnrichmentSingleResult (class in dae.enrichment_tool.event_counters) 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) 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) 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.gpf_instance.adjustments.adjust_command.AdjustmentsCommand method) (dae.gpf_instance.adjustments.adjust_duckdb_storage.AdjustDuckDbStorageCommand method) (dae.gpf_instance.adjustments.adjust_impala_storage.AdjustImpalaStorageCommand method) (dae.gpf_instance.adjustments.gpf_instance_adjustments.DefaultGenotypeStorage method) (dae.gpf_instance.adjustments.gpf_instance_adjustments.EnableDisableStudies method) (dae.gpf_instance.adjustments.gpf_instance_adjustments.InstanceIdCommand method) (dae.task_graph.executor.AbstractTaskGraphExecutor method) (dae.task_graph.executor.TaskGraphExecutor 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) 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) extend() (dae.pedigrees.pedigrees.Realization method)

F

F (dae.variants.attributes.Sex attribute) FAIL (dae.tools.gpf_validation_runner.TestStatus attribute) failed_attempt (users_api.models.AuthenticationLog attribute) 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.pheno.pheno_data.PhenotypeData property) (dae.pheno.pheno_data.PhenotypeGroup property) (dae.pheno.pheno_data.PhenotypeStudy property) (dae.studies.study.GenotypeData property) (dae.studies.study.GenotypeDataGroup property) (dae.studies.study.GenotypeDataStudy property) (studies.response_transformer.ResponseTransformer property) (studies.study_wrapper.WDAEStudy property) families_of_persons() (dae.pedigrees.families_data.FamiliesData method) FamiliesData (class in dae.pedigrees.families_data) 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_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_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) FamilyDelegate (class in dae.variants.family_variant) 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) 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.genomic_scores.CnvCollection method) fetch_family_variants() (dae.variants_loaders.parquet.loader.ParquetLoader method) fetch_region() (dae.genomic_resources.genomic_scores.AlleleScore method) (dae.genomic_resources.genomic_scores.PositionScore method) fetch_scores() (dae.genomic_resources.genomic_scores.AlleleScore method) (dae.genomic_resources.genomic_scores.PositionScore method) fetch_scores_agg() (dae.genomic_resources.genomic_scores.AlleleScore 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 (users_api.serializers.UserSerializer.Meta attribute) (users_api.serializers.UserWithoutEmailSerializer.Meta attribute) 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.gene_sets.gene_sets_db.GeneSetResourceSchema attribute) (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.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) (dae.pheno.common.InstrumentDescriptionsConfig attribute) (dae.pheno.common.MeasureDescriptionsConfig attribute) (dae.pheno.pheno_import.ImportInstrument attribute) 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 (users_api.views.UserViewSet attribute) 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) 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) 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) force_type_inference() (in module dae.pheno.prepare.measure_classifier) ForgotPassword (class in users_api.views) form (users_api.views.BasePasswordView attribute) (users_api.views.ResetPassword attribute) (users_api.views.SetPassword attribute) FORMAT_DEF (dae.genomic_resources.genomic_position_table.table_inmemory.InmemoryGenomicPositionTable 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_config() (dae.pheno.storage.PhenotypeStorage 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) from_json() (dae.genomic_scores.scores.ScoreDesc static method) (dae.person_sets.person_sets.PersonSet static method) (dae.person_sets.PersonSet static 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.genomic_resources.genomic_scores.AlleleScore.Mode static method) (dae.variants.attributes.Inheritance static method) (dae.variants.attributes.Role static method) (dae.variants.attributes.Sex static method) (dae.variants.attributes.Status static method) (dae.variants.attributes.Zygosity 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_row() (dae.pheno.common.ImportManifest 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_study() (dae.common_reports.family_report.FamiliesReport static method) from_table() (dae.pheno.common.ImportManifest 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) (dae.variants.attributes.Zygosity 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.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_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_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_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 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) 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) GeneProfileDBWriter (class in dae.gene_profile.db) generate_gp() (in module dae.gene_profile.generate_gene_profile) generate_import_manifests() (dae.pheno.pheno_data.PhenotypeData method) (dae.pheno.pheno_data.PhenotypeGroup method) (dae.pheno.pheno_data.PhenotypeStudy method) 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) 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) 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) GeneSetCollectionImpl (class in dae.gene_sets.implementations.gene_sets_impl) GeneSetResourceSchema (class in dae.gene_sets.gene_sets_db) GeneSetsDb (class in dae.gene_sets.gene_sets_db) 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 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 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) GenomicScoreImplementation (class in dae.genomic_resources.implementations.genomic_scores_impl) GenomicScoresRegistry (class in dae.genomic_scores.scores) genotype (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) genotype_browser module, [1] genotype_data (studies.study_wrapper.WDAEStudy property) 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) 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() (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) (users_api.views.BasePasswordView method) (users_api.views.FederationCredentials method) (users_api.views.ForgotPassword method) (users_api.views.UserGpStateView method) (users_api.views.WdaeLoginView method) 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_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_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_phenotype_storage_ids() (dae.pheno.storage.PhenotypeStorageRegistry method) get_all_phenotype_storages() (dae.pheno.storage.PhenotypeStorageRegistry 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_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_cache_path() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_children() (dae.person_sets.person_sets.PersonSet method) (dae.person_sets.PersonSet 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_ids() (dae.pheno.pheno_data.PhenotypeData method) (dae.pheno.pheno_data.PhenotypeGroup method) (dae.pheno.pheno_data.PhenotypeStudy method) (studies.study_wrapper.WDAEStudy 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) 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.pheno.pheno_data.PhenotypeData 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) 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_data_dir() (dae.