Index

A

AboutDescriptionView (class in gpf_instance.views) abspath() (in module gain.utils.fs_utils) abstract (users_api.models.BaseVerificationCode.Meta attribute) AbstractDuckDbImportStorage (class in gpf.duckdb_storage.duckdb_import_storage) AbstractDuckDbStorage (class in gpf.duckdb_storage.duckdb_genotype_storage) AbstractLiftoverAnnotator (class in gain.annotation.liftover_annotator) AbstractRunner (class in gpf.tools.gpf_validation_runner) acgt_genome() (in module gain.testing.acgt_import) acgt_gpf() (in module gpf.testing.acgt_import) acgt_grr() (in module gain.testing.acgt_import) adapt() (gpf.query_variants.query_runners.QueryRunner method) add() (gain.genomic_resources.aggregators.Aggregator method) (gain.genomic_resources.repository.Manifest method) add_annotator() (gain.annotation.annotation_pipeline.AnnotationPipeline method) add_argparser_arguments() (gain.annotation.annotation_genomic_context_cli.CLIAnnotationContextProvider method) (gain.genomic_resources.genomic_context.DefaultRepositoryContextProvider method) (gain.genomic_resources.genomic_context_base.GenomicContextProvider method) (gain.genomic_resources.genomic_context_cli.CLIGenomicContextProvider method) (gpf.genotype_storage.genotype_storage_genomic_context_cli.CLIGenotypeStorageContextProvider method) (gpf.gpf_instance_plugin.gpf_instance_context_plugin.GPFInstanceContextProvider method) add_arguments() (gain.task_graph.cli_tools.TaskGraphCli static method) (gpf.gpf_instance.adjustments.adjust_duckdb_storage.AdjustDuckDbStorageCommand static method) (gpf.gpf_instance.adjustments.adjust_impala_storage.AdjustImpalaStorageCommand static method) (users_api.management.commands.dataset_groups.Command method) (users_api.management.commands.datasets_export.Command method) (users_api.management.commands.datasets_restore.Command method) (users_api.management.commands.unlock_user.Command method) (users_api.management.commands.user_create.Command method) (users_api.management.commands.user_set_name.Command method) (users_api.management.commands.user_setpasswd.Command method) (users_api.management.commands.users_add.Command method) (users_api.management.commands.users_export.Command method) (users_api.management.commands.users_group_add.Command method) (users_api.management.commands.users_group_remove.Command method) (users_api.management.commands.users_remove.Command method) (users_api.management.commands.users_restore.Command method) (users_api.management.commands.users_show.Command method) add_common_annotation_arguments() (in module gain.annotation.annotate_utils) add_count() (gain.genomic_resources.statistics.min_max.MinMaxValue method) add_gene() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) add_group_perm_to_dataset() (in module datasets_api.permissions) add_group_perm_to_user() (in module datasets_api.permissions) add_input_files_to_task_graph() (in module gain.annotation.annotate_utils) add_measure_task() (gpf.pheno.prepare_data.PreparePhenoBrowserBase method) add_members() (gpf.pedigrees.family.Family method) add_missing_members() (gpf.pedigrees.pedigrees.FamilyConnections static method) add_missing_parquet_fields() (in module gpf.parquet.parquet_writer) add_page() (gpf.pedigrees.drawing.PDFLayoutDrawer method) add_parent() (gpf.studies.study.GenotypeData method) add_pheno_common_inference() (in module gpf.pheno.pheno_import) add_rank() (gpf.pedigrees.pedigrees.Individual method) add_ranks() (gpf.pedigrees.pedigrees.FamilyConnections method) add_record_to_annotable_arguments() (in module gain.annotation.record_to_annotatable) add_relation() (datasets_api.models.DatasetHierarchy class method) add_score_aggregator_documentation() (gain.annotation.score_annotator.GenomicScoreAnnotatorBase method) add_tagger() (gpf.pedigrees.family_tag_builder.FamilyTagsBuilder method) add_task() (gain.task_graph.graph.TaskGraph method) add_tasks() (gain.task_graph.graph.TaskGraph method) add_to_parser() (gpf.variants_loaders.raw.loader.CLIArgument method) add_unnest_in_join() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method) (gpf.query_variants.sql.schema2.base_query_builder.Dialect static method) add_value() (gain.genomic_resources.histogram.CategoricalHistogram method) (gain.genomic_resources.histogram.NullHistogram method) (gain.genomic_resources.histogram.NumberHistogram