Index

A

abspath() (in module dae.utils.fs_utils) abstract (users_api.models.BaseVerificationCode.Meta attribute) AbstractRunner (class in dae.tools.gpf_validation_runner) acgt_gpf() (in module dae.testing) 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_context_arguments() (dae.genomic_resources.genomic_context.CLIGenomicContext static method) add_members() (dae.pedigrees.family.Family method) add_missing_members() (dae.pedigrees.pedigrees.FamilyConnections static method) add_page() (dae.pedigrees.drawing.PDFLayoutDrawer method) 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.gene.gene_sets_db.GeneSetCollection method) (dae.genomic_resources.gene_models.GeneModels method) add_tagger() (dae.pedigrees.family_tag_builder.FamilyTagsBuilder method) add_to_parser() (dae.variants_loaders.raw.loader.CLIArgument method) add_unnest_in_join() (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) adjust_chrom_prefix() (in module dae.variants_loaders.raw.flexible_variant_loader) adjust_dataset() (dae.tools.gpf_instance_adjustments.EnableDisableStudies method) (dae.tools.gpf_instance_adjustments.StudyConfigsAdjustmentCommand method) adjust_study() (dae.tools.gpf_instance_adjustments.DefaultGenotypeStorage method) (dae.tools.gpf_instance_adjustments.EnableDisableStudies method) (dae.tools.gpf_instance_adjustments.StudyConfigsAdjustmentCommand method) AdjustDuckDbStorageCommand (class in dae.tools.gpf_instance_adjustments) AdjustImpalaStorageCommand (class in dae.tools.gpf_instance_adjustments) AdjustmentsCommand (class in dae.tools.gpf_instance_adjustments) affected (dae.variants.attributes.Status attribute) AFFECTED_DAD (dae.pedigrees.family.FamilyTag attribute) AFFECTED_MOM (dae.pedigrees.family.FamilyTag attribute) AFFECTED_PRB (dae.pedigrees.family.FamilyTag attribute) AFFECTED_SIB (dae.pedigrees.family.FamilyTag attribute) aggregate_gene_values() (dae.annotation.gene_score_annotator.GeneScoreAnnotator method) Aggregator (class in dae.genomic_resources.aggregators) all (dae.enrichment_tool.event_counters.EnrichmentResult attribute) (dae.enrichment_tool.event_counters.EventCountersResult attribute) (dae.enrichment_tool.event_counters.EventsResult attribute) (dae.enrichment_tool.event_counters.VariantEventsResult attribute) all() (dae.query_variants.attributes_query.StringQueryToTreeTransformer method) (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) ALL_ATTRIBUTE_IDXS (dae.effect_annotation.cli.AnnotationAttributes attribute) all_count() (dae.pheno.graphs.GraphColumn method) all_labels() (dae.pedigrees.family.FamilyTag static method) all_regions() (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) Allele (class in dae.variants.core) Allele.Type (class in dae.variants.core) allele_aggregator (dae.genomic_resources.genomic_scores.AlleleScoreAggr attribute) (dae.genomic_resources.genomic_scores.AlleleScoreQuery attribute) (dae.genomic_resources.genomic_scores.ScoreDef attribute) allele_count (dae.variants.family_variant.FamilyVariant property) (dae.variants.variant.SummaryVariant property) allele_events (dae.enrichment_tool.genotype_helper.VariantEvent attribute) allele_in_members (dae.variants.family_variant.FamilyAllele property) allele_in_roles (dae.variants.family_variant.FamilyAllele property) allele_in_sexes (dae.variants.family_variant.FamilyAllele property) allele_in_statuses (dae.variants.family_variant.FamilyAllele property) allele_index (dae.variants.family_variant.FamilyAllele property) (dae.variants.variant.SummaryAllele property) allele_indexes (dae.variants.family_variant.FamilyVariant property) allele_type (dae.variants.core.Allele property) (dae.variants.family_variant.FamilyAllele property) allele_type_from_cshl_variant() (in module dae.variants.variant) allele_type_from_name() (in module dae.variants.variant) AlleleEffects (class in dae.effect_annotation.effect) AlleleEvent (class in dae.enrichment_tool.genotype_helper) AlleleParquetSerializer (class in dae.parquet.schema2.serializers) alleles (dae.variants.family_variant.FamilyVariant property) (dae.variants.variant.SummaryVariant property) AlleleScore (class in dae.genomic_resources.genomic_scores) AlleleScoreAggr (class in dae.genomic_resources.genomic_scores) AlleleScoreAnnotator (class in dae.annotation.score_annotator) AlleleScoreQuery (class in dae.genomic_resources.genomic_scores) allowed_datasets (users_api.models.WdaeUser property) alt (dae.annotation.annotatable.VCFAllele property) (dae.genomic_resources.genomic_scores.ScoreLine property)

alt_alleles (dae.variants.variant.SummaryVariant property) alternative (dae.annotation.annotatable.VCFAllele property) (dae.variants.core.Allele property) (dae.variants.family_variant.FamilyAllele property) (dae.variants.variant.SummaryVariant property) AndNode (class in dae.query_variants.attributes_query) AndNode() (dae.query_variants.attributes_query.QueryTreeToBitwiseLambdaTransformer method) (dae.query_variants.attributes_query.QueryTreeToLambdaTransformer method) (dae.query_variants.attributes_query.QueryTreeToSQLBitwiseTransformer static method) Annotatable (class in dae.annotation.annotatable) Annotatable.Type (class in dae.annotation.annotatable) annotate() (dae.annotation.annotate_columns.AnnotateColumnsTool static method) (dae.annotation.annotate_vcf.AnnotateVCFTool static method) (dae.annotation.annotation_pipeline.AnnotationPipeline method) (dae.annotation.annotation_pipeline.Annotator method) (dae.annotation.annotation_pipeline.InputAnnotableAnnotatorDecorator method) (dae.annotation.annotation_pipeline.ReannotationPipeline method) (dae.annotation.annotation_pipeline.ValueTransformAnnotatorDecorator method) (dae.annotation.annotator_base.AnnotatorBase method) (dae.annotation.gene_score_annotator.GeneScoreAnnotator method) (dae.annotation.score_annotator.AlleleScoreAnnotator method) (dae.annotation.score_annotator.PositionScoreAnnotatorBase method) (dae.effect_annotation.annotator.EffectAnnotator method) annotate_allele() (dae.effect_annotation.annotator.EffectAnnotator method) annotate_cnv() (dae.effect_annotation.annotator.EffectAnnotator method) annotate_region() (dae.effect_annotation.annotator.EffectAnnotator method) annotate_summary_allele() (dae.annotation.annotation_pipeline.ReannotationPipeline method) annotate_variant() (dae.effect_annotation.annotator.EffectAnnotator static method) AnnotateColumnsTool (class in dae.annotation.annotate_columns) AnnotateVCFTool (class in dae.annotation.annotate_vcf) annotation_schema (dae.variants_loaders.raw.loader.AnnotationPipelineDecorator property) (dae.variants_loaders.raw.loader.VariantsLoader property) (dae.variants_loaders.raw.loader.VariantsLoaderDecorator property) AnnotationAttributes (class in dae.effect_annotation.cli) AnnotationConfigParser (class in dae.annotation.annotation_factory) AnnotationConfigurationError AnnotationDecorator (class in dae.variants_loaders.raw.loader) AnnotationDependencyGraph (dae.annotation.annotation_pipeline.ReannotationPipeline attribute) AnnotationEffect (class in dae.effect_annotation.effect) AnnotationPipeline (class in dae.annotation.annotation_pipeline) AnnotationPipelineDecorator (class in dae.variants_loaders.raw.loader) AnnotationRequestFactory (class in dae.effect_annotation.annotator) Annotator (class in dae.annotation.annotation_pipeline) annotator_id (dae.annotation.annotation_pipeline.AnnotatorInfo attribute) AnnotatorBase (class in dae.annotation.annotator_base) AnnotatorDecorator (class in dae.annotation.annotation_pipeline) AnnotatorInfo (class in dae.annotation.annotation_pipeline) any() (dae.query_variants.attributes_query.StringQueryToTreeTransformer method) (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) append() (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_summary_allele() (dae.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) apply() (dae.person_filters.CriteriaFilter method) (dae.person_filters.FamilyFilter method) (dae.person_filters.PersonFilter method) (dae.person_filters.PhenoFilter method) apply_to_df() (dae.person_filters.FamilyFilter method) (dae.person_filters.PersonFilter method) (dae.person_filters.PersonFilterRange method) (dae.person_filters.PersonFilterSet method) apply_to_family() (dae.pedigrees.layout.Layout method) are_mates() (dae.pedigrees.pedigrees.Individual method) are_siblings() (dae.pedigrees.pedigrees.Individual method) arg() (dae.query_variants.attributes_query.BitwiseTreeTransformer method) (dae.query_variants.attributes_query.StringQueryToTreeTransformer method) ARGUMENT (dae.variants_loaders.raw.loader.ArgumentType attribute) ArgumentType (class in dae.variants_loaders.raw.loader) array_item_suffix() (dae.query_variants.sql.schema2.base_query_builder.Dialect static method) atom() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) atomlist() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) AttributeInfo (class in dae.annotation.annotation_pipeline) attributes (dae.annotation.annotation_pipeline.Annotator property) (dae.annotation.annotation_pipeline.AnnotatorInfo attribute) (dae.variants.family_variant.FamilyAllele property) (dae.variants.variant.SummaryAllele 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

bars (dae.genomic_resources.histogram.CategoricalHistogram property) BaseAnnotationRequest (class in dae.effect_annotation.annotation_request) BaseGeneSetCollection (class in dae.gene.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) BaseQueryTransformerMatcher (class in dae.query_variants.attributes_query) BaseTreeTransformer (class in dae.query_variants.attributes_query) BaseVerificationCode (class in users_api.models) BaseVerificationCode.Meta (class in users_api.models) BATCH_ROWS (dae.parquet.schema2.parquet_io.ContinuousParquetFileWriter attribute) 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) bitmask2inheritance() (in module dae.variants.attributes) BitwiseTreeTransformer (class in dae.query_variants.attributes_query) browsable_figure_path() (dae.pheno.prepare_data.PreparePhenoBrowserBase method) Bucket (class in dae.import_tools.import_tools) bucket_index() (dae.import_tools.import_tools.MakefilePartitionHelper method) BUFFER_MAXSIZE (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) build() (dae.annotation.record_to_annotatable.CSHLAlleleRecordToAnnotatable method) (dae.annotation.record_to_annotatable.RecordToAnnotable method) (dae.annotation.record_to_annotatable.RecordToCNVAllele method) (dae.annotation.record_to_annotatable.RecordToPosition method) (dae.annotation.record_to_annotatable.RecordToRegion method) (dae.annotation.record_to_annotatable.RecordToVcfAllele method) (dae.annotation.record_to_annotatable.VcfLikeRecordToVcfAllele method) (dae.gpf_instance.gpf_instance.GPFInstance static method) (dae.gpf_instance.GPFInstance static method) (dae.pheno.db.PhenoDb method) (dae.pheno.graphs.GraphColumn static method) build_aggregator() (in module dae.genomic_resources.aggregators) build_allele_score_annotator() (in module dae.annotation.score_annotator) build_and_save() (dae.common_reports.common_report.CommonReport static method) build_annotation_filename() (dae.variants_loaders.raw.loader.AnnotationDecorator static method) build_annotation_pipeline() (dae.import_tools.import_tools.ImportProject method) (in module dae.annotation.annotation_factory) build_arguments_dict() (dae.variants_loaders.raw.loader.CLILoader method) (dae.variants_loaders.raw.loader.VariantsLoaderDecorator method) build_array_join() (dae.query_variants.sql.schema2.base_query_builder.Dialect method) build_backend() (dae.genotype_storage.genotype_storage.GenotypeStorage method) (dae.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage method) build_batch() (dae.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) build_browser() (dae.pheno.db.PhenoDb 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_collection() (dae.gene.denovo_gene_set_collection_factory.DenovoGeneSetCollectionFactory class method) build_config() (dae.configuration.study_config_builder.StudyConfigBuilder 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_dependency_graph() (dae.annotation.annotation_pipeline.ReannotationPipeline 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_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_runner() (dae.inmemory_storage.raw_variants.RawFamilyVariants 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) build_gene_models_from_resource() (in module dae.genomic_resources.gene_models) build_gene_score_annotator() (in module dae.annotation.gene_score_annotator) build_gene_set_collection_from_file() (in module dae.gene.gene_sets_db) build_gene_set_collection_from_resource() (in module dae.gene.gene_sets_db) build_genomic_position_table() (in module dae.genomic_resources.genomic_position_table) 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_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_instrument() (dae.pheno.prepare.pheno_prepare.PrepareVariables method) build_instrument_values_tables() (dae.pheno.db.PhenoDb method) build_instruments_and_measures_table() (dae.pheno.db.PhenoDb method) build_liftover_annotator() (in module dae.annotation.liftover_annotator) build_local_resource() (in module dae.genomic_resources.fsspec_protocol) build_manifest() (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) build_meta_measure() (dae.pheno.prepare.pheno_prepare.ClassifyMeasureTask 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_pedigree() (dae.pheno.prepare.pheno_prepare.PreparePersons method) build_person_set_collection_query() (dae.inmemory_storage.raw_variants.RawFamilyVariants static method) build_pheno_browser() (in module dae.tools.pheno2browser) build_pheno_common() (dae.pheno.prepare.pheno_prepare.PrepareVariables 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_regression() (dae.pheno.prepare_data.PreparePhenoBrowserBase method) build_report() (dae.common_reports.common_report.CommonReport static method) build_resource_file_state() (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) build_resource_implementation() (in module dae.genomic_resources.repository_factory) 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_score_aggregator_documentation() (dae.annotation.score_annotator.AlleleScoreAnnotator method) (dae.annotation.score_annotator.GenomicScoreAnnotatorBase method) (dae.annotation.score_annotator.NPScoreAnnotator method) (dae.annotation.score_annotator.PositionScoreAnnotator method) build_score_from_resource() (in module dae.genomic_resources.genomic_scores) build_summary_allele_batch_dict() (dae.parquet.schema2.serializers.AlleleParquetSerializer method) build_summary_schema() (dae.parquet.schema2.serializers.AlleleParquetSerializer class method) build_summary_variants_query_runner() (dae.inmemory_storage.raw_variants.RawFamilyVariants method) build_table() (dae.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) build_table_name() (dae.query_variants.sql.schema2.base_query_builder.Dialect method) build_target_chromosomes() (dae.import_tools.import_tools.MakefilePartitionHelper static method) build_values_categorical_distribution() (dae.pheno.prepare_data.PreparePhenoBrowserBase method) build_values_ordinal_distribution() (dae.pheno.prepare_data.PreparePhenoBrowserBase method) build_values_other_distribution() (dae.pheno.prepare_data.PreparePhenoBrowserBase method) build_values_violinplot() (dae.pheno.prepare_data.PreparePhenoBrowserBase method) build_variables() (dae.pheno.prepare.pheno_prepare.PrepareVariables method) build_variants_loader_pipeline() (dae.import_tools.import_tools.ImportProject method) build_vcf_allele() (dae.variants.core.Allele static method)