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage method) get_dataset() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance 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) 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_default_phenotype_storage() (dae.pheno.storage.PhenotypeStorageRegistry method) 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_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.CountAggregator 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_collection_count_statistics() (dae.gene_sets.implementations.gene_sets_impl.GeneSetCollectionImpl 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_per_gene_hist_filename() (dae.gene_sets.gene_sets_db.GeneSetCollection 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_genes_per_gene_set_hist_filename() (dae.gene_sets.gene_sets_db.GeneSetCollection 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) (in module dae.pheno.pheno_import) 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.implementations.gene_sets_impl.GeneSetCollectionImpl 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.CnvCollectionImplementation 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_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) get_leaf_children() (dae.studies.study.GenotypeData method) get_leaves() (dae.pheno.pheno_data.PhenotypeGroup 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) 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_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) (users_api.models.ResetPasswordCode method) (users_api.models.SetPasswordCode method) get_next_by_time() (users_api.models.AuthenticationLog method) 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) get_or_create_resource() (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) get_out_attributes() (dae.effect_annotation.cli.AnnotationAttributes method) get_output_parquet_files_dir() (in module dae.pheno.pheno_import) 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_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_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_person_color() (dae.person_sets.person_sets.PersonSetCollection static method) (dae.person_sets.PersonSetCollection static method) get_person_roles() (dae.pheno.pheno_data.PhenotypeData method) (dae.pheno.pheno_data.PhenotypeGroup method) get_person_set() (dae.person_sets.person_sets.PersonSetCollection method) (dae.person_sets.PersonSetCollection method) get_person_set_collection() (dae.pheno.pheno_data.PhenotypeData method) (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_persons() (dae.pheno.pheno_data.PhenotypeData method) get_persons_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_pheno_browser_images_dir() (in module dae.pheno.pheno_data) get_pheno_cache_path() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) 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_phenotype_storage() (dae.pheno.storage.PhenotypeStorageRegistry method) get_pipeline() (dae.annotation.context.CLIAnnotationContext static method) get_previous_by_created_at() (users_api.models.BaseVerificationCode method) (users_api.models.ResetPasswordCode method) (users_api.models.SetPasswordCode method) get_previous_by_time() (users_api.models.AuthenticationLog method) get_processing_annotation_batch_size() (dae.import_tools.import_tools.ImportProject method) 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_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_registered_genomic_context() (in module dae.genomic_resources.genomic_context) 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) 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) 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.implementations.gene_sets_impl.GeneSetCollectionImpl 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.CnvCollection static method) (dae.genomic_resources.genomic_scores.GenomicScore 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_selected_counting_models() (dae.enrichment_tool.enrichment_helper.EnrichmentHelper static method) get_selected_person_set_collections() (dae.enrichment_tool.enrichment_helper.EnrichmentHelper static method) get_sequence() (dae.genomic_resources.reference_genome.ReferenceGenome method) get_serializer_class() (users_api.views.UserViewSet method) 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_statistics_info() (dae.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation method) (dae.gene_scores.implementations.gene_scores_impl.GeneScoreImplementation method) (dae.gene_sets.implementations.gene_sets_impl.GeneSetCollectionImpl 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.CnvCollectionImplementation 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_statistics_template_data() (dae.genomic_resources.resource_implementation.InfoImplementationMixin method) get_stats() (dae.person_sets.person_sets.PersonSetCollection method) (dae.person_sets.PersonSetCollection 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_task_dir() (dae.annotation.annotate_utils.AnnotationTool static method) (dae.annotation.format_handlers.AbstractFormat static method) get_template() (dae.gene_scores.implementations.gene_scores_impl.GeneScoreImplementation method) (dae.gene_sets.implementations.gene_sets_impl.GeneSetCollectionImpl 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_info() (in module users_api.views) 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_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.GeneProfileDBWriter method) gpf_instance module gpf_instance (dae.pheno.common.PhenoImportConfig attribute) gpf_instance.apps module gpf_instance.gpf_instance 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) GPFInstanceConfig (class in dae.pheno.common) 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 GPStatistic (class in dae.gene_profile.statistic) GpUserState (class in users_api.models) gpuserstate (users_api.models.WdaeUser attribute) GpUserState.DoesNotExist GpUserState.MultipleObjectsReturned GraphColumn (class in dae.pheno.graphs) group_post_delete() (in module users_api.models) group_pre_delete() (in module users_api.models) grouping() (dae.query_variants.attribute_queries.AttributeQueryTransformerFunction method) (dae.query_variants.attribute_queries.AttributeQueryTransformerSQL method) groups (users_api.models.WdaeUser attribute) groups_api module groups_api.migrations module 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.user_set_name.Command method) (users_api.management.commands.user_setpasswd.Command method) (users_api.management.commands.users_remove.Command method) (users_api.management.commands.users_show.Command method) handle_measure_inference_tasks() (in module dae.pheno.pheno_import) has_affected_status_queries() (dae.inmemory_storage.raw_variants.RawMemoryVariants method) (dae.query_variants.base_query_variants.QueryVariants method) (dae.query_variants.base_query_variants.QueryVariantsBase 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_cnv (dae.studies.study.GenotypeData property) has_coding_bins() (dae.parquet.partition_descriptor.PartitionDescriptor method) has_complex (dae.studies.study.GenotypeData property) has_denovo (dae.studies.study.GenotypeData property) (dae.studies.study.GenotypeDataGroup property) has_denovo_variants() (dae.import_tools.import_tools.ImportProject method) has_descriptions (dae.pheno.browser.PhenoBrowser 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_partitions() (dae.parquet.partition_descriptor.PartitionDescriptor method) has_pheno_data (studies.study_wrapper.WDAEStudy property) 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) (dae.studies.study.GenotypeDataGroup property) has_unlimited_download (users_api.models.WdaeUser property) 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.import_tools.import_tools.ImportProject method) (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) has_zygosity (dae.studies.study.GenotypeData property) hashsum() (in module dae.utils.filehash) 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.user_set_name.Command attribute) (users_api.management.commands.user_setpasswd.Command attribute) (users_api.management.commands.users_remove.Command attribute) (users_api.management.commands.users_show.Command attribute) heterozygous (dae.variants.attributes.Zygosity 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) histogram_configs (dae.pheno.common.PhenoImportConfig attribute) histogram_type (dae.pheno.common.InferenceConfig attribute) (dae.pheno.prepare.measure_classifier.InferenceReport attribute) HistogramError histograms (dae.gene_sets.gene_sets_db.GeneSetResourceSchema attribute) HistogramStatisticMixin (class in dae.genomic_resources.histogram) homozygous (dae.variants.attributes.Zygosity attribute)