method) (gain.genomic_resources.implementations.reference_genome_impl.ChromosomeStatistic method) (gain.genomic_resources.implementations.reference_genome_impl.GenomeStatistic method) (gain.genomic_resources.statistics.base_statistic.Statistic method) (gain.genomic_resources.statistics.min_max.MinMaxValue method) add_variant_count() (in module gpf.gene_profile.generate_gene_profile) adjust_chrom_prefix() (in module gpf.variants_loaders.raw.flexible_variant_loader) adjust_dataset() (gpf.gpf_instance.adjustments.gpf_instance_adjustments.EnableDisableStudies method) (gpf.gpf_instance.adjustments.gpf_instance_adjustments.StudyConfigsAdjustmentCommand method) adjust_study() (gpf.gpf_instance.adjustments.gpf_instance_adjustments.DefaultGenotypeStorage method) (gpf.gpf_instance.adjustments.gpf_instance_adjustments.EnableDisableStudies method) (gpf.gpf_instance.adjustments.gpf_instance_adjustments.StudyConfigsAdjustmentCommand method) adjust_verbosity() (gain.utils.verbosity_configuration.VerbosityConfiguration static method) adjust_zero_based_line() (in module gain.genomic_resources.genomic_position_table.table) AdjustDuckDbStorageCommand (class in gpf.gpf_instance.adjustments.adjust_duckdb_storage) AdjustImpalaStorageCommand (class in gpf.gpf_instance.adjustments.adjust_impala_storage) AdjustmentsCommand (class in gpf.gpf_instance.adjustments.adjust_command) admin() (in module conftest) admin_client() (in module conftest) affected (gpf.variants.attributes.Status attribute) AFFECTED_DAD (gpf.pedigrees.family.FamilyTag attribute) AFFECTED_MOM (gpf.pedigrees.family.FamilyTag attribute) AFFECTED_PRB (gpf.pedigrees.family.FamilyTag attribute) AFFECTED_SIB (gpf.pedigrees.family.FamilyTag attribute) affected_statues (gpf.studies.study.PSCQueryAdjustments attribute) aggregate() (gain.genomic_resources.aggregators.Aggregator method) aggregate_gene_values() (gain.annotation.gene_score_annotator.GeneScoreAnnotator method) Aggregator (class in gain.genomic_resources.aggregators) aliases() (gpf.variants.attributes.Sex static method) align_na_results() (gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapter static method) (pheno_tool_api.adapter.PhenoToolAdapter static method) all (gpf.enrichment_tool.event_counters.EnrichmentResult attribute) (gpf.enrichment_tool.event_counters.EventCountersResult attribute) (gpf.enrichment_tool.event_counters.EventsResult attribute) (gpf.enrichment_tool.event_counters.VariantEventsResult attribute) all() (gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method) (gpf.query_variants.attribute_queries.SyntaxSugarTransformer method) ALL_ATTRIBUTE_IDXS (gain.effect_annotation.cli.AnnotationAttributes attribute) all_count() (gpf.pheno.graphs.GraphColumn method) all_labels() (gpf.pedigrees.family.FamilyTag static method) all_region_bins() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) all_regions() (gain.genomic_resources.gene_models.transcript_models.TranscriptModel method) (gain.genomic_resources.gene_models.TranscriptModel method) all_regions_from_chrom() (in module gain.utils.regions) all_tag_labels() (gpf.pedigrees.family.Person method) all_tags() (gpf.pedigrees.family.FamilyTag static method) alla_genome() (in module gain.testing.alla_import) alla_gpf() (in module gpf.testing.alla_import) alla_grr() (in module gain.testing.alla_import) Allele (class in gpf.variants.core) Allele.Type (class in gpf.variants.core) allele_aggregator (gain.genomic_resources.genomic_scores.AlleleScoreAggr attribute) (gain.genomic_resources.genomic_scores.AlleleScoreQuery attribute) (gain.genomic_resources.genomic_scores.ScoreDef attribute) allele_count (gpf.variants.family_variant.FamilyVariant property) (gpf.variants.variant.SummaryVariant property) allele_events (gpf.enrichment_tool.genotype_helper.VariantEvent attribute) allele_in_members (gpf.variants.family_variant.FamilyAllele property) allele_in_roles (gpf.variants.family_variant.FamilyAllele property) allele_in_sexes (gpf.variants.family_variant.FamilyAllele property) allele_in_statuses (gpf.variants.family_variant.FamilyAllele property) allele_index (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.variant.SummaryAllele property) allele_indexes (gpf.variants.family_variant.FamilyVariant property) allele_type (gpf.variants.core.Allele property) (gpf.variants.family_variant.FamilyAllele