C

cache_resources() (in module dae.genomic_resources.cached_repository) 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_dbfile_hashsum() (in module dae.tools.pheno2browser) calc_distribution_report() (dae.pheno.prepare.measure_classifier.ClassifierReport method) calc_frames() (dae.genomic_resources.gene_models.TranscriptModel method) calc_info_hash() (dae.gene.gene_sets_db.GeneSetCollection method) (dae.genomic_resources.gene_models.GeneModels method) calc_inheritance_trio() (dae.variants.family_variant.FamilyAllele class method) calc_statistics_hash() (dae.gene.gene_sets_db.GeneSetCollection method) (dae.genomic_resources.gene_models.GeneModels method) calculate_simple_best_state() (in module dae.variants.family_variant) camelize_string() (in module dae.utils.helpers) can_extend() (dae.pedigrees.pedigrees.Realization method) categorical (dae.pheno.common.MeasureType attribute) CategoricalHistogram (class in dae.genomic_resources.histogram) CategoricalHistogramConfig (class in dae.genomic_resources.histogram) cds_len() (dae.genomic_resources.gene_models.TranscriptModel method) cds_regions() (dae.effect_annotation.annotation_request.BaseAnnotationRequest 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_male_prb_family() (in module dae.pedigrees.family_tag_builder) check_mendelian_trio() (dae.variants.family_variant.FamilyAllele static method) check_missing_dad_family() (in module dae.pedigrees.family_tag_builder) check_missing_mom_family() (in module dae.pedigrees.family_tag_builder) check_multiplex_family() (in module dae.pedigrees.family_tag_builder) check_nuclear_family() (in module dae.pedigrees.family_tag_builder) check_omission_trio() (dae.variants.family_variant.FamilyAllele static method) check_phenotype_data_config() (in module dae.pheno.common) check_quad_family() (in module dae.pedigrees.family_tag_builder) check_simplex_family() (in module dae.pedigrees.family_tag_builder) check_stop_codon() (dae.effect_annotation.effect_checkers.frame_shift.FrameShiftEffectChecker method) (dae.effect_annotation.effect_checkers.utr.UTREffectChecker method) check_tag() (in module dae.pedigrees.family_tag_builder) check_trio_family() (in module dae.pedigrees.family_tag_builder) check_unaffected_dad_family() (in module dae.pedigrees.family_tag_builder) check_unaffected_mom_family() (in module dae.pedigrees.family_tag_builder) check_unaffected_prb_family() (in module dae.pedigrees.family_tag_builder) check_unaffected_sib_family() (in module dae.pedigrees.family_tag_builder) check_update_manifest() (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) CHECK_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) ChildrenBySex (class in dae.person_sets) ChildrenStats (class in dae.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) CHROM (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) chrom (dae.genomic_resources.genomic_scores.ScoreLine property) (dae.variants.core.Allele property) (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) (dae.variants.variant.SummaryVariant property) chrom_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) CHUNK_SIZE (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol attribute) ClassifierReport (class in dae.pheno.prepare.measure_classifier) classify() (dae.pheno.prepare.measure_classifier.MeasureClassifier method) ClassifyMeasureTask (class in dae.pheno.prepare.pheno_prepare) CLEAN_UP_COLUMNS (dae.variants_loaders.raw.loader.AnnotationDecorator attribute) clear() (dae.genomic_resources.aggregators.Aggregator method) (dae.genomic_resources.genomic_position_table.LineBuffer method) clear_instrument_values_tables() (dae.pheno.db.PhenoDb method) clear_instruments_table() (dae.pheno.db.PhenoDb method) clear_measures_table() (dae.pheno.db.PhenoDb method) clear_tags() (dae.pedigrees.family_tag_builder.FamilyTagsBuilder method) cli() (in module dae.annotation.annotate_columns) (in module dae.annotation.annotate_vcf) (in module dae.tools.annotate_variants) (in module dae.tools.gpf_instance_adjustments) 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_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) CLIError 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.effect_annotator.EffectAnnotatorAdapter method) (dae.annotation.liftover_annotator.LiftOverAnnotator method) (dae.annotation.normalize_allele_annotator.NormalizeAlleleAnnotator method) (dae.annotation.score_annotator.GenomicScoreAnnotatorBase method) (dae.effect_annotation.cli.VariantColumnInputFile method) (dae.effect_annotation.cli.VariantColumnOutputFile method) (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable method) (dae.genomic_resources.genomic_scores.GenomicScore method) (dae.genomic_resources.reference_genome.ReferenceGenome method) (dae.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) (dae.parquet.schema2.parquet_io.VariantsParquetWriter method) (dae.query_variants.query_runners.QueryResult method) (dae.query_variants.query_runners.QueryRunner method) (dae.studies.study.GenotypeData method) (dae.tools.gpf_instance_adjustments.AdjustmentsCommand method) (dae.utils.debug_closing.closing method) (dae.variants_loaders.cnv.loader.CNVLoader method) (dae.variants_loaders.dae.loader.DaeTransmittedLoader method) (dae.variants_loaders.dae.loader.DenovoLoader method) (dae.variants_loaders.raw.loader.AnnotationPipelineDecorator method) (dae.variants_loaders.raw.loader.EffectAnnotationDecorator method) (dae.variants_loaders.raw.loader.VariantsLoader method) (dae.variants_loaders.raw.loader.VariantsLoaderDecorator method) (dae.variants_loaders.vcf.loader.SingleVcfLoader method) (dae.variants_loaders.vcf.loader.VcfLoader method)

closing (class in dae.utils.debug_closing) cnv (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) CNVAllele (class in dae.annotation.annotatable) 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) 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_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_person_collection_attributes() (dae.person_sets.PersonSetCollection method) collect_resource_entries() (dae.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) collection_id (dae.person_sets.PSCQuery attribute) collections_descriptions (dae.gene.gene_sets_db.GeneSetsDb property) column_counts() (in module dae.pheno.graphs) column_name (dae.common_reports.denovo_report.EffectCell property) combine() (dae.person_sets.PersonSetCollection static method) (dae.variants.variant.VariantDesc static method) (in module dae.annotation.annotate_columns) (in module dae.annotation.annotate_vcf) CommonReport (class in dae.common_reports.common_report) complement() (dae.effect_annotation.annotation_request.NegativeStrandAnnotationRequest static method) (in module dae.utils.variant_utils) COMPLEX (dae.annotation.annotatable.Annotatable.Type attribute) complex (dae.variants.core.Allele.Type attribute) compute_md5_sum() (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) ConcatAggregator (class in dae.genomic_resources.aggregators) config_json() (dae.person_sets.PersonSetCollection method) ConfigDumper (class in dae.configuration.study_config_builder) 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.genomic_position_table.LineBuffer method) (dae.utils.regions.Region method) ContainsNode (class in dae.query_variants.attributes_query) ContainsNode() (dae.query_variants.attributes_query.QueryTreeToBitwiseLambdaTransformer method) (dae.query_variants.attributes_query.QueryTreeToLambdaTransformer method) (dae.query_variants.attributes_query.QueryTreeToSQLBitwiseTransformer method) 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.MeasureType attribute) ContinuousParquetFileWriter (class in dae.parquet.schema2.parquet_io) CONTROL (dae.pedigrees.family.FamilyTag attribute) convert_size() (in module dae.utils.helpers) convert_to_numeric() (dae.pheno.prepare.measure_classifier.MeasureClassifier static method) (in module dae.pheno.prepare.measure_classifier) convert_to_string() (dae.pheno.prepare.measure_classifier.MeasureClassifier static method) (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.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.gene_sets_db.GeneSet attribute) count_variant() (dae.common_reports.denovo_report.EffectCell method) (dae.common_reports.denovo_report.EffectRow method) CounterBase (class in dae.enrichment_tool.event_counters) CreatableSlugRelatedField (class in users_api.serializers) create() (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_all_tables() (dae.pheno.db.PhenoDb method) create_annotation_request() (dae.effect_annotation.annotator.AnnotationRequestFactory static method) create_default_measure() (dae.pheno.prepare.pheno_prepare.ClassifyMeasureTask static method) (dae.pheno.prepare.pheno_prepare.PrepareVariables static method) 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_intronic_effect() (dae.effect_annotation.effect.EffectFactory class method) create_intronic_non_coding_effect() (dae.effect_annotation.effect.EffectFactory class method) create_negative_strand_effect() (dae.effect_annotation.effect_checkers.promoter.PromoterEffectChecker method) create_positive_strand_effect() (dae.effect_annotation.effect_checkers.promoter.PromoterEffectChecker method) create_reference_allele() (dae.variants.variant.SummaryAllele static method) create_sandwich_instance() (dae.pedigrees.pedigrees.FamilyConnections method) create_superuser() (users_api.models.WdaeUserManager 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) CreateView (class in dae.utils.sql_utils) CriteriaFilter (class in dae.person_filters) 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) 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_vcf module dae.annotation.annotation_factory module dae.annotation.annotation_pipeline module dae.annotation.annotator_base module dae.annotation.context module dae.annotation.effect_annotator module dae.annotation.gene_score_annotator module dae.annotation.liftover_annotator module dae.annotation.normalize_allele_annotator module dae.annotation.record_to_annotatable module dae.annotation.score_annotator module, [1] 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_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.dask 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.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.event_counters module dae.enrichment_tool.genotype_helper module dae.gene module dae.gene.denovo_gene_set_collection module dae.gene.denovo_gene_set_collection_factory module dae.gene.denovo_gene_sets_db module dae.gene.gene_sets_db module dae.gene.gene_term module dae.gene.utils module dae.genomic_resources module dae.genomic_resources.aggregators module dae.genomic_resources.cached_repository module dae.genomic_resources.cli module dae.genomic_resources.fsspec_protocol module dae.genomic_resources.gene_models module dae.genomic_resources.genomic_context module dae.genomic_resources.genomic_position_table module dae.genomic_resources.genomic_scores module dae.genomic_resources.group_repository module dae.genomic_resources.histogram module dae.genomic_resources.reference_genome module dae.genomic_resources.repository module dae.genomic_resources.repository_factory module dae.genomic_resources.testing module dae.genotype_storage module dae.genotype_storage.genotype_storage module dae.genotype_storage.genotype_storage_registry module dae.gpf_instance module dae.gpf_instance.gpf_instance module dae.gpf_instance_plugin module dae.gpf_instance_plugin.gpf_instance_context_plugin module dae.import_tools module dae.import_tools.import_tools module dae.inmemory_storage module dae.inmemory_storage.inmemory_genotype_storage module dae.inmemory_storage.inmemory_import_storage module dae.inmemory_storage.raw_variants module dae.parquet module dae.parquet.schema2 module dae.parquet.schema2.parquet_io module dae.parquet.schema2.serializers module dae.pedigrees module dae.pedigrees.drawing 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_sets module dae.pheno module dae.pheno.common module dae.pheno.db module dae.pheno.graphs module dae.pheno.prepare module