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) (dae.pheno.common.PhenoImportConfig attribute) (users_api.models.AuthenticationLog attribute) (users_api.models.GpUserState attribute) (users_api.models.ResetPasswordCode attribute) (users_api.models.SetPasswordCode attribute) (users_api.models.WdaeUser attribute) id_to_position (dae.pedigrees.layout.Layout property) import_config (dae.pheno.common.ImportManifest attribute) 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) ImportConfigNormalizer (class in dae.import_tools.import_tools) ImportInstrument (class in dae.pheno.pheno_import) ImportManifest (class in dae.pheno.common) ImportProject (class in dae.import_tools.import_tools) ImportStorage (class in dae.import_tools.import_tools) in_start_codons() (dae.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) (dae.effect_annotation.annotation_request.PositiveStrandAnnotationRequest method) inc() (dae.utils.stats_collection.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) infer_measures() (in module dae.pheno.pheno_import) inference_config (dae.pheno.common.PhenoImportConfig attribute) inference_reference_impl() (in module dae.pheno.prepare.measure_classifier) inference_report (dae.pheno.pheno_import.MeasureReport attribute) InferenceConfig (class in dae.pheno.common) InferenceReport (class in dae.pheno.prepare.measure_classifier) 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) InfoImplementationMixin.FileEntry (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_in_members (dae.variants.family_variant.FamilyAllele property) 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) init_vcf_loaders() (dae.variants_loaders.vcf.loader.VcfLoader method) initial (datasets_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) (dae.pheno.common.PhenoImportConfig attribute) 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.GeneProfileDBWriter method) insert_gps() (dae.gene_profile.db.GeneProfileDBWriter method) InstanceIdCommand (class in dae.gpf_instance.adjustments.gpf_instance_adjustments) Instrument (class in dae.pheno.pheno_data) instrument (dae.pheno.common.DataDictionaryConfig attribute) (dae.pheno.common.InstrumentConfig attribute) (dae.pheno.common.InstrumentDictionaryConfig attribute) instrument_column (dae.pheno.common.DataDictionaryConfig attribute) (dae.pheno.common.InstrumentDictionaryConfig attribute) instrument_description (dae.pheno.pheno_import.MeasureReport attribute) instrument_dictionary (dae.pheno.common.PhenoImportConfig attribute) instrument_files (dae.pheno.common.PhenoImportConfig attribute) instrument_name (dae.pheno.common.RegressionMeasure attribute) (dae.pheno.pheno_import.MeasureReport attribute) InstrumentConfig (class in dae.pheno.common) InstrumentDescriptionsConfig (class in dae.pheno.common) InstrumentDictionaryConfig (class in dae.pheno.common) instruments (dae.pheno.pheno_data.PhenotypeData property) 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) 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_browser_outdated() (dae.pheno.pheno_data.PhenotypeData method) is_cached() (dae.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection 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_genotype (studies.study_wrapper.WDAEStudy property) is_gr_id_token() (in module dae.genomic_resources.repository) is_group (dae.pheno.pheno_data.PhenotypeData property) (dae.pheno.pheno_data.PhenotypeGroup property) (dae.studies.study.GenotypeData property) (dae.studies.study.GenotypeDataGroup property) (dae.studies.study.GenotypeDataStudy property) (studies.study_wrapper.StudyWrapper property) (studies.study_wrapper.WDAEStudy 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_older_than() (dae.pheno.common.ImportManifest method) is_open() (dae.annotation.annotation_pipeline.Annotator method) (dae.annotation.annotation_pipeline.AnnotatorDecorator method) (dae.annotation.score_annotator.GenomicScoreAnnotatorBase method) (dae.genomic_resources.genomic_scores.GenomicScore method) (dae.genomic_resources.liftover_chain.LiftoverChain method) (dae.genomic_resources.reference_genome.ReferenceGenome 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_phenotype (studies.study_wrapper.WDAEStudy property) 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) 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_superuser (users_api.models.WdaeUser attribute) 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) is_valid_family() (dae.pedigrees.pedigrees.FamilyConnections static method) is_version_constraint_satisfied() (in module dae.genomic_resources.repository) 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) (in module utils.streaming_response_util)

J

jitter (dae.pheno.common.RegressionMeasure attribute) 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) label_rotation (dae.gene_sets.gene_sets_db.CategoricalHistogramSchema attribute) (dae.genomic_resources.histogram.CategoricalHistogramConfig attribute) labels (dae.gene_sets.gene_sets_db.MetaSchema attribute) 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) 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) legend_json() (dae.person_sets.person_sets.PersonSetCollection method) (dae.person_sets.PersonSetCollection method) 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) 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) literal() (dae.query_variants.attribute_queries.AttributeQueryTransformerFunction method) (dae.query_variants.attribute_queries.AttributeQueryTransformerSQL method) (dae.query_variants.attribute_queries.AttributeQueryTransformerSQLLegacy method) 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_dict() (dae.configuration.gpf_config_parser.GPFConfigParser class method) load_config_raw() (dae.configuration.gpf_config_parser.GPFConfigParser class method) load_configurations() (dae.pheno.registry.PhenoRegistry static method) load_definition_file() (in module dae.genomic_resources.repository_factory) 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_histogram_configs() (in module dae.pheno.pheno_import) load_inference_configs() (in module dae.pheno.pheno_import) load_instrument_description_file() (in module dae.pheno.pheno_import) load_instrument_descriptions() (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_description_file() (in module dae.pheno.pheno_import) load_measure_descriptions() (in module dae.pheno.pheno_import) 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_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) log_filter() (in module utils.logger) logout() (in module users_api.views)