property) allele_type_from_cshl_variant() (in module gpf.variants.variant) allele_type_from_name() (in module gpf.variants.variant) AlleleEffects (class in gain.effect_annotation.effect) AlleleEvent (class in gpf.enrichment_tool.genotype_helper) AlleleParquetSerializer (class in gpf.parquet.schema2.serializers) ALLELES (gain.genomic_resources.genomic_scores.AlleleScore.Mode attribute) alleles (gpf.variants.family_variant.FamilyVariant property) (gpf.variants.variant.SummaryVariant property) alleles_mode() (gain.genomic_resources.genomic_scores.AlleleScore method) AlleleScore (class in gain.genomic_resources.genomic_scores) AlleleScore.Mode (class in gain.genomic_resources.genomic_scores) AlleleScoreAggr (class in gain.genomic_resources.genomic_scores)

AlleleScoreAnnotator (class in gain.annotation.score_annotator) AlleleScoreQuery (class in gain.genomic_resources.genomic_scores) AllMemberDetailsView (class in family_api.views) allow_only_whole_values_y (gain.genomic_resources.histogram.CategoricalHistogramConfig attribute) allowed_datasets (users_api.models.WdaeUser property) alt (gain.annotation.annotatable.VCFAllele property) (gain.genomic_resources.genomic_position_table.Line attribute) (gain.genomic_resources.genomic_position_table.line.Line attribute) (gain.genomic_resources.genomic_position_table.line.LineBase attribute) ALT (gain.genomic_resources.genomic_position_table.table.GenomicPositionTable attribute) alt (gain.genomic_resources.genomic_scores.ScoreLine property) alt_alleles (gpf.variants.variant.SummaryVariant property) alt_key (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (gain.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) alternative (gain.annotation.annotatable.VCFAllele property) (gpf.variants.core.Allele property) (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.variant.SummaryVariant property) ancestor (datasets_api.models.Dataset attribute) (datasets_api.models.DatasetHierarchy attribute) ancestor_id (datasets_api.models.DatasetHierarchy attribute) and_() (gpf.query_variants.attribute_queries.AttributeQueryTransformerFunction method) (gpf.query_variants.attribute_queries.AttributeQueryTransformerSQL method) (gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method) Annotatable (class in gain.annotation.annotatable) annotatable (gain.annotation.processing_pipeline.Annotation attribute) Annotatable.Type (class in gain.annotation.annotatable) annotate() (gain.annotation.annotation_pipeline.AnnotationPipeline method) (gain.annotation.annotation_pipeline.Annotator method) (gain.annotation.annotation_pipeline.InputAnnotableAnnotatorDecorator method) (gain.annotation.annotation_pipeline.ValueTransformAnnotatorDecorator method) (gain.annotation.annotator_base.AnnotatorBase method) (gain.annotation.cnv_collection_annotator.CnvCollectionAnnotator method) (gain.annotation.debug_annotator.HelloWorldAnnotator method) (gain.annotation.effect_annotator.EffectAnnotatorAdapter method) (gain.annotation.gene_score_annotator.GeneScoreAnnotator method) (gain.annotation.score_annotator.AlleleScoreAnnotator method) (gain.annotation.score_annotator.PositionScoreAnnotator method) (gain.annotation.simple_effect_annotator.SimpleEffectAnnotator method) (gain.effect_annotation.annotator.EffectAnnotator method) annotate_allele() (gain.effect_annotation.annotator.EffectAnnotator method) annotate_cnv() (gain.effect_annotation.annotator.EffectAnnotator method) annotate_columns() (in module gain.annotation.annotate_columns) annotate_region() (gain.effect_annotation.annotator.EffectAnnotator method) annotate_variant() (gain.effect_annotation.annotator.EffectAnnotator static method) annotate_vcf() (in module gain.annotation.annotate_vcf) Annotation (class in gain.annotation.processing_pipeline) ANNOTATION_CONFIG_GRAMMAR (gain.annotation.annotation_config.AnnotationConfigParser attribute) annotation_schema (gpf.variants_loaders.raw.loader.VariantsLoader property) (gpf.variants_loaders.raw.loader.VariantsLoaderDecorator property) AnnotationAttributes (class in gain.effect_annotation.cli) AnnotationConfigParser (class in gain.annotation.annotation_config) AnnotationConfigurationError AnnotationEffect (class in gain.effect_annotation.effect) AnnotationPipeline (class in gain.annotation.annotation_pipeline) AnnotationPipelineAnnotatablesBatchFilter (class