dae.pheno.prepare.measure_classifier module dae.pheno.prepare.pheno_prepare module dae.pheno.prepare_data module dae.pheno.utils module dae.pheno.utils.commons module dae.pheno.utils.lin_regress module dae.pheno_tool module dae.pheno_tool.tool module dae.query_variants module dae.query_variants.attributes_query module dae.query_variants.attributes_query_inheritance module dae.query_variants.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.family_builder module dae.query_variants.sql.schema2.summary_builder module dae.studies module dae.studies.study module dae.studies.variants_db module dae.testing module dae.testing.import_helpers module dae.testing.setup_helpers module dae.tools module dae.tools.annotate_variants module dae.tools.create_sqlite_gene_set module dae.tools.cshl2vcf module dae.tools.draw_pedigree module dae.tools.generate_denovo_gene_sets module dae.tools.gpf_instance_adjustments module dae.tools.gpf_validation_runner module dae.tools.grr_cache_repo module dae.tools.ped2ped module dae.tools.phase module dae.tools.pheno2browser module dae.tools.simple_family2pedigree module dae.tools.simple_study_import module dae.tools.vcfinfo_extractor module dae.utils module dae.utils.dae_utils module dae.utils.debug_closing module dae.utils.dict_utils module dae.utils.filehash module dae.utils.fixtures module dae.utils.fs_utils module dae.utils.helpers module dae.utils.progress module dae.utils.regions module dae.utils.sql_utils module dae.utils.statistics module dae.utils.variant_utils module dae.utils.verbosity_configuration module dae.variants module dae.variants.attributes module dae.variants.core module dae.variants.family_variant module dae.variants.variant module dae.variants_loaders module dae.variants_loaders.cnv module dae.variants_loaders.cnv.flexible_cnv_loader module dae.variants_loaders.cnv.loader module dae.variants_loaders.dae module dae.variants_loaders.dae.loader module dae.variants_loaders.raw module dae.variants_loaders.raw.flexible_variant_loader module dae.variants_loaders.raw.loader module dae.variants_loaders.vcf module dae.variants_loaders.vcf.loader module dae2vcf_variant() (in module dae.utils.dae_utils) 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) data_reset() (dae.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) DatasetSerializer (class in users_api.serializers) date_joined (users_api.models.WdaeUser attribute) dd() (in module dae.gene.gene_term) deauthenticate() (users_api.models.WdaeUser method) decorate() (dae.annotation.annotation_pipeline.InputAnnotableAnnotatorDecorator static method) (dae.annotation.annotation_pipeline.ValueTransformAnnotatorDecorator static method) (dae.variants_loaders.raw.loader.StoredAnnotationDecorator static method) DEFAULT_AGGREGATOR_TYPE (dae.annotation.gene_score_annotator.GeneScoreAnnotator attribute) DEFAULT_COMPRESSION (dae.parquet.schema2.parquet_io.ContinuousParquetFileWriter attribute) default_config() (dae.genomic_resources.histogram.CategoricalHistogramConfig static method) (dae.genomic_resources.histogram.NullHistogramConfig static method) (dae.genomic_resources.histogram.NumberHistogramConfig static method) (in module dae.pheno.common) default_setters (dae.configuration.gpf_config_parser.GPFConfigValidator attribute) DefaultBox (class in dae.configuration.gpf_config_parser) DefaultGenotypeStorage (class in dae.tools.gpf_instance_adjustments) DefaultRepositoryContextProvider (class in dae.genomic_resources.genomic_context) definition (dae.genomic_resources.repository.GenomicResourceRepo property) degree() (dae.pedigrees.pedigrees.Realization method) del_loader_prefix() (dae.import_tools.import_tools.ImportProject static method) delete() (users_api.views.FederationCredentials method) delete_resource_file() (dae.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) denovo (dae.testing.import_helpers.StudyInputLayout attribute) (dae.testing.StudyInputLayout attribute) (dae.variants.attributes.Inheritance attribute) (dae.variants.attributes.TransmissionType attribute) denovo() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) denovo_gene_set_cache_file() (dae.gene.denovo_gene_set_collection_factory.DenovoGeneSetCollectionFactory static method) denovo_gene_sets_db (dae.gpf_instance.gpf_instance.GPFInstance property) (dae.gpf_instance.GPFInstance 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.denovo_gene_set_collection) DenovoGeneSetCollectionFactory (class in dae.gene.denovo_gene_set_collection_factory) DenovoGeneSetsDb (class in dae.gene.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) desc (dae.gene.gene_sets_db.GeneSet attribute) (dae.genomic_resources.genomic_scores.ScoreDef attribute) description (dae.annotation.annotation_pipeline.AttributeInfo attribute) (dae.studies.study.GenotypeData property) deserialize() (dae.genomic_resources.histogram.CategoricalHistogram static method) (dae.genomic_resources.histogram.NullHistogram static method) (dae.genomic_resources.histogram.NumberHistogram static method) destroy() (users_api.views.UserViewSet method) details (dae.variants.family_variant.FamilyAllele property) (dae.variants.variant.SummaryAllele property) (dae.variants.variant.SummaryVariant property) Dialect (class in dae.query_variants.sql.schema2.base_query_builder) DictAggregator (class in dae.genomic_resources.aggregators) diff() (dae.pedigrees.family.Person method) difference() (in module dae.utils.regions) display_name (dae.variants.attributes.Role property) DISTRIBUTION_CUTOFF (dae.pheno.prepare.measure_classifier.ClassifierReport attribute) do_annotate_variant() (dae.effect_annotation.annotator.EffectAnnotator method) documentation (dae.annotation.annotation_pipeline.AnnotatorInfo attribute) (dae.annotation.annotation_pipeline.AttributeInfo property) domain_json() (dae.person_sets.PersonSetCollection method) done() (dae.pheno.prepare.pheno_prepare.ClassifyMeasureTask method) (dae.pheno.prepare.pheno_prepare.MeasureValuesTask method) (dae.pheno.prepare.pheno_prepare.Task method) draw() (dae.pedigrees.drawing.OffsetLayoutDrawer method) draw_categorical_violin_distribution() (in module dae.pheno.graphs) draw_distribution() (in module dae.pheno.graphs) draw_families() (in module dae.tools.draw_pedigree) draw_families_report() (in module dae.tools.draw_pedigree) draw_linregres() (in module dae.pheno.graphs) draw_measure_violinplot() (in module dae.pheno.graphs) draw_ordinal_violin_distribution() (in module dae.pheno.graphs) draw_pedigree() (in module dae.tools.draw_pedigree) dump_browser_variable() (dae.pheno.prepare_data.PreparePhenoBrowserBase method) dump_config() (in module dae.pheno.common)

E

effect (dae.enrichment_tool.genotype_helper.GeneEffect attribute) effect_gene_symbols (dae.variants.variant.SummaryAllele property) (dae.variants.variant.SummaryVariant property) effect_genes (dae.enrichment_tool.genotype_helper.AlleleEvent attribute) (dae.variants.variant.SummaryAllele property) EFFECT_GROUPS (dae.effect_annotation.effect.EffectTypesMixin attribute) effect_severity() (dae.effect_annotation.effect.AnnotationEffect class method) EFFECT_TYPES (dae.effect_annotation.effect.EffectTypesMixin attribute) effect_types (dae.variants.variant.SummaryAllele property) (dae.variants.variant.SummaryVariant property) EFFECT_TYPES_MAPPING (dae.effect_annotation.effect.EffectTypesMixin attribute) EFFECT_TYPES_UI_NAMING (dae.effect_annotation.effect.EffectTypesMixin attribute) EffectAnnotationDecorator (class in dae.variants_loaders.raw.loader) EffectAnnotator (class in dae.effect_annotation.annotator) EffectAnnotatorAdapter (class in dae.annotation.effect_annotator) EffectAnnotatorBuilder (class in dae.effect_annotation.cli) EffectCell (class in dae.common_reports.denovo_report) EffectFactory (class in dae.effect_annotation.effect) EffectGene (class in dae.effect_annotation.effect) EffectRow (class in dae.common_reports.denovo_report) effects (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) EffectTranscript (class in dae.effect_annotation.effect) EffectTypesMixin (class in dae.effect_annotation.effect) ElementOfNode (class in dae.query_variants.attributes_query) ElementOfNode() (dae.query_variants.attributes_query.QueryTreeToLambdaTransformer method) email (users_api.models.AuthenticationLog attribute) (users_api.models.WdaeUser attribute) email_user() (users_api.models.WdaeUser method) empty() (dae.pheno.prepare.pheno_prepare.TaskQueue method) EnableDisableStudies (class in dae.tools.gpf_instance_adjustments) end (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)

EnrichmentResult (class in dae.enrichment_tool.event_counters) EnrichmentSingleResult (class in dae.enrichment_tool.event_counters) entries_to_delete (dae.genomic_resources.repository.ManifestUpdate attribute) entries_to_update (dae.genomic_resources.repository.ManifestUpdate attribute) ENUM_PROPERTIES (dae.parquet.schema2.serializers.AlleleParquetSerializer attribute) EqualsNode (class in dae.query_variants.attributes_query) EqualsNode() (dae.query_variants.attributes_query.QueryTreeToLambdaTransformer method) ERROR (dae.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.query_variants.sql.schema2.base_query_builder.Dialect static method) escape_quote_char() (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.tools.gpf_instance_adjustments.AdjustDuckDbStorageCommand method) (dae.tools.gpf_instance_adjustments.AdjustImpalaStorageCommand method) (dae.tools.gpf_instance_adjustments.AdjustmentsCommand method) (dae.tools.gpf_instance_adjustments.DefaultGenotypeStorage method) (dae.tools.gpf_instance_adjustments.EnableDisableStudies method) (dae.tools.gpf_instance_adjustments.InstanceIdCommand method) exists() (in module dae.utils.fs_utils) Exon (class in dae.genomic_resources.gene_models) expand_effect_types() (in module dae.effect_annotation.effect) Expression (class in dae.query_variants.attributes_query_inheritance) expression() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) extend() (dae.pedigrees.pedigrees.Realization method) extract_resource_ids_from_annotation() (in module dae.tools.grr_cache_repo)