M

M (dae.variants.attributes.Sex attribute) main() (dae.tools.gpf_validation_runner.MainRunner method) (in module dae.gene_profile.convert_gene_profile_to_duckdb) (in module dae.gene_profile.generate_gene_profile) (in module dae.genomic_resources.draw_score_histograms) (in module dae.import_tools.cli) (in module dae.pheno.build_pheno_browser) (in module dae.pheno.import_tools) (in module dae.pheno.pheno_import) (in module dae.pheno.update_pheno_descriptions) (in module dae.task_graph.demo_graphs_cli) (in module dae.tools.cnv_liftover) (in module dae.tools.dae2vcf) (in module dae.tools.dae_liftover) (in module dae.tools.denovo2vcf) (in module dae.tools.denovo_liftover) (in module dae.tools.draw_pedigree) (in module dae.tools.generate_common_report) (in module dae.tools.generate_denovo_gene_sets) (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.vcf2tsv) (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_filter_beta() (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_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) mat2str() (in module dae.utils.variant_utils) 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) 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 (dae.gene_sets.gene_sets_db.ViewRangeSchema 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_value (dae.pheno.prepare.measure_classifier.InferenceReport attribute) 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) (dae.genomic_resources.resource_implementation.InfoImplementationMixin.FileEntry attribute) md5sum() (in module dae.utils.filehash) MeanAggregator (class in dae.genomic_resources.aggregators) Measure (class in dae.pheno.pheno_data) measure_column (dae.pheno.common.DataDictionaryConfig attribute) measure_name (dae.pheno.pheno_import.MeasureReport attribute) measure_names (dae.pheno.common.RegressionMeasure attribute) measure_type (dae.pheno.pheno_import.MeasureReport attribute) MeasureDescriptionsConfig (class in dae.pheno.common) MeasureHistogramConfigs (class in dae.pheno.common) MeasureReport (class in dae.pheno.pheno_import) measures (dae.pheno.pheno_data.PhenotypeData property) measures_api module MeasureType (class in dae.pheno.common) MedianAggregator (class in dae.genomic_resources.aggregators) member_has_both_parents() (dae.pedigrees.family.Family method) member_has_dad() (dae.pedigrees.family.Family method) member_has_mom() (dae.pedigrees.family.Family method) member_has_parent() (dae.pedigrees.family.Family method) member_index (dae.pedigrees.family.Person property) member_is_child() (dae.pedigrees.family.Family method) member_is_parent() (dae.pedigrees.family.Family method) 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) 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_histogram_configs() (in module dae.pheno.pheno_import) 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.gene_sets.gene_sets_db.BaseResourceSchema attribute) (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) MetaSchema (class in dae.gene_sets.gene_sets_db) 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 query_state_save.migrations.0003_querystate_origin_querystate_timestamp) (class in users_api.migrations.0002_auto_20190424_0751) (class in users_api.migrations.0003_authenticationlog) min (dae.gene_sets.gene_sets_db.ViewRangeSchema attribute) min_individuals (dae.pheno.common.InferenceConfig attribute) (dae.pheno.prepare.measure_classifier.InferenceReport attribute) MIN_QUEUE_SIZE (dae.task_graph.executor.DaskExecutor attribute) min_rank (dae.pheno.common.RankRange attribute) min_value (dae.pheno.prepare.measure_classifier.InferenceReport 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_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 (users_api.serializers.UserSerializer.Meta attribute) (users_api.serializers.UserWithoutEmailSerializer.Meta attribute) 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.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.BaseResourceSchema attribute) (dae.gene_sets.gene_sets_db.CategoricalHistogramSchema attribute) (dae.gene_sets.gene_sets_db.GeneSetResourceSchema attribute) (dae.gene_sets.gene_sets_db.MetaSchema attribute) (dae.gene_sets.gene_sets_db.NumericHistogramSchema attribute) (dae.gene_sets.gene_sets_db.ViewRangeSchema 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.DataDictionaryConfig attribute) (dae.pheno.common.DestinationConfig attribute) (dae.pheno.common.GPFInstanceConfig attribute) (dae.pheno.common.ImportManifest attribute) (dae.pheno.common.InferenceConfig attribute) (dae.pheno.common.InstrumentConfig attribute) (dae.pheno.common.InstrumentDescriptionsConfig attribute) (dae.pheno.common.InstrumentDictionaryConfig attribute) (dae.pheno.common.MeasureDescriptionsConfig attribute) (dae.pheno.common.MeasureHistogramConfigs attribute) (dae.pheno.common.PhenoImportConfig attribute) (dae.pheno.common.RankRange attribute) (dae.pheno.common.RegressionMeasure attribute) (dae.pheno.common.StudyConfig attribute) (dae.pheno.pheno_import.MeasureReport attribute) (dae.pheno.prepare.measure_classifier.InferenceReport attribute) (dae.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute) (dae.query_variants.sql.schema2.sql_query_builder.ZygosityQuery 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.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.BaseResourceSchema attribute) (dae.gene_sets.gene_sets_db.CategoricalHistogramSchema attribute) (dae.gene_sets.gene_sets_db.GeneSetResourceSchema attribute) (dae.gene_sets.gene_sets_db.MetaSchema attribute) (dae.gene_sets.gene_sets_db.NumericHistogramSchema attribute) (dae.gene_sets.gene_sets_db.ViewRangeSchema 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.DataDictionaryConfig attribute) (dae.pheno.common.DestinationConfig attribute) (dae.pheno.common.GPFInstanceConfig attribute) (dae.pheno.common.ImportManifest attribute) (dae.pheno.common.InferenceConfig attribute) (dae.pheno.common.InstrumentConfig attribute) (dae.pheno.common.InstrumentDescriptionsConfig attribute) (dae.pheno.common.InstrumentDictionaryConfig attribute) (dae.pheno.common.MeasureDescriptionsConfig attribute) (dae.pheno.common.MeasureHistogramConfigs attribute) (dae.pheno.common.PhenoImportConfig attribute) (dae.pheno.common.RankRange attribute) (dae.pheno.common.RegressionMeasure attribute) (dae.pheno.common.StudyConfig attribute) (dae.pheno.pheno_import.MeasureReport attribute) (dae.pheno.prepare.measure_classifier.InferenceReport attribute) (dae.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute) (dae.query_variants.sql.schema2.sql_query_builder.ZygosityQuery 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.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.BaseResourceSchema attribute) (dae.gene_sets.gene_sets_db.CategoricalHistogramSchema attribute) (dae.gene_sets.gene_sets_db.GeneSetResourceSchema attribute) (dae.gene_sets.gene_sets_db.MetaSchema attribute) (dae.gene_sets.gene_sets_db.NumericHistogramSchema attribute) (dae.gene_sets.gene_sets_db.ViewRangeSchema 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.DataDictionaryConfig attribute) (dae.pheno.common.DestinationConfig attribute) (dae.pheno.common.GPFInstanceConfig attribute) (dae.pheno.common.ImportManifest attribute) (dae.pheno.common.InferenceConfig attribute) (dae.pheno.common.InstrumentConfig attribute) (dae.pheno.common.InstrumentDescriptionsConfig attribute) (dae.pheno.common.InstrumentDictionaryConfig attribute) (dae.pheno.common.MeasureDescriptionsConfig attribute) (dae.pheno.common.MeasureHistogramConfigs attribute) (dae.pheno.common.PhenoImportConfig attribute) (dae.pheno.common.RankRange attribute) (dae.pheno.common.RegressionMeasure attribute) (dae.pheno.common.StudyConfig attribute) (dae.pheno.pheno_import.MeasureReport attribute) (dae.pheno.prepare.measure_classifier.InferenceReport attribute) (dae.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute) (dae.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute) modified() (in module dae.utils.fs_utils) modify_tuple() (dae.configuration.gpf_config_parser.GPFConfigParser class method) module common_reports_api 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.docker_annotator dae.annotation.effect_annotator dae.annotation.format_handlers 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.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.convert_gene_profile_to_duckdb 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.implementations dae.gene_sets.implementations.gene_sets_impl dae.genomic_resources dae.genomic_resources.aggregators dae.genomic_resources.cached_repository dae.genomic_resources.cli 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.adjustments dae.gpf_instance.adjustments.adjust_command dae.gpf_instance.adjustments.adjust_duckdb_storage dae.gpf_instance.adjustments.adjust_impala_storage dae.gpf_instance.adjustments.gpf_instance_adjustments 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.annotation_serialization 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.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.browser dae.pheno.build_pheno_browser dae.pheno.common dae.pheno.db dae.pheno.graphs dae.pheno.import_tools 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.storage dae.pheno.update_pheno_descriptions 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.attribute_queries 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.dae2vcf dae.tools.dae_liftover dae.tools.denovo2vcf dae.tools.denovo_liftover dae.tools.draw_pedigree dae.tools.generate_common_report dae.tools.generate_denovo_gene_sets dae.tools.gpf_convert_study_config 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.vcf2tsv 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.stats_collection 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 dae.variants_loaders.vcf.serializer 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 enrichment_api family_api gene_profiles_api gene_scores gene_sets gene_view genomes_api genomic_scores_api genotype_browser, [1] gpf_instance gpf_instance.apps gpf_instance.gpf_instance gpfjs gpfjs.views groups_api groups_api.migrations measures_api person_sets_api pheno_browser_api pheno_tool_api 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.migrations.0003_querystate_origin_querystate_timestamp sentry studies studies.query_transformer studies.response_transformer studies.study_wrapper user_queries user_queries.admin user_queries.migrations users_api, [1] users_api.management users_api.management.commands users_api.management.commands.export_base users_api.management.commands.user_set_name users_api.management.commands.user_setpasswd users_api.management.commands.users_remove users_api.management.commands.users_show users_api.migrations users_api.migrations.0002_auto_20190424_0751 users_api.migrations.0003_authenticationlog users_api.models users_api.serializers users_api.urls users_api.validators users_api.views utils utils.datasets utils.email_regex utils.expand_gene_set utils.gene_sets utils.logger utils.password_requirements utils.query_params utils.streaming_response_util utils.testing wdae wdae.wgpf wdae.wsgi 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.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_resources.resource_implementation.InfoImplementationMixin.FileEntry 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.pheno.pheno_import.ImportInstrument attribute) (dae.studies.study.GenotypeData property) (gpf_instance.apps.WDAEConfig attribute) (studies.study_wrapper.WDAEStudy property) (users_api.models.WdaeUser attribute) names() (dae.genomic_resources.repository.Manifest method) nan (dae.pheno.prepare.measure_classifier.Convertible attribute) natural_order (dae.gene_sets.gene_sets_db.CategoricalHistogramSchema attribute) (dae.genomic_resources.histogram.CategoricalHistogramConfig attribute) NCBIGeneInfo (class in dae.gene_sets.gene_term) NEEDS_COMPUTE (dae.task_graph.cache.CacheRecordType attribute)