in gain.annotation.processing_pipeline) AnnotationPipelineAnnotatablesFilter (class in gain.annotation.processing_pipeline) AnnotationPipelineContextManager (class in gain.annotation.processing_pipeline) AnnotationPipelineImplementation (class in gain.genomic_resources.implementations.annotation_pipeline_impl) AnnotationPipelineVariantsBatchFilter (class in gpf.parquet.schema2.processing_pipeline) AnnotationPipelineVariantsFilter (class in gpf.parquet.schema2.processing_pipeline) AnnotationPipelineVariantsFilterMixin (class in gpf.parquet.schema2.processing_pipeline) AnnotationPreamble (class in gain.annotation.annotation_config) AnnotationRequestFactory (class in gain.effect_annotation.annotator) annotations (gain.annotation.processing_pipeline.AnnotationsWithSource attribute) AnnotationsWithSource (class in gain.annotation.processing_pipeline) AnnotationsWithSourceBatchFilter (class in gain.annotation.processing_pipeline) AnnotationsWithSourceFilter (class in gain.annotation.processing_pipeline) Annotator (class in gain.annotation.annotation_pipeline) annotator_id (gain.annotation.annotation_config.AnnotatorInfo attribute) AnnotatorBase (class in gain.annotation.annotator_base) AnnotatorDecorator (class in gain.annotation.annotation_pipeline) AnnotatorInfo (class in gain.annotation.annotation_config) annotators (gain.annotation.annotation_config.RawFullConfig attribute) anonymous_client() (in module conftest) any() (gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method) (gpf.query_variants.attribute_queries.SyntaxSugarTransformer method) append() (gain.genomic_resources.genomic_position_table.line.LineBuffer method) (gain.genomic_resources.genomic_position_table.LineBuffer method) (gpf.tools.gpf_validation_runner.TestSuite method) append_allele() (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) (gpf.parquet.schema2.variants_parquet_writer.ContinuousParquetFileWriter method) append_meta_to_parquet() (in module gpf.parquet.parquet_writer) apply() (gpf.person_filters.FamilyFilter method) (gpf.person_filters.person_filters.CriteriaFilter method) (gpf.person_filters.person_filters.FamilyFilter method) (gpf.person_filters.person_filters.PersonFilter method) (gpf.person_filters.person_filters.PhenoFilter method) (gpf.person_filters.PersonFilter method) (gpf.person_filters.PhenoFilter method) apply_family_heuristics() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) apply_mask() (gpf.utils.variant_utils.BitmaskEnumTranslator method) apply_summary_heuristics() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) apply_to_df() (gpf.person_filters.FamilyFilter method) (gpf.person_filters.person_filters.FamilyFilter method) (gpf.person_filters.person_filters.PersonFilter method) (gpf.person_filters.person_filters.PersonFilterRange method) (gpf.person_filters.person_filters.PersonFilterSet method) (gpf.person_filters.PersonFilter method) (gpf.person_filters.PersonFilterRange method) (gpf.person_filters.PersonFilterSet method) apply_to_family() (gpf.pedigrees.layout.Layout method) are_mates() (gpf.pedigrees.pedigrees.Individual method) are_siblings() (gpf.pedigrees.pedigrees.Individual method) args (gain.task_graph.graph.TaskDesc attribute) ARGUMENT (gpf.variants_loaders.raw.loader.ArgumentType attribute) ArgumentType (class in gpf.variants_loaders.raw.loader) array_item_suffix() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method) (gpf.query_variants.sql.schema2.base_query_builder.Dialect static method) as_directed_graph() (gain.task_graph.graph.TaskGraph method) attribute_type (gain.annotation.annotation_config.AttributeInfo attribute) (gain.annotation.annotation_pipeline.AttributeDesc attribute) AttributeDesc (class in gain.annotation.annotation_pipeline) AttributeInfo (class in gain.annotation.annotation_config) AttributeQueriesUnsupportedException AttributeQueryNotSupported AttributeQueryTransformer (class in gpf.query_variants.attribute_queries) AttributeQueryTransformerFunction (class in gpf.query_variants.attribute_queries) AttributeQueryTransformerSQL (class in gpf.query_variants.attribute_queries) AttributeQueryTransformerSQLLegacy (class in gpf.query_variants.attribute_queries) attributes (gain.annotation.annotation_config.AnnotatorInfo attribute) (gain.annotation.annotation_pipeline.Annotator property) (gain.genomic_resources.genomic_scores.CNV