F

F (dae.variants.attributes.Sex attribute) FAIL (dae.tools.gpf_validation_runner.TestStatus attribute) failed_attempt (users_api.models.AuthenticationLog attribute) failed_case_count (dae.tools.gpf_validation_runner.AbstractRunner property) (dae.tools.gpf_validation_runner.MainRunner property) families (dae.studies.study.GenotypeData property) (dae.studies.study.GenotypeDataGroup property) (dae.studies.study.GenotypeDataStudy property) 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) 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_attributes (dae.variants.family_variant.FamilyAllele property) family_best_state (dae.variants.family_variant.FamilyVariant property) family_bin (dae.pedigrees.family.Person property) 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_index (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) family_type (dae.pedigrees.family.Family property) family_variant_filter_duplicate_function() (dae.inmemory_storage.raw_variants.RawFamilyVariants class method) family_variant_filter_function() (dae.inmemory_storage.raw_variants.RawFamilyVariants class method) family_variants_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) 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) FamilyType (class in dae.pedigrees.family) FamilyVariant (class in dae.variants.family_variant) 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.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.LineBuffer method) (dae.genomic_resources.reference_genome.ReferenceGenome method) fetch_region() (dae.genomic_resources.genomic_scores.GenomicScore method) fetch_scores() (dae.genomic_resources.genomic_scores.AlleleScore method) (dae.genomic_resources.genomic_scores.NPScore method) (dae.genomic_resources.genomic_scores.PositionScore method) fetch_scores_agg() (dae.genomic_resources.genomic_scores.AlleleScore method) (dae.genomic_resources.genomic_scores.NPScore method) (dae.genomic_resources.genomic_scores.PositionScore method) 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 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.genomic_resources.repository.ResourceFileState attribute) files (dae.gene.gene_sets_db.GeneSetCollection property) (dae.genomic_resources.gene_models.GeneModels property) (dae.genomic_resources.reference_genome.ReferenceGenome property) filetype_parsers (dae.configuration.gpf_config_parser.GPFConfigParser attribute) 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.inmemory_storage.raw_variants.RawFamilyVariants static 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_summary_allele() (dae.inmemory_storage.raw_variants.RawFamilyVariants class method) filter_summary_variant() (dae.inmemory_storage.raw_variants.RawFamilyVariants class method) filterGenes() (dae.gene.gene_term.GeneTerms method) find_directory_with_a_file() (in module dae.utils.fs_utils) find_index() (dae.genomic_resources.genomic_position_table.LineBuffer 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) fit() (dae.pheno.utils.lin_regress.LinearRegression method) flexible_cnv_loader() (in module dae.variants_loaders.cnv.flexible_cnv_loader) flexible_denovo_load() (dae.variants_loaders.dae.loader.DenovoLoader method) flexible_pedigree_read() (dae.pedigrees.loader.FamiliesLoader static method) flexible_variant_loader() (in module dae.variants_loaders.raw.flexible_variant_loader) float_type() (dae.query_variants.sql.schema2.base_query_builder.Dialect static method) foobar_gpf() (in module dae.testing) force_extend() (dae.pedigrees.pedigrees.Realization method) ForgotPassword (class in users_api.views) form (users_api.views.BasePasswordView attribute) (users_api.views.ResetPassword attribute) (users_api.views.SetPassword attribute) FrameShiftEffectChecker (class in dae.effect_annotation.effect_checkers.frame_shift) frequencies (dae.variants.variant.SummaryVariant property) frequency (dae.variants.variant.SummaryAllele property) from_cnv() (dae.variants.variant.VariantDetails static method) from_dict() (dae.configuration.study_config_builder.TOMLDict static method) (dae.genomic_resources.histogram.CategoricalHistogram static method) (dae.genomic_resources.histogram.CategoricalHistogramConfig static method) (dae.genomic_resources.histogram.NullHistogram static method) (dae.genomic_resources.histogram.NullHistogramConfig static method) (dae.genomic_resources.histogram.NumberHistogram static method) (dae.genomic_resources.histogram.NumberHistogramConfig static method) from_effect_transcripts() (dae.effect_annotation.effect.EffectTranscript class method) from_effects() (dae.effect_annotation.effect.AlleleEffects class method) from_events_result() (dae.enrichment_tool.event_counters.EventCountersResult static method) from_families() (dae.common_reports.family_counter.FamiliesGroupCounters static method) (dae.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_file_content() (dae.genomic_resources.repository.Manifest static method) from_gene_effects() (dae.effect_annotation.effect.EffectGene class method) from_genotype_study() (dae.common_reports.denovo_report.DenovoReport static method) (dae.common_reports.family_report.FamiliesReport static method) from_json() (dae.person_sets.PersonSet static method) (dae.person_sets.PersonSetCollection 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.pedigrees.family.FamilyType 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) 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_records() (dae.pedigrees.family.Family static method) from_sets() (dae.pedigrees.pedigrees.SandwichInstance static method) from_simplified_effects() (dae.effect_annotation.effect.AlleleEffects class method) from_str() (dae.pheno.common.MeasureType static method) (dae.utils.regions.Region static method) from_string() (dae.annotation.annotatable.Annotatable static method) (dae.annotation.annotatable.Annotatable.Type static method) (dae.annotation.annotatable.CNVAllele static method) (dae.annotation.annotatable.Position static method) (dae.annotation.annotatable.Region static method) (dae.annotation.annotatable.VCFAllele static method) (dae.effect_annotation.effect.AlleleEffects static method) (dae.effect_annotation.effect.EffectGene static method) (dae.effect_annotation.effect.EffectTranscript static method) from_tuple() (dae.effect_annotation.effect.EffectGene class method) (dae.effect_annotation.effect.EffectTranscript class method) from_value() (dae.variants.attributes.Inheritance static method) (dae.variants.attributes.Role static method) (dae.variants.attributes.Sex static method) (dae.variants.attributes.Status static method) from_variants() (dae.common_reports.denovo_report.DenovoReportTable static method) from_vcf() (dae.variants.variant.VariantDetails static method) FrozenBox (class in dae.configuration.gpf_config_parser) FsspecReadOnlyProtocol (class in dae.genomic_resources.fsspec_protocol) FsspecReadWriteProtocol (class in dae.genomic_resources.fsspec_protocol) full_members (dae.pedigrees.family.Family property) full_variants (dae.inmemory_storage.raw_variants.RawMemoryVariants property) full_variants_iterator() (dae.inmemory_storage.raw_variants.RawFamilyVariants method) (dae.inmemory_storage.raw_variants.RawMemoryVariants method) (dae.variants_loaders.cnv.loader.CNVLoader method) (dae.variants_loaders.dae.loader.DenovoLoader method) (dae.variants_loaders.raw.loader.AnnotationPipelineDecorator method) (dae.variants_loaders.raw.loader.EffectAnnotationDecorator method) (dae.variants_loaders.raw.loader.StoredAnnotationDecorator method) (dae.variants_loaders.raw.loader.VariantsGenotypesLoader method) (dae.variants_loaders.raw.loader.VariantsLoader method) 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_models (dae.gpf_instance.gpf_instance.GPFInstance property) (dae.gpf_instance.GPFInstance property) gene_models_by_gene_name() (dae.genomic_resources.gene_models.GeneModels method) gene_models_by_location() (dae.genomic_resources.gene_models.GeneModels method) gene_names() (dae.genomic_resources.gene_models.GeneModels method) GENE_REGIONS_HEURISTIC_CUTOFF (dae.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute) GENE_REGIONS_HEURISTIC_EXTEND (dae.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute) gene_scores_db (dae.gpf_instance.gpf_instance.GPFInstance property) (dae.gpf_instance.GPFInstance property) gene_sets_db (dae.gpf_instance.gpf_instance.GPFInstance property) (dae.gpf_instance.GPFInstance property) GeneEffect (class in dae.enrichment_tool.genotype_helper) GeneEventsCounter (class in dae.enrichment_tool.event_counters) GeneModels (class in dae.genomic_resources.gene_models) GeneModelsParser (class in dae.genomic_resources.gene_models) generate_chrom_targets() (dae.import_tools.import_tools.MakefilePartitionHelper method) generate_import_task_graph() (dae.import_tools.import_tools.ImportStorage method) (dae.inmemory_storage.inmemory_import_storage.InmemoryImportStorage method) generate_instrument_table_name() (in module dae.pheno.db) generate_variants_targets() (dae.import_tools.import_tools.MakefilePartitionHelper method) generated (dae.pedigrees.family.Person property) generation_ranks() (dae.pedigrees.pedigrees.IndividualGroup method) GeneScoreAnnotator (class in dae.annotation.gene_score_annotator) GeneSet (class in dae.gene.gene_sets_db) GeneSetCollection (class in dae.gene.gene_sets_db) GeneSetsDb (class in dae.gene.gene_sets_db) GeneTerms (class in dae.gene.gene_term) genetic_model (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) GeneticModel (class in dae.variants.attributes) genomic_scores (dae.gpf_instance.gpf_instance.GPFInstance property) (dae.gpf_instance.GPFInstance property) GenomicContext (class in dae.genomic_resources.genomic_context) GenomicContextProvider (class in dae.genomic_resources.genomic_context) 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) 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) genotype (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) genotype_browser module genotype_browser.urls module genotype_browser.views module genotype_data_persons() (dae.pheno_tool.tool.PhenoToolHelper method) genotype_data_variants() (dae.pheno_tool.tool.PhenoToolHelper method) genotype_storages (dae.gpf_instance.gpf_instance.GPFInstance property) (dae.gpf_instance.GPFInstance property) GenotypeBrowserQueryView (class in genotype_browser.views) 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.Line method) (dae.genomic_resources.genomic_position_table.VCFLine method) (dae.pheno.prepare.pheno_prepare.TaskQueue 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.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_denovo_gene_sets() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance 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.denovo_gene_set_collection.DenovoGeneSetCollection class method) (dae.gene.denovo_gene_sets_db.DenovoGeneSetsDb method) (dae.gene.gene_sets_db.BaseGeneSetCollection method) (dae.gene.gene_sets_db.GeneSetCollection method) (dae.gene.gene_sets_db.GeneSetsDb method) (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_all_genotype_data() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) (dae.studies.variants_db.VariantsDb method) get_all_genotype_group_configs() (dae.studies.variants_db.VariantsDb method) get_all_genotype_group_ids() (dae.studies.variants_db.VariantsDb method) get_all_genotype_groups() (dae.studies.variants_db.VariantsDb method) get_all_genotype_storage_ids() (dae.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) get_all_genotype_storages() (dae.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) get_all_genotype_studies() (dae.studies.variants_db.VariantsDb method) get_all_genotype_study_configs() (dae.studies.variants_db.VariantsDb method) get_all_genotype_study_ids() (dae.studies.variants_db.VariantsDb method) get_all_ids() (dae.studies.variants_db.VariantsDb method) get_all_phenotype_data() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_all_records() (dae.genomic_resources.genomic_position_table.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.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_vcf.AnnotateVCFTool 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_bbox() (dae.pedigrees.layout.Layout method) get_bit_and_str() (in module dae.query_variants.attributes_query) get_browser_measure() (dae.pheno.db.PhenoDb method) get_children() (dae.person_sets.PersonSet method) get_children_by_sex() (dae.person_sets.PersonSet method) get_children_count() (dae.person_sets.PersonSet method) get_children_stats() (dae.person_sets.PersonSet method) get_chrom_length() (dae.genomic_resources.reference_genome.ReferenceGenome method) get_chromosome_length() (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable method) get_chromosome_length_tabix() (in module dae.utils.regions) get_chromosomes() (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable method) 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_columns() (dae.pedigrees.family.Family 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) get_config() (dae.genomic_resources.genomic_scores.GenomicScore method) (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) (dae.studies.variants_db.VariantsDb 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_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_genotype_storage() (dae.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) get_default_grr_definition() (in module dae.genomic_resources.repository_factory) get_default_grr_definition_path() (in module dae.genomic_resources.repository_factory) get_denovo_events() (dae.enrichment_tool.genotype_helper.GenotypeHelper method) get_denovo_gene_set() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_denovo_gene_sets() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) 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.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_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_families() (dae.pheno.db.PhenoDb method) get_family_pedigree() (in module dae.common_reports.family_counter) 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.TabixGenomicPositionTable 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_files() (dae.genomic_resources.repository.Manifest method) get_final() (dae.genomic_resources.aggregators.Aggregator method) (dae.genomic_resources.aggregators.ConcatAggregator method) (dae.genomic_resources.aggregators.DictAggregator method) (dae.genomic_resources.aggregators.JoinAggregator method) (dae.genomic_resources.aggregators.ListAggregator method) (dae.genomic_resources.aggregators.MaxAggregator method) (dae.genomic_resources.aggregators.MeanAggregator method) (dae.genomic_resources.aggregators.MedianAggregator method) (dae.genomic_resources.aggregators.MinAggregator method) (dae.genomic_resources.aggregators.ModeAggregator method)

get_frame() (dae.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) (dae.effect_annotation.annotation_request.PositiveStrandAnnotationRequest method) get_gene_models() (dae.effect_annotation.cli.EffectAnnotatorBuilder method) (dae.genomic_resources.genomic_context.GenomicContext method) get_gene_score() (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_set() (dae.gene.denovo_gene_set_collection.DenovoGeneSetCollection class method) (dae.gene.denovo_gene_sets_db.DenovoGeneSetsDb method) (dae.gene.gene_sets_db.BaseGeneSetCollection method) (dae.gene.gene_sets_db.GeneSetCollection method) (dae.gene.gene_sets_db.GeneSetsDb method) (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_gene_set_collection_ids() (dae.gene.gene_sets_db.GeneSetsDb method) get_gene_set_descriptions() (dae.gene.denovo_gene_sets_db.DenovoGeneSetsDb method) get_gene_set_ids() (dae.gene.denovo_gene_sets_db.DenovoGeneSetsDb method) (dae.gene.gene_sets_db.GeneSetsDb method) get_gene_sets_collections() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_gene_sets_types_legend() (dae.gene.denovo_gene_set_collection.DenovoGeneSetCollection 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.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) 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_gp_configuration() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_gp_statistic() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_gpf_instance() (dae.import_tools.import_tools.ImportProject method) get_graph() (dae.pedigrees.pedigrees.FamilyConnections method) get_grr() (dae.effect_annotation.cli.EffectAnnotatorBuilder method) get_header() (dae.effect_annotation.cli.VariantColumnInputFile method) get_histogram_file() (dae.genomic_resources.histogram.HistogramStatisticMixin static method) get_histogram_filename() (dae.genomic_resources.genomic_scores.GenomicScore method) get_histogram_image_file() (dae.genomic_resources.histogram.HistogramStatisticMixin static method) get_histogram_image_filename() (dae.genomic_resources.genomic_scores.GenomicScore method) get_histogram_image_url() (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_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.gene.gene_sets_db.GeneSetCollection method) (dae.genomic_resources.gene_models.GeneModels method) get_input_filenames() (dae.import_tools.import_tools.ImportProject method) get_instrument_column_names() (dae.pheno.db.PhenoDb 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_line_iterator() (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable 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_maximal_set() (dae.pedigrees.pedigrees.Realization method) get_measure_column_names() (dae.pheno.db.PhenoDb method) get_measure_column_names_reverse() (dae.pheno.db.PhenoDb method) get_measures() (dae.pheno.db.PhenoDb 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_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_nucleotides_count_to_full_codon() (dae.effect_annotation.annotation_request.BaseAnnotationRequest static method) get_number_range() (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_parents() (dae.person_sets.PersonSet method) get_parquet_dataset_dir() (dae.import_tools.import_tools.ImportProject method) get_partition_descriptor() (dae.import_tools.import_tools.ImportProject method) get_pedigree() (dae.import_tools.import_tools.ImportProject method) get_pedigree_column_names() (in module dae.pedigrees.family) get_pedigree_filename() (dae.import_tools.import_tools.ImportProject method) get_pedigree_loader() (dae.import_tools.import_tools.ImportProject method) get_pedigree_params() (dae.import_tools.import_tools.ImportProject method) get_person_color() (dae.person_sets.PersonSetCollection static method) get_person_set() (dae.person_sets.PersonSetCollection method) get_person_set_collection() (dae.studies.study.GenotypeData method) get_person_set_collection_legend() (dae.gene.denovo_gene_set_collection.DenovoGeneSetCollection method) get_person_set_of_person() (dae.person_sets.PersonSetCollection method) get_persons() (dae.pheno.db.PhenoDb method) (dae.pheno.prepare.pheno_prepare.PrepareBase method) get_phenotype_data() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_phenotype_data_config() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) get_phenotype_data_ids() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance 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_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.TabixGenomicPositionTable method) get_reference_genome() (dae.genomic_resources.genomic_context.GenomicContext method) get_refernce_genome() (dae.effect_annotation.cli.EffectAnnotatorBuilder method) get_regression() (dae.pheno.db.PhenoDb method) get_regression_values() (dae.pheno.db.PhenoDb method) get_remaining_lockout_time() (users_api.models.AuthenticationLog static 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.fsspec_protocol.FsspecReadOnlyProtocol 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.fsspec_protocol.FsspecReadOnlyProtocol method) get_row_group_size() (dae.import_tools.import_tools.ImportProject method) get_schema() (dae.gene.gene_sets_db.GeneSetCollection static method) (dae.genomic_resources.gene_models.GeneModels static method) (dae.genomic_resources.genomic_scores.AlleleScore static method) (dae.genomic_resources.genomic_scores.GenomicScore static method) (dae.genomic_resources.genomic_scores.NPScore static method) (dae.genomic_resources.genomic_scores.PositionScore static method) (dae.genomic_resources.reference_genome.ReferenceGenome static method) get_score() (dae.genomic_resources.genomic_scores.ScoreLine method) get_score_definition() (dae.genomic_resources.genomic_scores.GenomicScore method) get_score_histogram() (dae.genomic_resources.genomic_scores.GenomicScore 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.gene_models.GeneModels method) get_stats() (dae.person_sets.PersonSetCollection method) get_storage_types() (dae.genotype_storage.genotype_storage.GenotypeStorage class method) (dae.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage class method) get_studies_ids() (dae.studies.study.GenotypeData method) (dae.studies.study.GenotypeDataGroup method) (dae.studies.study.GenotypeDataStudy method) get_summary() (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) get_sym_2_fn() (in module dae.enrichment_tool.event_counters) get_template() (dae.gene.gene_sets_db.GeneSetCollection method) (dae.genomic_resources.gene_models.GeneModels 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_pipeline.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_pipeline.ParamsUsageMonitor method) get_user_info() (in module users_api.views) get_values() (dae.effect_annotation.cli.AnnotationAttributes method) get_variant_loader() (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_version_str() (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) getCleanGeneId() (in module dae.gene.utils) getDims() (in module dae.tools.phase) getGenes() (in module dae.gene.utils) getGeneTermAtt() (in module dae.gene.utils) getNsTokens() (in module dae.gene.utils) glob() (in module dae.utils.fs_utils) GPFConfigParser (class in dae.configuration.gpf_config_parser) GPFConfigValidator (class in dae.configuration.gpf_config_parser) GPFInstance (class in dae.gpf_instance) (class in dae.gpf_instance.gpf_instance) GPFInstanceGenomicContext (class in dae.gpf_instance_plugin.gpf_instance_context_plugin) GPFInstanceGenomicContextProvider (class in dae.gpf_instance_plugin.gpf_instance_context_plugin) GraphColumn (class in dae.pheno.graphs) GreaterThanEqNode (class in dae.query_variants.attributes_query) GreaterThanNode (class in dae.query_variants.attributes_query) group_post_delete() (in module users_api.models) group_pre_delete() (in module users_api.models) groups (users_api.models.WdaeUser attribute) 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)