neg() (dae.query_variants.attribute_queries.AttributeQueryTransformerFunction method) (dae.query_variants.attribute_queries.AttributeQueryTransformerSQL method) NegativeStrandAnnotationRequest (class in dae.effect_annotation.annotation_request) 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_genome_1() (in module dae.conftest) normalize_genome_2() (in module dae.conftest) 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) NOTSET (dae.tools.gpf_validation_runner.TestStatus attribute) ns_tokens (dae.gene_sets.gene_term.NCBIGeneInfo attribute) NUCLEAR (dae.pedigrees.family.FamilyTag attribute) NuclearCode (class in dae.effect_annotation.gene_codes) NullHistogram (class in dae.genomic_resources.histogram) NullHistogramConfig (class in dae.genomic_resources.histogram) number_config (dae.pheno.common.MeasureHistogramConfigs attribute) number_of_bins (dae.gene_sets.gene_sets_db.NumericHistogramSchema attribute) (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) NumericHistogramSchema (class in dae.gene_sets.gene_sets_db)

O

oauth2_provider_accesstoken (users_api.models.WdaeUser attribute) oauth2_provider_application (users_api.models.WdaeUser attribute) oauth2_provider_grant (users_api.models.WdaeUser attribute) oauth2_provider_idtoken (users_api.models.WdaeUser attribute) oauth2_provider_refreshtoken (users_api.models.WdaeUser attribute) objects (users_api.models.AuthenticationLog attribute) (users_api.models.GpUserState attribute) (users_api.models.ResetPasswordCode attribute) (users_api.models.SetPasswordCode attribute) (users_api.models.WdaeUser attribute) 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) open() (dae.annotation.annotation_pipeline.AnnotationPipeline method) (dae.annotation.annotation_pipeline.Annotator method) (dae.annotation.annotation_pipeline.AnnotatorDecorator method) (dae.annotation.annotator_base.AnnotatorBase method) (dae.annotation.cnv_collection_annotator.CnvCollectionAnnotator method) (dae.annotation.docker_annotator.DockerAnnotator method) (dae.annotation.effect_annotator.EffectAnnotatorAdapter method) (dae.annotation.format_handlers.AbstractFormat method) (dae.annotation.format_handlers.ColumnsFormat method) (dae.annotation.format_handlers.ParquetFormat method) (dae.annotation.format_handlers.VCFFormat 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.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.CnvCollection method) (dae.genomic_resources.genomic_scores.GenomicScore method) (dae.genomic_resources.genomic_scores.PositionScore method) (dae.genomic_resources.liftover_chain.LiftoverChain method) (dae.genomic_resources.reference_genome.ReferenceGenome method) (dae.variants_loaders.vcf.serializer.VcfSerializer 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_file() (in module dae.pheno.pheno_import) 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) (query_state_save.migrations.0003_querystate_origin_querystate_timestamp.Migration attribute) (users_api.migrations.0002_auto_20190424_0751.Migration attribute) (users_api.migrations.0003_authenticationlog.Migration attribute) OPTION (dae.variants_loaders.raw.loader.ArgumentType attribute) or_() (dae.query_variants.attribute_queries.AttributeQueryTransformerFunction method) (dae.query_variants.attribute_queries.AttributeQueryTransformerSQL method) ordinal (dae.pheno.common.InferenceConfig attribute) (dae.pheno.common.MeasureType attribute) other (dae.pheno.common.MeasureType attribute) (dae.variants.attributes.Inheritance attribute) other_parent() (dae.pedigrees.pedigrees.MatingUnit method) overlap_enrichment_result_dict() (in module dae.enrichment_tool.event_counters) overlap_event_counts() (in module dae.enrichment_tool.event_counters)