attribute) (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.variant.SummaryAllele property) (gpf.variants.variant.SummaryVariant property) augment_accessibility() (in module datasets_api.views) augment_with_groups() (in module datasets_api.views) augment_with_parents() (in module datasets_api.views) auth_token (users_api.models.WdaeUser attribute) authenticate() (utils.authentication.GPFOAuth2Authentication method) (utils.authentication.ReadOnlyDBAuthentication method) (utils.authentication.SessionAuthenticationWithUnauthenticatedCSRF method) authentication_classes (groups_api.views.GroupsViewSet attribute) (query_base.query_base.QueryBaseView attribute) (users_api.views.FederationCredentials attribute) (users_api.views.UserViewSet attribute) AuthenticationLog (class in users_api.models) AuthenticationLog.DoesNotExist AuthenticationLog.MultipleObjectsReturned autosomal (gpf.variants.attributes.GeneticModel attribute) autosomal_broken (gpf.variants.attributes.GeneticModel attribute)

B

backend (gpf.studies.study.GenotypeDataStudy property) background_id (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground property) (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property) background_type (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground property) (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property) backup_schema2_study() (in module gpf.parquet.schema2.annotate_schema2_parquet) base_dir (gpf.duckdb_storage.duckdb_storage_config.DuckDbConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbParquetConf attribute) (gpf.schema2_storage.schema2_layout.Schema2DatasetLayout attribute) BASE_DOC_URL (gain.annotation.annotator_base.AnnotatorBase attribute) base_fields (users_api.forms.WdaeLoginForm attribute) (users_api.forms.WdaePasswordForgottenForm attribute) (users_api.forms.WdaeRegisterPasswordForm attribute) (users_api.forms.WdaeResetPasswordForm attribute) BaseAnnotationRequest (class in gain.effect_annotation.annotation_request) BaseCommonReportsHelper (class in common_reports_api.common_reports_helper) BaseDatasetPermissionsView (class in datasets_api.views) BaseEnrichmentBackground (class in gpf.enrichment_tool.base_enrichment_background) BaseEnrichmentBuilder (class in enrichment_api.enrichment_builder) BaseEnrichmentHelper (class in enrichment_api.enrichment_helper) BaseEnrichmentResourceBackground (class in gpf.enrichment_tool.base_enrichment_background) BaseGeneSetCollection (class in gain.gene_sets.gene_set) BaseGenotypeBrowserRunner (class in gpf.tools.gpf_validation_runner) basename (groups_api.views.GroupsViewSet attribute) (users_api.views.UserViewSet attribute) BasePasswordView (class in users_api.views) BasePhenoBrowserHelper (class in pheno_browser_api.pheno_browser_helper) BaseQueryBuilder (class in gpf.query_variants.sql.schema2.base_query_builder) BaseResourceSchema (class in gain.gene_sets.gene_set) BaseVerificationCode (class in users_api.models) BaseVerificationCode.Meta (class in users_api.models) basic_liftover_allele() (in module gain.annotation.liftover_annotator) basic_liftover_variant() (in module gain.annotation.liftover_annotator) BasicLiftoverAnnotator (class in gain.annotation.liftover_annotator) batch_annotate() (gain.annotation.annotation_pipeline.AnnotationPipeline method) (gain.annotation.annotation_pipeline.Annotator method) (gain.annotation.annotator_base.AnnotatorBase method) BATCH_ROWS (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter attribute) BATCH_SIZE (gpf.schema2_storage.schema2_import_storage.Schema2ImportStorage attribute) bcf_liftover_allele() (in module gain.annotation.liftover_annotator) bcf_liftover_variant() (in module gain.annotation.liftover_annotator) BcfLiftoverAnnotator (class in gain.annotation.liftover_annotator) bedfile2regions() (in module gain.utils.regions) BedRegion (class in gain.utils.regions) begin (gain.utils.regions.BedRegion property) (gain.utils.regions.Region property) best2gt() (in module gpf.utils.variant_utils) best_st (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) best_state (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) BigWigLine (class in gain.genomic_resources.genomic_position_table) (class in gain.genomic_resources.genomic_position_table.line) BigWigTable (class in gain.genomic_resources.genomic_position_table) (class