H

half_sibling (dae.variants.attributes.Role attribute) handle_measure() (dae.pheno.prepare_data.PreparePhenoBrowserBase method) handle_regressions() (dae.pheno.prepare_data.PreparePhenoBrowserBase method) has_annotation_file() (dae.variants_loaders.raw.loader.AnnotationDecorator static method) has_attr() (dae.pedigrees.family.Person method) has_attribute() (dae.variants.family_variant.FamilyAllele method) (dae.variants.variant.SummaryAllele method) (dae.variants.variant.SummaryVariant method) has_both_parents() (dae.pedigrees.family.Person method) has_cnv (dae.studies.study.GenotypeData property) has_complex (dae.studies.study.GenotypeData property) has_dad() (dae.pedigrees.family.Person method) has_denovo (dae.studies.study.GenotypeData property) has_denovo_gene_sets() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) has_denovo_variants() (dae.import_tools.import_tools.ImportProject method) has_descriptions (dae.pheno.db.PhenoDb property) has_families_cache() (dae.studies.study.GenotypeDataGroup method) has_gene_score() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) has_gene_set_collection() (dae.gene.gene_sets_db.GeneSetsDb method) (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) has_genotype_storage() (dae.import_tools.import_tools.ImportProject method)

has_members() (dae.pedigrees.family.Family method) has_missing_parent() (dae.pedigrees.family.Person method) has_mom() (dae.pedigrees.family.Person method) has_no_parent() (dae.pedigrees.family.Person method) has_parent() (dae.pedigrees.family.Person method) has_phenotype_data() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) has_tag() (dae.pedigrees.family.Person method) has_transmitted (dae.studies.study.GenotypeData 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) has_view_range() (dae.genomic_resources.histogram.NumberHistogramConfig method) has_wildcard() (dae.annotation.annotation_factory.AnnotationConfigParser static method) hashsum() (in module dae.utils.filehash) header_line() (dae.pheno.prepare.measure_classifier.ClassifierReport static method) hist_conf (dae.genomic_resources.genomic_scores.ScoreDef attribute) HistogramError HistogramStatisticMixin (class in dae.genomic_resources.histogram) http_process_test_server() (in module dae.genomic_resources.testing) http_threaded_test_server() (in module dae.genomic_resources.testing)

I

id (users_api.models.AuthenticationLog attribute) (users_api.models.ResetPasswordCode attribute) (users_api.models.SetPasswordCode attribute) (users_api.models.WdaeUser attribute) id_to_position (dae.pedigrees.layout.Layout property) ImportConfigNormalizer (class in dae.import_tools.import_tools) 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.statistics.StatsCollection method) include_reference (dae.import_tools.import_tools.ImportProject property) increase_indent() (dae.configuration.study_config_builder.ConfigDumper method) indel (dae.variants.core.Allele.Type attribute) index (dae.import_tools.import_tools.Bucket attribute) 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) 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) Inheritance (class in dae.variants.attributes) inheritance_converter() (in module dae.query_variants.attributes_query) inheritance_in_members (dae.variants.family_variant.FamilyAllele property) InheritanceTransformer (class in dae.query_variants.attributes_query_inheritance) init_gpf_instance_genomic_context_plugin() (in module dae.gpf_instance_plugin.gpf_instance_context_plugin) init_test_gpf_instance_genomic_context_plugin() (in module dae.gpf_instance_plugin.gpf_instance_context_plugin) 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) InputAnnotableAnnotatorDecorator (class in dae.annotation.annotation_pipeline) InstanceIdCommand (class in dae.tools.gpf_instance_adjustments) int_type() (dae.query_variants.sql.schema2.base_query_builder.Dialect static method) internal (dae.annotation.annotation_pipeline.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_child() (dae.pedigrees.family.Person method) is_closed() (dae.query_variants.query_runners.QueryRunner method) is_cnv() (dae.variants.core.Allele.Type class method) is_coding() (dae.genomic_resources.gene_models.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_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) is_empty_field() (dae.common_reports.people_counter.PeopleCounter method) is_gr_id_token() (in module dae.genomic_resources.repository) is_group (dae.studies.study.GenotypeData property) (dae.studies.study.GenotypeDataGroup property) (dae.studies.study.GenotypeDataStudy property) is_in_interval_order() (dae.pedigrees.pedigrees.Realization method) is_individual() (dae.pedigrees.pedigrees.Individual method) (dae.pedigrees.pedigrees.IndividualGroup method) is_loaded() (dae.genomic_resources.gene_models.GeneModels method) is_maximal() (dae.pedigrees.pedigrees.Realization method) is_nan() (in module dae.pheno.prepare.measure_classifier) is_numeric() (dae.pheno.common.MeasureType static method) is_open() (dae.annotation.annotation_pipeline.Annotator method) (dae.annotation.annotation_pipeline.AnnotatorDecorator method) (dae.annotation.score_annotator.GenomicScoreAnnotatorBase method) (dae.genomic_resources.genomic_scores.GenomicScore method) (dae.genomic_resources.reference_genome.ReferenceGenome method) is_parent() (dae.pedigrees.family.Person method) is_pedigree_only() (dae.person_sets.PersonSetCollection method) is_pseudoautosomal() (dae.genomic_resources.reference_genome.ReferenceGenome method) is_read_only() (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_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) iterator_to_json() (in module users_api.views)

J

join() (in module dae.utils.fs_utils) join_gene_models() (in module dae.genomic_resources.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)

L

label (dae.pedigrees.family.FamilyTag property) (dae.pheno.graphs.GraphColumn property) LARGE_DELETION (dae.annotation.annotatable.Annotatable.Type attribute) large_deletion (dae.variants.core.Allele.Type attribute) LARGE_DPI (dae.pheno.prepare_data.PreparePhenoBrowserBase attribute) LARGE_DUPLICATION (dae.annotation.annotatable.Annotatable.Type attribute) large_duplication (dae.variants.core.Allele.Type attribute) large_values_desc (dae.genomic_resources.genomic_scores.ScoreDef 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) LeafNode (class in dae.query_variants.attributes_query) LessThanEqNode (class in dae.query_variants.attributes_query) LessThanNode (class in dae.query_variants.attributes_query) lgd_gene_effects() (dae.effect_annotation.effect.AnnotationEffect class method) liftover_allele() (dae.annotation.liftover_annotator.LiftOverAnnotator method) liftover_cnv() (dae.annotation.liftover_annotator.LiftOverAnnotator method) liftover_position() (dae.annotation.liftover_annotator.LiftOverAnnotator method) liftover_region() (dae.annotation.liftover_annotator.LiftOverAnnotator method) LiftOverAnnotator (class in dae.annotation.liftover_annotator) Line (class in dae.genomic_resources.genomic_position_table) (class in dae.pedigrees.layout) LinearRegression (class in dae.pheno.utils.lin_regress) LineBuffer (class in dae.genomic_resources.genomic_position_table) list() (users_api.views.UserViewSet method) ListAggregator (class in dae.genomic_resources.aggregators) load() (dae.common_reports.common_report.CommonReport static 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)

load_collection() (dae.gene.denovo_gene_set_collection_factory.DenovoGeneSetCollectionFactory class method) load_config() (dae.configuration.gpf_config_parser.GPFConfigParser class method) load_config_raw() (dae.configuration.gpf_config_parser.GPFConfigParser class method) load_definition_file() (in module dae.genomic_resources.repository_factory) load_descriptions() (dae.pheno.prepare.pheno_prepare.PrepareVariables static method) load_directory_configs() (dae.configuration.gpf_config_parser.GPFConfigParser class method) load_families_cache() (dae.studies.study.GenotypeDataGroup method) load_gene_sets() (dae.gene.gene_sets_db.GeneSetCollection method) load_histogram() (in module dae.genomic_resources.histogram) load_instrument() (dae.pheno.prepare.pheno_prepare.PrepareVariables method) load_manifest() (dae.genomic_resources.cached_repository.CachingProtocol method) (dae.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) load_measure() (dae.pheno.prepare_data.PreparePhenoBrowserBase method) load_pedigree_file() (dae.pedigrees.loader.FamiliesLoader static method) load_resource_file_state() (dae.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) load_simple_families_file() (dae.pedigrees.loader.FamiliesLoader static method) load_yaml() (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) loadNCBIGeneInfo() (in module dae.gene.utils) 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_filename (dae.pheno.prepare.pheno_prepare.PrepareVariables property) log_header() (dae.pheno.prepare.pheno_prepare.PrepareVariables method) log_line() (dae.pheno.prepare.measure_classifier.ClassifierReport method) log_measure() (dae.pheno.prepare.pheno_prepare.PrepareVariables method) logical_and() (dae.query_variants.attributes_query.BitwiseTreeTransformer method) (dae.query_variants.attributes_query.StringQueryToTreeTransformer method) (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) logical_or() (dae.query_variants.attributes_query.BitwiseTreeTransformer method) (dae.query_variants.attributes_query.StringQueryToTreeTransformer method) (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) logout() (in module users_api.views)