P

PAGE_SIZE (dae.gene_profile.db.GeneProfileDB attribute) (dae.pheno.browser.PhenoBrowser attribute) 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.studies.study.GenotypeData property) (studies.study_wrapper.WDAEStudy property) parents_id() (dae.pedigrees.family_role_builder.Mating static method) parents_zygosity (dae.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute) ParquetFormat (class in dae.annotation.format_handlers) 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) 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.dae2vcf) (in module dae.tools.dae_liftover) (in module dae.tools.denovo2vcf) (in module dae.tools.denovo_liftover) (in module dae.tools.simple_family2pedigree) (in module dae.tools.stats_liftover) (in module dae.tools.vcf2tsv) (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_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) 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) password_reset() (users_api.views.UserViewSet method) 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 (dae.pheno.common.DataDictionaryConfig attribute) (dae.pheno.common.GPFInstanceConfig attribute) (dae.pheno.common.InstrumentConfig attribute) (dae.pheno.common.InstrumentDictionaryConfig attribute) (users_api.models.BaseVerificationCode attribute) (users_api.models.ResetPasswordCode attribute) (users_api.models.SetPasswordCode attribute) 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.PhenoImportConfig 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 (users_api.views.UserViewSet attribute) Person (class in dae.pedigrees.family) person_column (dae.pheno.common.InstrumentConfig attribute) (dae.pheno.common.PhenoImportConfig attribute) (dae.pheno.pheno_import.ImportInstrument attribute) person_ids (dae.studies.study.PSCQueryAdjustments attribute) person_ids() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) person_set_collections (dae.pheno.common.StudyConfig attribute) (dae.pheno.pheno_data.PhenotypeData property) (dae.pheno.pheno_data.PhenotypeGroup property) (dae.pheno.pheno_data.PhenotypeStudy property) (dae.studies.study.GenotypeData property) (studies.study_wrapper.StudyWrapper property) person_sets_api 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_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_cli_parser() (in module dae.pheno.build_pheno_browser) (in module dae.pheno.import_tools) (in module dae.pheno.pheno_import) (in module dae.pheno.update_pheno_descriptions) pheno_id (dae.pheno.pheno_data.PhenotypeData property) pheno_tool_api module PhenoBrowser (class in dae.pheno.browser) 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) PhenoImportConfig (class in dae.pheno.common) 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) PhenoToolHelper (class in dae.pheno_tool.tool) phenotype (dae.studies.study.GenotypeData property) PHENOTYPE_ATTRS (studies.response_transformer.ResponseTransformer attribute) phenotype_data (studies.study_wrapper.WDAEStudy property) phenotype_storages (dae.gpf_instance.gpf_instance.GPFInstance property) (dae.gpf_instance.GPFInstance property) PhenotypeData (class in dae.pheno.pheno_data) PhenotypeGroup (class in dae.pheno.pheno_data) PhenotypeStorage (class in dae.pheno.storage) PhenotypeStorageRegistry (class in dae.pheno.storage) PhenotypeStudy (class in dae.pheno.pheno_data) plot() (dae.genomic_resources.histogram.CategoricalHistogram method) (dae.genomic_resources.histogram.NullHistogram method) (dae.genomic_resources.histogram.NumberHistogram method) plot_function (dae.gene_sets.gene_sets_db.CategoricalHistogramSchema attribute) (dae.gene_sets.gene_sets_db.NumericHistogramSchema attribute) (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.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.CNV attribute) (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.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.CNV attribute) (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.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) PositionScoreQuery (class in dae.genomic_resources.genomic_scores) PositiveStrandAnnotationRequest (class in dae.effect_annotation.annotation_request) possible_denovo (dae.variants.attributes.Inheritance attribute) possible_omission (dae.variants.attributes.Inheritance attribute) possiblePersonPhasing() (in module dae.tools.phase) possiblePersonPhasingR() (in module dae.tools.phase) post() (users_api.views.BasePasswordView method) (users_api.views.FederationCredentials method) (users_api.views.ForgotPassword method) (users_api.views.RESTLoginView method) (users_api.views.UserGpStateView method) (users_api.views.WdaeLoginView method) prb (dae.variants.attributes.Role attribute) preamble (dae.annotation.annotation_config.RawFullConfig attribute) prepare_for_annotation() (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) PreparePhenoBrowserBase (class in dae.pheno.prepare_data) print() (dae.annotation.annotation_pipeline.AnnotationPipeline method) (dae.annotation.annotation_pipeline.ReannotationPipeline 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() (dae.annotation.format_handlers.AbstractFormat method) process_batched() (dae.annotation.format_handlers.AbstractFormat method) process_config() (dae.configuration.gpf_config_parser.GPFConfigParser static method) process_config_raw() (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_utils) 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) PSCQueryAdjustments (class in dae.studies.study) pseudo_autosomal (dae.variants.attributes.GeneticModel attribute) pub_med (dae.studies.study.GenotypeData property) put() (users_api.views.FederationCredentials method) 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_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_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.migrations.0003_querystate_origin_querystate_timestamp module

query_summary_variants() (dae.duckdb_storage.duckdb2_variants.DuckDb2Variants method) (dae.inmemory_storage.raw_variants.RawFamilyVariants method) (dae.query_variants.base_query_variants.QueryVariants 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.QueryVariants 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) 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) QueryTransformer (class in studies.query_transformer) QueryVariants (class in dae.query_variants.base_query_variants) QueryVariantsBase (class in dae.query_variants.base_query_variants) 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_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) recurrency (dae.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) (dae.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) 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_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_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_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) 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) (dae.pheno.storage.PhenotypeStorageRegistry method) register_enrichment_builder() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) register_genotype_data() (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_storage() (dae.pheno.storage.PhenotypeStorageRegistry method)