in gain.genomic_resources.genomic_position_table.table_bigwig) bitmask2inheritance() (in module gpf.variants.attributes) BitmaskEnumTranslator (class in gpf.utils.variant_utils) blob_column() (gpf.parquet.schema2.serializers.AlleleParquetSerializer method) (gpf.parquet.schema2.serializers.FamilyAlleleParquetSerializer method) (gpf.parquet.schema2.serializers.SummaryAlleleParquetSerializer method) bold_red (gpf_web.default_settings.CustomFormatter attribute) broken (datasets_api.models.Dataset attribute) broken_families (gpf.pedigrees.families_data.FamiliesData property) browsable_figure_path() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method) browser (gpf.pheno.pheno_data.PhenotypeData property) Bucket (class in gpf.import_tools.import_tools) bucket_url (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute) BUFFER_MAXSIZE (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (gain.genomic_resources.genomic_position_table.table_tabix.TabixGenomicPositionTable attribute) build() (enrichment_api.enrichment_builder.EnrichmentBuilder method) (gain.annotation.record_to_annotatable.CSHLAlleleRecordToAnnotatable method) (gain.annotation.record_to_annotatable.DaeAlleleRecordToAnnotatable method) (gain.annotation.record_to_annotatable.RecordToAnnotable method) (gain.annotation.record_to_annotatable.RecordToCNVAllele method) (gain.annotation.record_to_annotatable.RecordToPosition method) (gain.annotation.record_to_annotatable.RecordToRegion method) (gain.annotation.record_to_annotatable.RecordToVcfAllele method) (gain.annotation.record_to_annotatable.VcfLikeRecordToVcfAllele method) (gpf.gpf_instance.gpf_instance.GPFInstance static method) (gpf.gpf_instance.GPFInstance static method) (gpf.pheno.graphs.GraphColumn static method) (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) build_aggregator() (in module gain.genomic_resources.aggregators) build_allele_record_dict() (gpf.parquet.schema2.serializers.AlleleParquetSerializer method) (gpf.parquet.schema2.serializers.FamilyAlleleParquetSerializer method) (gpf.parquet.schema2.serializers.SummaryAlleleParquetSerializer method) build_allele_score_annotator() (in module gain.annotation.score_annotator) build_and_query() (in module gain.genomic_resources.explore_grr_search) build_and_save() (gpf.pheno.pheno_data.PhenotypeData method) (gpf.studies.study.GenotypeData method) build_annotatable_from_dict() (in module gain.annotation.record_to_annotatable) build_annotation_filename() (in module gpf.inmemory_storage.annotation_serialization) build_annotation_pipeline() (gpf.import_tools.import_tools.ImportProject method) (in module gain.annotation.annotation_factory) build_annotator() (in module gain.annotation.debug_annotator) build_arguments_dict() (gpf.variants_loaders.raw.loader.CLILoader method) (gpf.variants_loaders.raw.loader.VariantsLoaderDecorator method) build_array_join() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect method) (gpf.query_variants.sql.schema2.base_query_builder.Dialect method) build_attribute_help() (gain.annotation.score_annotator.GenomicScoreAnnotatorBase method) build_backend() (gpf.genotype_storage.genotype_storage.GenotypeStorage method) build_batch() (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) build_blob_schema() (gpf.parquet.schema2.serializers.SummaryAlleleParquetSerializer class method) build_cache() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) build_chrom_mapping() (in module gain.genomic_resources.utils) build_chrom_mapping_annotator() (in module gain.annotation.chrom_mapping_annotator) build_cli_arguments() (gpf.variants_loaders.raw.loader.CLILoader class method) (gpf.variants_loaders.raw.loader.VariantsLoaderDecorator class method) build_cli_arguments_parser() (gpf.tools.liftover_tools.CNVLiftoverTool method) (gpf.tools.liftover_tools.DaeLiftoverTool method) (gpf.tools.liftover_tools.DenovoLiftoverTool method) (gpf.tools.liftover_tools.LiftoverTool method) (gpf.tools.liftover_tools.VCFLiftoverTool method) build_cli_genomic_context() (in module gain.annotation.annotate_utils) build_cnv_allele() (gpf.variants.core.Allele static method) build_cnv_collection_annotator() (in module gain.annotation.cnv_collection_annotator) build_coding_length_background() (in module gpf.enrichment_tool.build_coding_length_enrichment_background) build_collection() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection static method) (gpf.gene_sets.denovo_gene_set_helpers.DenovoGeneSetHelpers class method) build_config() (gpf.configuration.study_config_builder.StudyConfigBuilder method) build_configuration() (gpf.gene_profile.db.GeneProfileDBWriter class method) build_content_file() (gain.