M

M (dae.variants.attributes.Sex attribute) main() (dae.tools.gpf_validation_runner.MainRunner method) (in module dae.tools.create_sqlite_gene_set) (in module dae.tools.draw_pedigree) (in module dae.tools.generate_denovo_gene_sets) (in module dae.tools.gpf_validation_runner) (in module dae.tools.ped2ped) (in module dae.tools.pheno2browser) (in module dae.tools.simple_family2pedigree) (in module dae.tools.simple_study_import) (in module dae.tools.vcfinfo_extractor) MainRunner (class in dae.tools.gpf_validation_runner) make_pedigree_filter() (in module dae.person_filters) make_pheno_filter() (in module dae.person_filters) make_validation_runner() (dae.tools.gpf_validation_runner.MainRunner method) MakefilePartitionHelper (class in dae.import_tools.import_tools) 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.variants.attributes.Sex attribute) male_female_colors() (in module dae.pheno.graphs) male_female_legend() (in module dae.pheno.graphs) MALE_PRB (dae.pedigrees.family.FamilyTag attribute) males_count() (dae.pheno.graphs.GraphColumn method) Manifest (class in dae.genomic_resources.repository) manifest (dae.genomic_resources.repository.ManifestUpdate attribute) ManifestEntry (class in dae.genomic_resources.repository) ManifestUpdate (class in dae.genomic_resources.repository) mat2str() (in module dae.utils.variant_utils) match() (dae.query_variants.attributes_query.Matcher method) match_labels_query() (dae.annotation.annotation_factory.AnnotationConfigParser static method) matched_alleles (dae.variants.variant.SummaryVariant property) matched_alleles_indexes (dae.variants.variant.SummaryVariant property) matched_gene_effects (dae.variants.variant.SummaryVariant property) Matcher (class in dae.query_variants.attributes_query) maternal_aunt (dae.variants.attributes.Role attribute) maternal_cousin (dae.variants.attributes.Role attribute) maternal_grandfather (dae.variants.attributes.Role attribute) maternal_grandmother (dae.variants.attributes.Role attribute) maternal_half_sibling (dae.variants.attributes.Role attribute) maternal_uncle (dae.variants.attributes.Role attribute) Mating (class in dae.pedigrees.family_role_builder) MatingUnit (class in dae.pedigrees.pedigrees) MAX_CHARS (dae.pheno.prepare.measure_classifier.ClassifierReport attribute) MAX_CHILD_NUMBER (dae.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute) max_rank() (dae.pedigrees.pedigrees.FamilyConnections method) MAX_SHOWN_VARIANTS (genotype_browser.views.GenotypeBrowserQueryView attribute) max_x (dae.pedigrees.layout.Layout.BBox attribute) max_y (dae.pedigrees.layout.Layout.BBox attribute) MaxAggregator (class in dae.genomic_resources.aggregators) md5 (dae.genomic_resources.repository.ManifestEntry attribute) (dae.genomic_resources.repository.ResourceFileState attribute) md5sum() (in module dae.utils.filehash) MeanAggregator (class in dae.genomic_resources.aggregators) MeasureClassifier (class in dae.pheno.prepare.measure_classifier) MeasureType (class in dae.pheno.common) MeasureValuesTask (class in dae.pheno.prepare.pheno_prepare) MedianAggregator (class in dae.genomic_resources.aggregators) member_index (dae.pedigrees.family.Person property) 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_index() (dae.pedigrees.family.Family method) mendelian (dae.variants.attributes.Inheritance attribute) mendelian() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) merge() (dae.genomic_resources.histogram.CategoricalHistogram method) (dae.genomic_resources.histogram.NullHistogram method) (dae.genomic_resources.histogram.NumberHistogram method) merge_config() (dae.configuration.gpf_config_parser.GPFConfigParser static method) merge_configs() (dae.person_sets.PersonSetCollection static method) meta_measures() (dae.pheno.prepare.measure_classifier.MeasureClassifier static method) min_x (dae.pedigrees.layout.Layout.BBox attribute) min_y (dae.pedigrees.layout.Layout.BBox attribute) MinAggregator (class in dae.genomic_resources.aggregators) missing (dae.pedigrees.family.Person property) (dae.variants.attributes.Inheritance attribute) missing() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) MISSING_DAD (dae.pedigrees.family.FamilyTag attribute) MISSING_MOM (dae.pedigrees.family.FamilyTag attribute) Mode (class in dae.genomic_resources.repository) mode() (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) ModeAggregator (class in dae.genomic_resources.aggregators) model (users_api.serializers.UserSerializer.Meta attribute) (users_api.serializers.UserWithoutEmailSerializer.Meta attribute) modified() (in module dae.utils.fs_utils) modify_tuple() (dae.configuration.gpf_config_parser.GPFConfigParser class method) module dae dae.annotation dae.annotation.annotatable dae.annotation.annotate_columns dae.annotation.annotate_vcf dae.annotation.annotation_factory dae.annotation.annotation_pipeline dae.annotation.annotator_base dae.annotation.context dae.annotation.effect_annotator dae.annotation.gene_score_annotator dae.annotation.liftover_annotator dae.annotation.normalize_allele_annotator dae.annotation.record_to_annotatable dae.annotation.score_annotator, [1] 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_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.dask 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.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.event_counters dae.enrichment_tool.genotype_helper dae.gene dae.gene.denovo_gene_set_collection dae.gene.denovo_gene_set_collection_factory dae.gene.denovo_gene_sets_db dae.gene.gene_sets_db dae.gene.gene_term dae.gene.utils dae.genomic_resources dae.genomic_resources.aggregators dae.genomic_resources.cached_repository dae.genomic_resources.cli dae.genomic_resources.fsspec_protocol dae.genomic_resources.gene_models dae.genomic_resources.genomic_context dae.genomic_resources.genomic_position_table dae.genomic_resources.genomic_scores dae.genomic_resources.group_repository dae.genomic_resources.histogram dae.genomic_resources.reference_genome dae.genomic_resources.repository dae.genomic_resources.repository_factory dae.genomic_resources.testing dae.genotype_storage dae.genotype_storage.genotype_storage dae.genotype_storage.genotype_storage_registry dae.gpf_instance dae.gpf_instance.gpf_instance dae.gpf_instance_plugin dae.gpf_instance_plugin.gpf_instance_context_plugin dae.import_tools dae.import_tools.import_tools dae.inmemory_storage dae.inmemory_storage.inmemory_genotype_storage dae.inmemory_storage.inmemory_import_storage dae.inmemory_storage.raw_variants dae.parquet dae.parquet.schema2 dae.parquet.schema2.parquet_io dae.parquet.schema2.serializers dae.pedigrees dae.pedigrees.drawing 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_sets dae.pheno dae.pheno.common dae.pheno.db dae.pheno.graphs dae.pheno.prepare dae.pheno.prepare.measure_classifier dae.pheno.prepare.pheno_prepare dae.pheno.prepare_data dae.pheno.utils dae.pheno.utils.commons dae.pheno.utils.lin_regress dae.pheno_tool dae.pheno_tool.tool dae.query_variants dae.query_variants.attributes_query dae.query_variants.attributes_query_inheritance 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.family_builder dae.query_variants.sql.schema2.summary_builder dae.studies dae.studies.study dae.studies.variants_db dae.testing dae.testing.import_helpers dae.testing.setup_helpers dae.tools dae.tools.annotate_variants dae.tools.create_sqlite_gene_set dae.tools.cshl2vcf dae.tools.draw_pedigree dae.tools.generate_denovo_gene_sets dae.tools.gpf_instance_adjustments dae.tools.gpf_validation_runner dae.tools.grr_cache_repo dae.tools.ped2ped dae.tools.phase dae.tools.pheno2browser dae.tools.simple_family2pedigree dae.tools.simple_study_import dae.tools.vcfinfo_extractor dae.utils dae.utils.dae_utils dae.utils.debug_closing dae.utils.dict_utils dae.utils.filehash dae.utils.fixtures dae.utils.fs_utils dae.utils.helpers dae.utils.progress dae.utils.regions dae.utils.sql_utils dae.utils.statistics dae.utils.variant_utils dae.utils.verbosity_configuration dae.variants dae.variants.attributes dae.variants.core dae.variants.family_variant dae.variants.variant dae.variants_loaders dae.variants_loaders.cnv dae.variants_loaders.cnv.flexible_cnv_loader dae.variants_loaders.cnv.loader dae.variants_loaders.dae dae.variants_loaders.dae.loader dae.variants_loaders.raw dae.variants_loaders.raw.flexible_variant_loader dae.variants_loaders.raw.loader dae.variants_loaders.vcf dae.variants_loaders.vcf.loader genotype_browser genotype_browser.urls genotype_browser.views users_api users_api.models users_api.serializers users_api.urls users_api.validators users_api.views

mom (dae.variants.attributes.Role attribute) MULTIGENERATIONAL (dae.pedigrees.family.FamilyType attribute) MULTIPLEX (dae.pedigrees.family.FamilyTag attribute) (dae.pedigrees.family.FamilyType attribute) mutation_type() (dae.effect_annotation.effect_checkers.protein_change.ProteinChangeEffectChecker method)

N

name (dae.annotation.annotation_pipeline.AttributeInfo attribute) (dae.gene.gene_sets_db.GeneSet attribute) (dae.genomic_resources.repository.ManifestEntry attribute) (dae.studies.study.GenotypeData property) (users_api.models.WdaeUser attribute) names() (dae.genomic_resources.repository.Manifest method) (in module dae.pheno.graphs) nan (dae.pheno.prepare.measure_classifier.Convertible attribute) negation() (dae.query_variants.attributes_query.BitwiseTreeTransformer method) (dae.query_variants.attributes_query.StringQueryToTreeTransformer method) negative_primitive() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) NegativeStrandAnnotationRequest (class in dae.effect_annotation.annotation_request) NegPrimitive (class in dae.query_variants.attributes_query_inheritance) NO_RANK (dae.pedigrees.pedigrees.Individual attribute) non_numeric (dae.pheno.prepare.measure_classifier.Convertible attribute) normalization_rules (dae.configuration.gpf_config_parser.GPFConfigValidator attribute) normalize() (dae.annotation.annotation_factory.AnnotationConfigParser static method) (dae.import_tools.import_tools.ImportConfigNormalizer method) normalize_allele() (in module dae.annotation.normalize_allele_annotator) NormalizeAlleleAnnotator (class in dae.annotation.normalize_allele_annotator) not_role() (dae.variants.attributes.Role static method)

not_sequenced (dae.pedigrees.family.Person property) NotNode (class in dae.query_variants.attributes_query) NotNode() (dae.query_variants.attributes_query.QueryTreeToLambdaTransformer method) (dae.query_variants.attributes_query.QueryTreeToSQLBitwiseTransformer static method) NOTSET (dae.tools.gpf_validation_runner.TestStatus attribute) NPScore (class in dae.genomic_resources.genomic_scores) NPScoreAggr (class in dae.genomic_resources.genomic_scores) NPScoreAnnotator (class in dae.annotation.score_annotator) NPScoreQuery (class in dae.genomic_resources.genomic_scores) nuc_aggregator (dae.genomic_resources.genomic_scores.ScoreDef attribute) NUCLEAR (dae.pedigrees.family.FamilyTag attribute) NuclearCode (class in dae.effect_annotation.gene_codes) nucleotide_aggregator (dae.genomic_resources.genomic_scores.NPScoreAggr attribute) (dae.genomic_resources.genomic_scores.NPScoreQuery attribute) NullHistogram (class in dae.genomic_resources.histogram) NullHistogramConfig (class in dae.genomic_resources.histogram) number_of_bins (dae.genomic_resources.histogram.NumberHistogramConfig attribute) number_of_children_with_event (dae.common_reports.denovo_report.EffectCell property) number_of_observed_events (dae.common_reports.denovo_report.EffectCell property) NumberHistogram (class in dae.genomic_resources.histogram) NumberHistogramConfig (class in dae.genomic_resources.histogram) numeric (dae.pheno.prepare.measure_classifier.Convertible attribute)

O

oauth2_provider_accesstoken (users_api.models.WdaeUser attribute) 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.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) omission() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) open() (dae.annotation.annotation_pipeline.AnnotationPipeline method) (dae.annotation.annotation_pipeline.Annotator method) (dae.annotation.annotation_pipeline.AnnotatorDecorator method) (dae.annotation.effect_annotator.EffectAnnotatorAdapter method) (dae.annotation.liftover_annotator.LiftOverAnnotator method) (dae.annotation.normalize_allele_annotator.NormalizeAlleleAnnotator method) (dae.annotation.score_annotator.GenomicScoreAnnotatorBase method) (dae.genomic_resources.genomic_position_table.TabixGenomicPositionTable method) (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable method) (dae.genomic_resources.genomic_scores.AlleleScore method) (dae.genomic_resources.genomic_scores.GenomicScore method) (dae.genomic_resources.genomic_scores.NPScore method) (dae.genomic_resources.genomic_scores.PositionScore method) (dae.genomic_resources.reference_genome.ReferenceGenome method)

open_raw_file() (dae.genomic_resources.cached_repository.CachingProtocol method) (dae.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) open_tabix_file() (dae.genomic_resources.cached_repository.CachingProtocol method) (dae.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) open_vcf_file() (dae.genomic_resources.cached_repository.CachingProtocol method) (dae.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (dae.genomic_resources.GenomicResource method) (dae.genomic_resources.repository.GenomicResource method) (dae.genomic_resources.repository.ReadOnlyRepositoryProtocol method) OPTION (dae.variants_loaders.raw.loader.ArgumentType attribute) ordinal (dae.pheno.common.MeasureType attribute) OrNode (class in dae.query_variants.attributes_query) OrNode() (dae.query_variants.attributes_query.QueryTreeToBitwiseLambdaTransformer method) (dae.query_variants.attributes_query.QueryTreeToLambdaTransformer method) (dae.query_variants.attributes_query.QueryTreeToSQLBitwiseTransformer static method) OTHER (dae.pedigrees.family.FamilyType attribute) other (dae.pheno.common.MeasureType attribute) (dae.variants.attributes.Inheritance attribute) other() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) other_parent() (dae.pedigrees.pedigrees.MatingUnit method) overlap_enrichment_result_dict() (in module dae.enrichment_tool.event_counters) overlap_event_counts() (in module dae.enrichment_tool.event_counters)

P

parameters (dae.annotation.annotation_pipeline.AnnotatorInfo attribute) (dae.annotation.annotation_pipeline.AttributeInfo attribute) ParamsUsageMonitor (class in dae.annotation.annotation_pipeline) parent (dae.variants.attributes.Role attribute) parents (dae.studies.study.GenotypeData property) parents_id() (dae.pedigrees.family_role_builder.Mating 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_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.tools.simple_family2pedigree) 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_factory.AnnotationConfigParser static method) parse_config_file() (dae.annotation.annotation_factory.AnnotationConfigParser static method) parse_gr_id_version_token() (in module dae.genomic_resources.repository) parse_minimal() (dae.annotation.annotation_factory.AnnotationConfigParser static method) parse_raw() (dae.annotation.annotation_factory.AnnotationConfigParser static method) parse_raw_attribute_config() (dae.annotation.annotation_factory.AnnotationConfigParser static method) parse_raw_attributes() (dae.annotation.annotation_factory.AnnotationConfigParser static method) parse_resource_id_version() (in module dae.genomic_resources.repository) parse_short() (dae.annotation.annotation_factory.AnnotationConfigParser static method) parse_str() (dae.annotation.annotation_factory.AnnotationConfigParser static method) partial_update() (users_api.views.UserViewSet method) 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 (users_api.models.BaseVerificationCode attribute) (users_api.models.ResetPasswordCode attribute) (users_api.models.SetPasswordCode attribute) path_to_fixtures() (in module dae.utils.fixtures) PDFLayoutDrawer (class in dae.pedigrees.drawing) PED_COLUMNS_REQUIRED (dae.pheno.prepare.pheno_prepare.PrepareCommon attribute) pedigree (dae.testing.import_helpers.StudyInputLayout attribute) (dae.testing.StudyInputLayout attribute) peek_first() (dae.genomic_resources.genomic_position_table.LineBuffer method) peek_last() (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) permission_classes (users_api.views.UserViewSet attribute) Person (class in dae.pedigrees.family) PERSON_ID (dae.pheno.prepare.pheno_prepare.PrepareCommon attribute) person_set_collections (dae.studies.study.GenotypeData property) PersonFilter (class in dae.person_filters) PersonFilterRange (class in dae.person_filters) PersonFilterSet (class in dae.person_filters) persons (dae.enrichment_tool.genotype_helper.AlleleEvent attribute) PersonSet (class in dae.person_sets) PersonSetCollection (class in dae.person_sets) PersonSetCollection.Source (class in dae.person_sets) phase() (in module dae.tools.phase) PhenoDb (class in dae.pheno.db) PhenoFilter (class in dae.person_filters) PhenoFilterRange (class in dae.person_filters) PhenoFilterSet (class in dae.person_filters) PhenoResult (class in dae.pheno_tool.tool)