register_preexisting_user() (users_api.models.WdaeUser method) register_storage_config() (dae.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) (dae.pheno.storage.PhenotypeStorageRegistry method) register_storages_configs() (dae.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) (dae.pheno.storage.PhenotypeStorageRegistry method) register_study_config() (dae.pheno.registry.PhenoRegistry method) regression_display_names (dae.pheno.browser.PhenoBrowser property) regression_display_names_with_ids (dae.pheno.browser.PhenoBrowser property) regression_ids (dae.pheno.browser.PhenoBrowser property) RegressionMeasure (class in dae.pheno.common) regressions (dae.pheno.common.StudyConfig attribute) 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) 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) 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_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) reset() (dae.genomic_resources.gene_models.gene_models.GeneModels method) (dae.genomic_resources.gene_models.GeneModels method) reset_password() (users_api.models.WdaeUser method) reset_regions() (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) ResetPasswordCode (class in users_api.models) resetpasswordcode (users_api.models.WdaeUser attribute) ResetPasswordCode.DoesNotExist ResetPasswordCode.MultipleObjectsReturned resolve_repeated_attributes() (in module dae.annotation.annotation_factory) resolve_tags() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) resource (dae.genomic_resources.resource_implementation.InfoImplementationMixin attribute) resource_builder() (in module dae.genomic_resources.testing) resource_format (dae.gene_sets.gene_sets_db.GeneSetResourceSchema attribute) 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.gene_sets.gene_sets_db.GeneSetResourceSchema 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) ResponseTransformer (class in studies.response_transformer) RESTLoginView (class in users_api.views) 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) 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.studies.study.PSCQueryAdjustments attribute) roles() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) 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.annotation.docker_annotator.DockerAnnotator method) (dae.annotation.reannotate_instance.ReannotateInstanceTool 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) 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.browser.PhenoBrowser method) (dae.utils.stats_collection.StatsCollection 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_descriptions() (in module dae.pheno.update_pheno_descriptions) 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_instrument_descriptions() (dae.pheno.browser.PhenoBrowser method) (dae.pheno.db.PhenoDb method) save_liftover_stats() (in module dae.tools.stats_liftover) save_manifest() (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) save_measure_descriptions() (dae.pheno.browser.PhenoBrowser method) (dae.pheno.db.PhenoDb method) save_ped_df_to_parquet() (in module dae.parquet.parquet_writer) save_pedigree() (dae.pedigrees.loader.FamiliesLoader static method) save_regression() (dae.pheno.browser.PhenoBrowser method) save_regression_values() (dae.pheno.browser.PhenoBrowser 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.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 (users_api.views.UserViewSet attribute) search_measures() (dae.pheno.browser.PhenoBrowser method) (dae.pheno.pheno_data.PhenotypeData method) select_events_in_person_set() (dae.enrichment_tool.event_counters.CounterBase method) selected_family_tags (dae.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute) 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) send_reset_email() (in module users_api.models) send_reset_inactive_acc_email() (in module users_api.models) send_verif_email() (in module users_api.models) sentry module 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) (dae.variants_loaders.vcf.serializer.VcfSerializer 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 (users_api.views.UserViewSet attribute) 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_context() (users_api.validators.SomeSuperuserLeftValidator method) 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_negative_stats() (dae.pheno_tool.tool.PhenoResult method) set_password() (users_api.models.WdaeUser method) 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) 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) SetPasswordCode (class in users_api.models) setpasswordcode (users_api.models.WdaeUser attribute) SetPasswordCode.DoesNotExist SetPasswordCode.MultipleObjectsReturned 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_zygosity (dae.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute) sexes (dae.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) (dae.gene_sets.denovo_gene_sets_config.SexesCriteria attribute) (dae.studies.study.PSCQueryAdjustments 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) 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) (dae.pheno.registry.PhenoRegistry method) (dae.pheno.storage.PhenotypeStorage method) (dae.pheno.storage.PhenotypeStorageRegistry method) sib (dae.variants.attributes.Role attribute) SibshipUnit (class in dae.pedigrees.pedigrees) sign() (in module dae.utils.fs_utils) 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) SingleCriteria (class in dae.gene_sets.denovo_gene_sets_config) SingleVcfLoader (class in dae.variants_loaders.vcf.loader) size (dae.genomic_resources.genomic_scores.CNV property) (dae.genomic_resources.repository.ManifestEntry attribute) (dae.genomic_resources.repository.ResourceFileState attribute) (dae.genomic_resources.resource_implementation.InfoImplementationMixin.FileEntry attribute) SIZE (dae.pedigrees.layout.IndividualWithCoordinates attribute) size() (dae.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) skip (dae.pheno.common.InferenceConfig attribute) skip_pedigree_measures (dae.pheno.common.PhenoImportConfig 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) 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) start (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.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.stats_collection) Status (class in dae.variants.attributes) status (dae.pedigrees.family.Person property) status_zygosity (dae.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute) statuses() (dae.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) 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_dir (dae.pheno.common.DestinationConfig attribute) storage_id (dae.pheno.common.DestinationConfig attribute) 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) 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) string_type() (dae.query_variants.sql.schema2.base_query_builder.Dialect static method) stringify() (in module dae.annotation.format_handlers) studies module studies.query_transformer module studies.response_transformer module studies.study_wrapper module study (dae.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute) (dae.schema2_storage.schema2_layout.Schema2DatasetLayout attribute) study_config (dae.pheno.common.PhenoImportConfig 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.WDAEStudy 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) StudyConfig (class in dae.pheno.common) StudyConfigBuilder (class in dae.configuration.study_config_builder) StudyConfigsAdjustmentCommand (class in dae.gpf_instance.adjustments.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) SUBSTITUTIONS (dae.genomic_resources.genomic_scores.AlleleScore.Mode attribute) substitutions_mode() (dae.genomic_resources.genomic_scores.AlleleScore method) 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_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) 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) SyntaxSugarTransformer (class in dae.query_variants.attribute_queries)