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) build_default_histogram_conf() (in module gain.genomic_resources.histogram) build_demo_graph() (in module gain.task_graph.demo_graphs_cli) build_descs_from_score() (gain.gene_scores.gene_scores.GeneScoresDb static method) build_effect_annotator() (gain.effect_annotation.cli.EffectAnnotatorBuilder method) (in module gain.annotation.effect_annotator) build_effect_types() (gain.effect_annotation.effect.EffectTypesMixin class method) build_effect_types_groups() (gain.effect_annotation.effect.EffectTypesMixin class method)

build_effect_types_list() (gain.effect_annotation.effect.EffectTypesMixin class method) build_empty_histogram() (in module gain.genomic_resources.histogram) build_enrichment_event_counts_cache() (in module gpf.enrichment_tool.enrichment_cache_builder) build_families_data() (in module gpf.pedigrees.testing) build_families_data_from_pedigree() (gpf.pedigrees.loader.FamiliesLoader static method) build_families_report() (in module gpf.tools.draw_pedigree) build_family() (in module gpf.pedigrees.testing) build_family_layout() (in module gpf.tools.draw_pedigree) build_family_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor method) build_family_schema() (in module gpf.parquet.schema2.serializers) build_family_variants_query() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) build_family_variants_query_runner() (gpf.duckdb_storage.duckdb2_variants.DuckDb2Variants method) (gpf.inmemory_storage.raw_variants.RawFamilyVariants method) (gpf.parquet_storage.storage.ParquetLoaderVariants method) (gpf.query_variants.base_query_variants.QueryVariants method) (gpf.query_variants.sql.schema2.base_variants.SqlSchema2Variants method) build_filesystem_test_protocol() (in module gain.genomic_resources.testing) build_filesystem_test_repository() (in module gain.genomic_resources.testing) build_filesystem_test_resource() (in module gain.genomic_resources.testing) build_from_config() (gpf.import_tools.import_tools.ImportProject static method) build_from_file() (gpf.import_tools.import_tools.ImportProject static method) build_fsspec_protocol() (in module gain.genomic_resources.fsspec_protocol) build_fts_query() (in module gain.genomic_resources.explore_grr_search) build_gene_models_from_file() (in module gain.genomic_resources.gene_models) (in module gain.genomic_resources.gene_models.gene_models_factory) build_gene_models_from_resource() (in module gain.genomic_resources.gene_models) (in module gain.genomic_resources.gene_models.gene_models_factory) build_gene_models_from_resource_id() (in module gain.genomic_resources.gene_models) (in module gain.genomic_resources.gene_models.gene_models_factory) build_gene_regions() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) build_gene_score_annotator() (in module gain.annotation.gene_score_annotator) build_gene_score_from_resource() (in module gain.gene_scores.gene_scores) build_gene_score_from_resource_id() (in module gain.gene_scores.gene_scores) build_gene_score_implementation_from_resource() (in module gain.gene_scores.implementations.gene_scores_impl) build_gene_set_annotator() (in module gain.annotation.gene_set_annotator) build_gene_set_collection_from_file() (in module gain.gene_sets.gene_set) build_gene_set_collection_from_resource() (in module gain.gene_sets.gene_set) build_gene_set_collection_from_resource_id() (in module gain.gene_sets.gene_set) build_gene_set_collection_implementation_from_resource() (in module gain.gene_sets.implementations.gene_sets_impl) build_gene_weights_enrichment_background() (in module gpf.enrichment_tool.resource_implementations.enrichment_resource_impl) build_genomic_position_table() (in module gain.genomic_resources.genomic_position_table) (in module gain.genomic_resources.genomic_position_table.utils) build_genomic_resource() (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) build_genomic_resource_group_repository() (in module