PhenoTool (class in dae.pheno_tool.tool) PhenoToolHelper (class in dae.pheno_tool.tool) phenotype (dae.studies.study.GenotypeData property) PID_COLUMN (dae.pheno.prepare.pheno_prepare.PrepareCommon attribute) plot() (dae.genomic_resources.histogram.CategoricalHistogram method) (dae.genomic_resources.histogram.NullHistogram method) (dae.genomic_resources.histogram.NumberHistogram method) Point (class in dae.pedigrees.layout) pop_first() (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.VCFGenomicPositionTable attribute) pos_begin (dae.genomic_resources.genomic_scores.ScoreLine property) pos_end (dae.annotation.annotatable.Annotatable property) POS_END (dae.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) pos_end (dae.genomic_resources.genomic_scores.ScoreLine property) Position (class in dae.annotation.annotatable) position (dae.annotation.annotatable.Annotatable property) POSITION (dae.annotation.annotatable.Annotatable.Type attribute) position (dae.variants.core.Allele property) (dae.variants.core.Allele.Type attribute) (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) (dae.variants.variant.SummaryVariant property) position_aggregator (dae.genomic_resources.genomic_scores.AlleleScoreAggr attribute) (dae.genomic_resources.genomic_scores.AlleleScoreQuery attribute) (dae.genomic_resources.genomic_scores.NPScoreAggr attribute) (dae.genomic_resources.genomic_scores.NPScoreQuery attribute) (dae.genomic_resources.genomic_scores.PositionScoreAggr attribute) (dae.genomic_resources.genomic_scores.PositionScoreQuery attribute) PositionScore (class in dae.genomic_resources.genomic_scores) PositionScoreAggr (class in dae.genomic_resources.genomic_scores) PositionScoreAnnotator (class in dae.annotation.score_annotator), [1] PositionScoreAnnotatorBase (class in dae.annotation.score_annotator) PositionScoreQuery (class in dae.genomic_resources.genomic_scores) PositiveStrandAnnotationRequest (class in dae.effect_annotation.annotation_request) possible_denovo (dae.variants.attributes.Inheritance attribute) possible_denovo() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) possible_omission (dae.variants.attributes.Inheritance attribute) possible_omission() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) possiblePersonPhasing() (in module dae.tools.phase) possiblePersonPhasingR() (in module dae.tools.phase) post() (genotype_browser.views.GenotypeBrowserQueryView method) (users_api.views.BasePasswordView method) (users_api.views.FederationCredentials method) (users_api.views.ForgotPassword method) (users_api.views.RESTLoginView method) (users_api.views.WdaeLoginView method) prb (dae.variants.attributes.Role attribute) PrepareBase (class in dae.pheno.prepare.pheno_prepare) PrepareCommon (class in dae.pheno.prepare.pheno_prepare) PreparePersons (class in dae.pheno.prepare.pheno_prepare) PreparePhenoBrowserBase (class in dae.pheno.prepare_data) PrepareVariables (class in dae.pheno.prepare.pheno_prepare) Primitive (class in dae.query_variants.attributes_query_inheritance) primitive() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) PriorityGenomicContext (class in dae.genomic_resources.genomic_context) process_config() (dae.configuration.gpf_config_parser.GPFConfigParser static method) produce_genotype() (dae.variants_loaders.dae.loader.DenovoLoader static method) produce_tabix_index() (in module dae.annotation.annotate_columns) progress() (in module dae.utils.progress) progress_nl() (in module dae.utils.progress) PromoterEffectChecker (class in dae.effect_annotation.effect_checkers.promoter) 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.LineBuffer method) PSCQuery (class in dae.person_sets) pseudo_autosomal (dae.variants.attributes.GeneticModel attribute) pub_med (dae.studies.study.GenotypeData property) put() (dae.pheno.prepare.pheno_prepare.TaskQueue method) (users_api.views.FederationCredentials method) pvalues (dae.pheno.utils.lin_regress.LinearRegression property)

Q

QUAD (dae.pedigrees.family.FamilyTag attribute) (dae.pedigrees.family.FamilyType attribute) query_gp_statistics() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) query_resources() (dae.annotation.annotation_factory.AnnotationConfigParser static method) query_result_summary_variants() (dae.studies.study.GenotypeData method) query_result_variants() (dae.studies.study.GenotypeData method) query_str() (dae.query_variants.attributes_query.Matcher method) query_summary_variants() (dae.inmemory_storage.raw_variants.RawFamilyVariants method) (dae.studies.study.GenotypeData method)

query_variants() (dae.inmemory_storage.raw_variants.RawFamilyVariants method) (dae.studies.study.GenotypeData method) QueryResult (class in dae.query_variants.query_runners) QueryRunner (class in dae.query_variants.query_runners) queryset (users_api.views.UserViewSet attribute) QueryTransformerMatcher (class in dae.query_variants.attributes_query) QueryTreeToBitwiseLambdaTransformer (class in dae.query_variants.attributes_query) QueryTreeToLambdaTransformer (class in dae.query_variants.attributes_query) QueryTreeToSQLBitwiseTransformer (class in dae.query_variants.attributes_query) QueryTreeToSQLTransformer (class in dae.query_variants.attributes_query) QUOTE (dae.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute)

R

raw (dae.pheno.common.MeasureType attribute) RawFamilyVariants (class in dae.inmemory_storage.raw_variants) RawMemoryVariants (class in dae.inmemory_storage.raw_variants) RawVariantsQueryRunner (class in dae.inmemory_storage.raw_variants) read_ewa_set_file() (in module dae.gene.gene_term) read_gmt_file() (in module dae.gene.gene_term) read_input() (in module dae.annotation.annotate_columns) read_mapping_file() (in module dae.gene.gene_term) read_only (dae.genotype_storage.genotype_storage.GenotypeStorage property) 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) Realization (class in dae.pedigrees.pedigrees) 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) 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) 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.family.Family method) (dae.pedigrees.family.Person method) ref (dae.annotation.annotatable.VCFAllele property) (dae.genomic_resources.genomic_scores.ScoreLine property) ref_allele (dae.variants.variant.SummaryVariant property) reference (dae.annotation.annotatable.VCFAllele property) (dae.variants.attributes.Inheritance attribute) (dae.variants.core.Allele property) (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) (dae.variants.variant.SummaryVariant property) reference() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) reference_genome (dae.gpf_instance.gpf_instance.GPFInstance property) (dae.gpf_instance.GPFInstance property) reference_genotype() (in module dae.utils.variant_utils) ReferenceGenome (class in dae.genomic_resources.reference_genome) 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.LineBuffer method) region_bin (dae.import_tools.import_tools.Bucket attribute) region_bins_count() (dae.import_tools.import_tools.MakefilePartitionHelper method) regions (dae.import_tools.import_tools.Bucket attribute) 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) register_genotype_data() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) (dae.studies.variants_db.VariantsDb method) register_genotype_storage() (dae.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) register_genotype_storage_factory() (in module dae.genotype_storage) register_import_storage_factory() (in module dae.import_tools.import_tools) register_preexisting_user() (users_api.models.WdaeUser method) register_storage_config() (dae.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) register_storages_configs() (dae.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) regression_display_names (dae.pheno.db.PhenoDb property) regression_display_names_with_ids (dae.pheno.db.PhenoDb property) regression_ids (dae.pheno.db.PhenoDb property) relabel_chromosomes() (dae.genomic_resources.gene_models.GeneModels method) reload() (dae.gene.denovo_gene_sets_db.DenovoGeneSetsDb method) (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) (dae.studies.variants_db.VariantsDb 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.PersonSetCollection static method) rename_gene_terms() (in module dae.gene.utils) renameGenes() (dae.gene.gene_term.GeneTerms method) repo_id (dae.genomic_resources.repository.GenomicResourceRepo property) REQUIRED_FIELDS (users_api.models.WdaeUser attribute) reset_password() (users_api.models.WdaeUser method) reset_regions() (dae.variants_loaders.cnv.loader.CNVLoader method) (dae.variants_loaders.dae.loader.DenovoLoader method) (dae.variants_loaders.raw.loader.VariantsGenotypesLoader method) (dae.variants_loaders.raw.loader.VariantsLoader method) (dae.variants_loaders.vcf.loader.VcfLoader method) ResetPassword (class in users_api.views) 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) resource_builder() (in module dae.genomic_resources.testing) resource_id (dae.genomic_resources.gene_models.GeneModels property) (dae.genomic_resources.reference_genome.ReferenceGenome property) resource_ids (dae.annotation.annotation_pipeline.Annotator property) ResourceFileState (class in dae.genomic_resources.repository) resources (dae.annotation.annotation_pipeline.Annotator property) (dae.annotation.annotation_pipeline.AnnotatorInfo attribute) RESTLoginView (class in users_api.views) retrieve() (users_api.views.UserViewSet method) 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_converter() (in module dae.query_variants.attributes_query) row() (dae.genomic_resources.genomic_position_table.Line method) (dae.genomic_resources.genomic_position_table.VCFLine method) rules (dae.configuration.gpf_config_parser.GPFConfigValidator attribute) run() (dae.inmemory_storage.raw_variants.RawVariantsQueryRunner method) (dae.pheno.prepare.pheno_prepare.ClassifyMeasureTask method) (dae.pheno.prepare.pheno_prepare.MeasureValuesTask method) (dae.pheno.prepare.pheno_prepare.Task method) (dae.pheno.prepare_data.PreparePhenoBrowserBase method) (dae.query_variants.query_runners.QueryRunner method) (dae.tools.gpf_validation_runner.GenotypeBrowserRunner method) run_validation() (users_api.serializers.UserSerializer method)

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) 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.gene_term.GeneTerms method) (dae.genomic_resources.gene_models.GeneModels method) (dae.pheno.db.PhenoDb method) (dae.utils.statistics.StatsCollection method) save_annotation_file() (dae.variants_loaders.raw.loader.AnnotationDecorator static method) save_families() (dae.pedigrees.loader.FamiliesLoader static method) save_families_cache() (dae.studies.study.GenotypeDataGroup method) save_fig() (dae.pheno.prepare_data.PreparePhenoBrowserBase method) save_index() (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) save_manifest() (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) save_pedigree() (dae.pedigrees.loader.FamiliesLoader static method) (dae.pheno.prepare.pheno_prepare.PreparePersons method) save_regression() (dae.pheno.db.PhenoDb method) save_regression_values() (dae.pheno.db.PhenoDb method) save_resource_file_state() (dae.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (dae.genomic_resources.repository.ReadWriteRepositoryProtocol method) save_study_config() (in module dae.import_tools.import_tools) scale() (dae.pedigrees.layout.Layout method) schema_family (dae.parquet.schema2.serializers.AlleleParquetSerializer property) schema_summary (dae.parquet.schema2.serializers.AlleleParquetSerializer property) score (dae.genomic_resources.genomic_scores.AlleleScoreAggr attribute) (dae.genomic_resources.genomic_scores.AlleleScoreQuery attribute) (dae.genomic_resources.genomic_scores.NPScoreAggr attribute) (dae.genomic_resources.genomic_scores.NPScoreQuery attribute) (dae.genomic_resources.genomic_scores.PositionScoreAggr attribute) (dae.genomic_resources.genomic_scores.PositionScoreQuery attribute) score_id (dae.genomic_resources.genomic_scores.ScoreDef attribute) ScoreDef (class in dae.genomic_resources.genomic_scores) ScoreLine (class in dae.genomic_resources.genomic_scores) search_fields (users_api.views.UserViewSet attribute) search_measures() (dae.pheno.db.PhenoDb method) search_measures_df() (dae.pheno.db.PhenoDb method) select_events_in_person_set() (dae.enrichment_tool.event_counters.CounterBase method) selected_person_sets (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) SEP1 (dae.variants_loaders.raw.loader.AnnotationDecorator attribute) SEP2 (dae.variants_loaders.raw.loader.AnnotationDecorator attribute) SEP3 (dae.variants_loaders.raw.loader.AnnotationDecorator attribute) serialize() (dae.genomic_resources.histogram.CategoricalHistogram method) (dae.genomic_resources.histogram.NullHistogram method) (dae.genomic_resources.histogram.NumberHistogram method) 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_matched_alleles() (dae.variants.variant.SummaryVariant method) set_measure() (dae.pheno.prepare.measure_classifier.ClassifierReport method) set_negative_stats() (dae.pheno_tool.tool.PhenoResult method) set_password() (users_api.models.WdaeUser method) 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_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_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_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_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_tabix() (in module dae.genomic_resources.testing) setup_vcf() (in module dae.genomic_resources.testing) (in module dae.testing) SEVERITY (dae.effect_annotation.effect.AnnotationEffect attribute) Sex (class in dae.variants.attributes) sex (dae.pedigrees.family.Person property) sex_converter() (in module dae.query_variants.attributes_query)