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_grr() (in module dae.conftest) (in module dae.testing.t4c8_import) t4c8_instance() (in module dae.conftest) t4c8_study_1() (in module dae.conftest) t4c8_study_1_ped() (in module dae.conftest) t4c8_study_1_pheno() (in module dae.conftest) t4c8_study_2() (in module dae.conftest) t4c8_study_3() (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) 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) tags_or_mode (dae.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute) tags_to_family_ids() (dae.query_variants.base_query_variants.QueryVariantsBase method) TagsQuery (class in dae.query_variants.sql.schema2.sql_query_builder) 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) (users_api.views.ResetPassword attribute) (users_api.views.SetPassword attribute) 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) 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) (users_api.serializers.DatasetSerializer method) 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() (users_api.serializers.DatasetSerializer method) (users_api.serializers.UserSerializer method) 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) 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_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_attribute_query_to_function() (in module dae.query_variants.attribute_queries) transform_attribute_query_to_sql_expression() (in module dae.query_variants.attribute_queries) transform_attribute_query_to_sql_expression_schema1() (in module dae.query_variants.attribute_queries) transform_cli_args() (in module dae.pheno.pheno_import) 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_pedigree_queries() (dae.person_sets.person_sets.PersonSetCollection method) (dae.person_sets.PersonSetCollection method) transform_request() (studies.study_wrapper.StudyWrapper method) transform_roles_to_single_role_string() (dae.query_variants.base_query_variants.QueryVariantsBase static method) transform_summary_variants() (studies.response_transformer.ResponseTransformer 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) 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.gene_sets.gene_sets_db.BaseResourceSchema attribute) (dae.gene_sets.gene_sets_db.CategoricalHistogramSchema attribute) (dae.gene_sets.gene_sets_db.NumericHistogramSchema 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) 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) undefined (dae.variants.attributes.Zygosity attribute) union() (in module dae.utils.regions) unique_regions() (in module dae.utils.regions) UNIQUE_VALUES_LIMIT (dae.genomic_resources.histogram.CategoricalHistogram attribute) unix_timestamp (dae.pheno.common.ImportManifest attribute) unknown (dae.variants.attributes.Inheritance attribute) (dae.variants.attributes.Role attribute) (dae.variants.attributes.TransmissionType attribute) unmap_chromosome() (dae.genomic_resources.genomic_position_table.table.GenomicPositionTable method) unregister_genotype_data() (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) (users_api.serializers.UserSerializer method) (users_api.views.UserViewSet method) 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.GeneProfileDBWriter method) 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_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 (users_api.models.BaseVerificationCode attribute) (users_api.models.GpUserState attribute) (users_api.models.ResetPasswordCode attribute) (users_api.models.SetPasswordCode attribute) user_id (users_api.models.BaseVerificationCode attribute) (users_api.models.GpUserState attribute) (users_api.models.ResetPasswordCode attribute) (users_api.models.SetPasswordCode attribute) user_permissions (users_api.models.WdaeUser attribute) user_queries module user_queries.admin module user_queries.migrations module

UserGpStateView (class in users_api.views) USERNAME_FIELD (users_api.models.WdaeUser attribute) userquery_set (users_api.models.WdaeUser attribute) users_api module, [1] users_api.management module users_api.management.commands module users_api.management.commands.export_base module users_api.management.commands.user_set_name module users_api.management.commands.user_setpasswd module users_api.management.commands.users_remove module users_api.management.commands.users_show module users_api.migrations module users_api.migrations.0002_auto_20190424_0751 module users_api.migrations.0003_authenticationlog module users_api.models module users_api.serializers module users_api.urls module users_api.validators module users_api.views module UserSerializer (class in users_api.serializers) UserSerializer.Meta (class in users_api.serializers) UserViewSet (class in users_api.views) UserWithoutEmailSerializer (class in users_api.serializers) UserWithoutEmailSerializer.Meta (class in users_api.serializers) utils module utils.datasets module utils.email_regex module utils.expand_gene_set module utils.gene_sets module utils.logger 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)

V

validate() (users_api.models.BaseVerificationCode method) (users_api.models.ResetPasswordCode method) (users_api.models.SetPasswordCode method) (users_api.serializers.UserSerializer method) 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.gene_sets.gene_sets_db.CategoricalHistogramSchema attribute) (dae.gene_sets.gene_sets_db.NumericHistogramSchema attribute) (dae.genomic_resources.histogram.CategoricalHistogramConfig attribute) value_type (dae.genomic_resources.genomic_scores.ScoreDef attribute) (dae.pheno.common.InferenceConfig attribute) (dae.pheno.prepare.measure_classifier.InferenceReport attribute) values (dae.person_sets.person_sets.PersonSetConfig attribute) (dae.person_sets.PersonSetConfig attribute) values() (dae.pedigrees.families_data.FamiliesData method) values_domain (dae.pheno.prepare.measure_classifier.InferenceReport attribute) 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_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) variants_filenames (dae.variants_loaders.dae.loader.DaeTransmittedLoader property) (dae.variants_loaders.raw.loader.VariantsLoader property) (dae.variants_loaders.vcf.loader.VcfLoader property) variants_loader_annotate_and_save() (in module dae.inmemory_storage.annotation_serialization) variants_loader_load_annotation() (in module dae.inmemory_storage.annotation_serialization) 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) vcffile_chromosomes() (in module dae.variants_loaders.vcf.loader) VCFFormat (class in dae.annotation.format_handlers) 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) VcfSerializer (class in dae.variants_loaders.vcf.serializer) VerbosityConfiguration (class in dae.utils.verbosity_configuration) verification_code_model (users_api.views.BasePasswordView attribute) (users_api.views.ResetPassword attribute) (users_api.views.SetPassword attribute) 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.gene_sets.gene_sets_db.NumericHistogramSchema attribute) (dae.genomic_resources.histogram.NumberHistogramConfig attribute) ViewRangeSchema (class in dae.gene_sets.gene_sets_db)

W

wdae module wdae.wgpf module wdae.wsgi module WDAEConfig (class in gpf_instance.apps) WdaeLoginView (class in users_api.views) wdaemanage module WDAEStudy (class in studies.study_wrapper) WdaeUser (class in users_api.models) WdaeUser.DoesNotExist WdaeUser.MultipleObjectsReturned WdaeUserManager (class in users_api.models)

web_format_str (dae.gene_sets.gene_sets_db.GeneSetResourceSchema attribute) web_label (dae.gene_sets.gene_sets_db.GeneSetResourceSchema attribute) WHERE (dae.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute) work_dir (dae.import_tools.import_tools.ImportProject property) (dae.pheno.common.PhenoImportConfig attribute) 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_reports_to_parquet() (in module dae.pheno.pheno_import) write_results() (in module dae.pheno.pheno_import) write_summary_variant() (dae.parquet.schema2.parquet_io.VariantsParquetWriter method) write_to_db() (dae.pheno.common.ImportManifest static method) write_to_parquet() (in module dae.pheno.pheno_import)

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.gene_sets.gene_sets_db.NumericHistogramSchema attribute) (dae.genomic_resources.histogram.NumberHistogramConfig attribute) x_min_log (dae.gene_sets.gene_sets_db.NumericHistogramSchema attribute) (dae.genomic_resources.histogram.NumberHistogramConfig attribute)

Y

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

year (dae.studies.study.GenotypeData property)

Z

zero_based_adjust() (in module dae.genomic_resources.genomic_position_table.table) Zygosity (class in dae.variants.attributes) zygosity_in_roles (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property)

zygosity_in_sexes (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) zygosity_in_status (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) ZygosityQuery (class in dae.query_variants.sql.schema2.sql_query_builder)