sfrom (dae.person_sets.PersonSetCollection.Source attribute) sha256sum() (in module dae.utils.filehash) short() (dae.variants.attributes.Sex method) (dae.variants.attributes.Status method) short_attributes() (dae.pheno.prepare.measure_classifier.ClassifierReport static method) short_header_line() (dae.pheno.prepare.measure_classifier.ClassifierReport static method) shutdown() (dae.genotype_storage.genotype_storage.GenotypeStorage method) (dae.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) (dae.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage method) sib (dae.variants.attributes.Role attribute) SibshipUnit (class in dae.pedigrees.pedigrees) sign() (in module dae.utils.fs_utils) simple_arg() (dae.query_variants.attributes_query.BitwiseTreeTransformer method) (dae.query_variants.attributes_query.StringQueryToTreeTransformer method) SimpleGenomicContext (class in dae.genomic_resources.genomic_context) SimpleGenomicContextProvider (class in dae.genomic_resources.genomic_context) SIMPLEX (dae.pedigrees.family.FamilyTag attribute) (dae.pedigrees.family.FamilyType attribute) simplify_effects() (dae.effect_annotation.effect.AnnotationEffect class method) SingleVcfLoader (class in dae.variants_loaders.vcf.loader) size (dae.genomic_resources.repository.ManifestEntry attribute) (dae.genomic_resources.repository.ResourceFileState attribute) SIZE (dae.pedigrees.layout.IndividualWithCoordinates attribute) size() (dae.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) 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.genomic_resources.genomic_scores.ScoreDef 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_pipeline.AttributeInfo 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) ssource (dae.person_sets.PersonSetCollection.Source attribute) staff_update() (in module users_api.models) start (dae.utils.regions.BedRegion property) (dae.utils.regions.Region property) start() (dae.genotype_storage.genotype_storage.GenotypeStorage method) (dae.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage method) (dae.query_variants.attributes_query.StringQueryToTreeTransformer method) (dae.query_variants.query_runners.QueryResult method) (dae.query_variants.query_runners.QueryRunner method) startCodons (dae.effect_annotation.gene_codes.NuclearCode attribute) StartLossEffectChecker (class in dae.effect_annotation.effect_checkers.start_loss) StatsCollection (class in dae.utils.statistics) Status (class in dae.variants.attributes) status (dae.pedigrees.family.Person property) step_dad (dae.variants.attributes.Role attribute) step_mom (dae.variants.attributes.Role attribute) stop (dae.utils.regions.BedRegion property) (dae.utils.regions.Region property) stopCodons (dae.effect_annotation.gene_codes.NuclearCode attribute) StopLossEffectChecker (class in dae.effect_annotation.effect_checkers.stop_loss) store_junit_results() (dae.tools.gpf_validation_runner.MainRunner static method) store_results() (dae.tools.gpf_validation_runner.GenotypeBrowserRunner method) (dae.tools.gpf_validation_runner.MainRunner method) StoredAnnotationDecorator (class in dae.variants_loaders.raw.loader) str2bool() (in module dae.utils.helpers) str2fgt() (in module dae.utils.variant_utils) str2gt() (in module dae.utils.variant_utils) str2mat() (in module dae.utils.variant_utils) str2mat_adjust_colsep() (in module dae.utils.variant_utils) STREAMING_CHUNK_SIZE (dae.pheno.db.PhenoDb attribute) streaming_search() (users_api.views.UserViewSet method) StringQueryToTreeTransformer (class in dae.query_variants.attributes_query) study_id (dae.import_tools.import_tools.ImportProject property) (dae.studies.study.GenotypeData property) (dae.testing.import_helpers.StudyInputLayout attribute) (dae.testing.StudyInputLayout attribute) study_id_from_path() (in module dae.utils.helpers) study_phenotype (dae.studies.study.GenotypeDataStudy property) study_type (dae.studies.study.GenotypeData property) study_update() (in module dae.testing) (in module dae.testing.import_helpers) StudyConfigBuilder (class in dae.configuration.study_config_builder) StudyConfigsAdjustmentCommand (class in dae.tools.gpf_instance_adjustments) StudyInputLayout (class in dae.testing) (class in dae.testing.import_helpers) SUBSTITUTION (dae.annotation.annotatable.Annotatable.Type attribute) substitution (dae.variants.core.Allele.Type 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_index (dae.variants.family_variant.FamilyAllele property) (dae.variants.family_variant.FamilyVariant property) (dae.variants.variant.SummaryAllele property) (dae.variants.variant.SummaryVariant property) summary_variant_filter_duplicate_function() (dae.inmemory_storage.raw_variants.RawFamilyVariants class method) summary_variant_filter_function() (dae.inmemory_storage.raw_variants.RawFamilyVariants class method) summary_variant_from_records() (dae.variants.variant.SummaryVariantFactory static method) summary_variant_from_vcf() (dae.variants.variant.SummaryVariantFactory static method) summary_variants_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) SUPPORTED_GENE_MODELS_FILE_FORMATS (dae.genomic_resources.gene_models.GeneModels attribute) svuid (dae.variants.variant.SummaryVariant property) syms (dae.gene.gene_sets_db.GeneSet attribute)

T

t4c8_gpf() (in module dae.testing) tabix_index_filename() (in module dae.utils.fs_utils) TabixGenomicPositionTable (class in dae.genomic_resources.genomic_position_table) 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_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) 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.pheno.prepare.pheno_prepare) TaskQueue (class in dae.pheno.prepare.pheno_prepare) template (users_api.views.BasePasswordView attribute) (users_api.views.ResetPassword attribute) (users_api.views.SetPassword attribute) test_frames() (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)

to_internal_value() (users_api.serializers.CreatableSlugRelatedField method) (users_api.serializers.DatasetSerializer method) to_json() (dae.pedigrees.family.Family method) (dae.pedigrees.family.Person method) (dae.person_sets.PersonSet method) (dae.person_sets.PersonSetCollection 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.pedigrees.loader.FamiliesLoader static method) to_value() (dae.variants.attributes.Role static method) (dae.variants.attributes.Sex static method) (dae.variants.attributes.Status static method) to_xml_element() (dae.tools.gpf_validation_runner.TestResult method) (dae.tools.gpf_validation_runner.TestSuite method) token_converter() (dae.query_variants.attributes_query.QueryTreeToSQLTransformer static method) tokenize() (dae.annotation.annotatable.Annotatable static method) TOMLDict (class in dae.configuration.study_config_builder) TOMLList (class in dae.configuration.study_config_builder) total (dae.person_sets.ChildrenStats property) total_len() (dae.genomic_resources.gene_models.TranscriptModel method) total_length() (in module dae.utils.regions) transcript_effects() (dae.effect_annotation.effect.AnnotationEffect class method) TranscriptModel (class in dae.genomic_resources.gene_models) transform() (dae.query_variants.attributes_query.BaseTreeTransformer method) transform_query_string_to_tree() (dae.query_variants.attributes_query.BaseQueryTransformerMatcher method) transform_tree_to_matcher() (dae.query_variants.attributes_query.QueryTransformerMatcher method) translate() (dae.pedigrees.layout.Layout method) transmission_type (dae.variants.family_variant.FamilyAllele property) (dae.variants.variant.SummaryAllele property) (dae.variants.variant.SummaryVariant property) TransmissionType (class in dae.variants.attributes) transmitted (dae.variants.attributes.TransmissionType attribute) TreeNode (class in dae.query_variants.attributes_query) trim_equal_ref_alt_parts() (dae.effect_annotation.variant.Variant method) trim_parsimonious() (in module dae.utils.variant_utils) trim_str_left() (in module dae.utils.variant_utils) trim_str_left_right() (in module dae.utils.variant_utils) trim_str_right() (in module dae.utils.variant_utils) trim_str_right_left() (in module dae.utils.variant_utils) TRIO (dae.pedigrees.family.FamilyTag attribute) (dae.pedigrees.family.FamilyType attribute) trios (dae.pedigrees.family.Family property) try_solve() (dae.pedigrees.pedigrees.SandwichSolver static method) tvalues (dae.pheno.utils.lin_regress.LinearRegression property) type (dae.annotation.annotation_pipeline.AnnotatorInfo attribute) (dae.annotation.annotation_pipeline.AttributeInfo attribute) (dae.genomic_resources.histogram.CategoricalHistogram attribute) (dae.genomic_resources.histogram.NullHistogram attribute) (dae.genomic_resources.histogram.NumberHistogram attribute) (dae.import_tools.import_tools.Bucket attribute) TYPE_DISPLAY_NAME (dae.variants.core.Allele attribute) types (dae.effect_annotation.effect.AlleleEffects property)

U

U (dae.variants.attributes.Sex attribute) 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) union() (in module dae.utils.regions) unique_regions() (in module dae.utils.regions) unknown (dae.variants.attributes.Inheritance attribute) (dae.variants.attributes.Role attribute) (dae.variants.attributes.TransmissionType attribute) unknown() (dae.query_variants.attributes_query_inheritance.InheritanceTransformer method) unregister_genotype_data() (dae.gpf_instance.gpf_instance.GPFInstance method) (dae.gpf_instance.GPFInstance method) (dae.studies.variants_db.VariantsDb method) unset_tag() (dae.pedigrees.family.Family method) (dae.pedigrees.family.Person method) (in module dae.pedigrees.family_tag_builder) unspecified (dae.enrichment_tool.event_counters.EnrichmentResult attribute) (dae.enrichment_tool.event_counters.EventCountersResult attribute) (dae.enrichment_tool.event_counters.EventsResult attribute) (dae.enrichment_tool.event_counters.VariantEventsResult attribute) (dae.person_sets.ChildrenBySex attribute) (dae.person_sets.ChildrenStats attribute) (dae.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.TranscriptModel method) update_header() (in module dae.annotation.annotate_vcf) update_indexes() (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.import_helpers) use_bit_and_function() (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) user (users_api.models.BaseVerificationCode attribute) (users_api.models.ResetPasswordCode attribute) (users_api.models.SetPasswordCode attribute) user_id (users_api.models.BaseVerificationCode attribute) (users_api.models.ResetPasswordCode attribute) (users_api.models.SetPasswordCode attribute) user_permissions (users_api.models.WdaeUser attribute) USERNAME_FIELD (users_api.models.WdaeUser attribute) userquery_set (users_api.models.WdaeUser attribute) users_api 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) utr3_len() (dae.genomic_resources.gene_models.TranscriptModel method) utr3_regions() (dae.genomic_resources.gene_models.TranscriptModel method) utr5_len() (dae.genomic_resources.gene_models.TranscriptModel method) utr5_regions() (dae.genomic_resources.gene_models.TranscriptModel 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.genotype_storage.genotype_storage.GenotypeStorage class method) (dae.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage 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.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage attribute) value_order (dae.genomic_resources.histogram.CategoricalHistogramConfig attribute) value_type (dae.genomic_resources.genomic_scores.ScoreDef attribute) values_domain() (dae.genomic_resources.histogram.CategoricalHistogram method) (dae.genomic_resources.histogram.NullHistogram method) (dae.genomic_resources.histogram.NumberHistogram method) VALUES_LIMIT (dae.genomic_resources.histogram.CategoricalHistogram attribute) 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_type (dae.variants.variant.SummaryAllele property) variant_type_converter() (in module dae.query_variants.attributes_query) variant_types (dae.variants.variant.SummaryVariant property) VariantColumnInputFile (class in dae.effect_annotation.cli) VariantColumnOutputFile (class in dae.effect_annotation.cli) VariantDesc (class in dae.variants.variant) VariantDetails (class in dae.variants.variant)

VariantEvent (class in dae.enrichment_tool.genotype_helper) VariantEventsResult (class in dae.enrichment_tool.event_counters) variants_filenames (dae.variants_loaders.dae.loader.DaeTransmittedLoader property) (dae.variants_loaders.raw.loader.VariantsLoader property) (dae.variants_loaders.vcf.loader.VcfLoader property) VariantsDb (class in dae.studies.variants_db) VariantsGenotypesLoader (class in dae.variants_loaders.raw.loader) VariantsLoader (class in dae.variants_loaders.raw.loader) VariantsLoaderDecorator (class in dae.variants_loaders.raw.loader) VariantsParquetWriter (class in dae.parquet.schema2.parquet_io) vcf (dae.testing.import_helpers.StudyInputLayout attribute) (dae.testing.StudyInputLayout attribute) vcf2cshl() (in module dae.variants.variant) vcf_import() (in module dae.testing) (in module dae.testing.import_helpers) vcf_study() (in module dae.testing) (in module dae.testing.import_helpers) VCFAllele (class in dae.annotation.annotatable) VcfFamiliesGenotypes (class in dae.variants_loaders.vcf.loader) VCFGenomicPositionTable (class in dae.genomic_resources.genomic_position_table) VcfLikeRecordToVcfAllele (class in dae.annotation.record_to_annotatable) VCFLine (class in dae.genomic_resources.genomic_position_table) VcfLoader (class in dae.variants_loaders.vcf.loader) 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) verify_pheno_folder() (dae.pheno.db.PhenoDb static method) version_string_to_suffix() (in module dae.genomic_resources.repository) version_tuple_to_string() (in module dae.genomic_resources.repository) version_tuple_to_suffix() (in module dae.genomic_resources.repository) view_max() (dae.genomic_resources.histogram.NumberHistogram method) view_min() (dae.genomic_resources.histogram.NumberHistogram method) view_range (dae.genomic_resources.histogram.NumberHistogram property) (dae.genomic_resources.histogram.NumberHistogramConfig attribute) visit_create_view() (in module dae.utils.sql_utils)

W

WdaeLoginView (class in users_api.views) WdaeUser (class in users_api.models) WdaeUser.DoesNotExist WdaeUser.MultipleObjectsReturned WdaeUserManager (class in users_api.models) WHERE (dae.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute) work() (dae.annotation.annotate_columns.AnnotateColumnsTool method) (dae.annotation.annotate_vcf.AnnotateVCFTool method)

work_dir (dae.import_tools.import_tools.ImportProject property) worst (dae.effect_annotation.effect.AlleleEffects property) worst_effect (dae.variants.variant.SummaryAllele property) worst_effect() (dae.effect_annotation.effect.AnnotationEffect class method) write_columns() (dae.effect_annotation.cli.VariantColumnOutputFile method) write_dataset() (dae.parquet.schema2.parquet_io.VariantsParquetWriter method) write_summary_variant() (dae.parquet.schema2.parquet_io.VariantsParquetWriter method)

X

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

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

Y

y (dae.pedigrees.layout.Point attribute) y_center (dae.pedigrees.layout.IndividualWithCoordinates property)

y_log_scale (dae.genomic_resources.histogram.CategoricalHistogramConfig attribute) (dae.genomic_resources.histogram.NumberHistogramConfig attribute) year (dae.studies.study.GenotypeData property)