gain.genomic_resources.repository_factory) build_genomic_resource_repository() (in module gain.genomic_resources.repository_factory) build_genomic_scores_registry() (gpf.genomic_scores.scores.GenomicScoresRegistry static method) build_genotype_data_all_datasets() (studies.study_wrapper.WDAEStudy static method) build_genotype_data_description() (studies.study_wrapper.WDAEAbstractStudy method) (studies.study_wrapper.WDAEStudy method) build_gtf_record() (in module gain.genomic_resources.gene_models.serialization) build_histogram_config() (in module gain.genomic_resources.histogram) build_http_test_protocol() (in module gain.genomic_resources.testing) build_id() (gpf.pedigrees.family_role_builder.Mating static method) build_import_project() (in module gpf.tools.simple_study_import) build_index_info() (gain.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) build_inmemory_protocol() (in module gain.genomic_resources.fsspec_protocol) build_inmemory_test_protocol() (in module gain.genomic_resources.testing) build_inmemory_test_repository() (in module gain.genomic_resources.testing) build_inmemory_test_resource() (in module gain.genomic_resources.testing) build_labels_query() (gain.annotation.annotation_config.AnnotationConfigParser static method) build_liftover_annotator() (in module gain.annotation.liftover_annotator) build_liftover_chain_from_resource() (in module gain.genomic_resources.liftover_chain) build_liftover_chain_from_resource_id() (in module gain.genomic_resources.liftover_chain) build_liftover_pipeline() (gpf.tools.liftover_tools.LiftoverTool method) build_local_resource() (in module gain.genomic_resources.fsspec_protocol) build_manifest() (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) build_normalize_allele_annotator() (in module gain.annotation.normalize_allele_annotator) build_not_query() (in module gain.genomic_resources.explore_grr_search) build_np_score_annotator() (in module gain.annotation.score_annotator) build_option() (gpf.variants_loaders.raw.loader.CLIArgument method) build_or_query() (in module gain.genomic_resources.explore_grr_search) build_output_path() (in module gain.annotation.annotate_utils) build_partitions() (in module gpf.gene_profile.generate_gene_profile) build_pheno_browser() (in module gpf.pheno.build_pheno_browser) build_phenotype_study() (gpf.pheno.storage.PhenotypeStorage method) build_pipeline_annotator() (in module gain.annotation.annotation_factory) build_position_allele() (gpf.variants.core.Allele static method) build_position_score_annotator() (in module gain.annotation.score_annotator) build_query() (gpf.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder method) build_rare_query() (in module gpf.gene_profile.generate_gene_profile) build_record_to_annotatable() (in module gain.annotation.record_to_annotatable) build_reference_genome_from_file() (in module gain.genomic_resources.reference_genome) build_reference_genome_from_resource() (in module gain.genomic_resources.reference_genome) build_reference_genome_from_resource_id() (in module gain.genomic_resources.reference_genome) build_regression() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method) build_report() (gpf.pheno.pheno_data.PhenotypeData method) (gpf.studies.study.GenotypeData method) build_report_description() (gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapter method) (pheno_tool_api.adapter.PhenoToolAdapter method) build_resource_file_state() (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) build_resource_implementation() (in module gain.genomic_resources.repository_factory) build_results() (enrichment_api.enrichment_builder.EnrichmentBuilder method) build_roles() (gpf.pedigrees.family_role_builder.FamilyRoleBuilder method) build_s3_test_bucket() (in module gain.genomic_resources.testing) build_s3_test_filesystem() (in module gain.genomic_resources.testing) build_s3_test_protocol() (in module gain.genomic_resources.testing) build_samocha_enrichment_background() (in module gpf.enrichment_tool.resource_implementations.enrichment_resource_impl) build_schema() (gpf.parquet.schema2.serializers.FamilyAlleleParquetSerializer class method) (gpf.parquet.schema2.serializers.SummaryAlleleParquetSerializer class method) (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) build_score_aggregator_documentation() (gain.annotation.score_annotator.AlleleScoreAnnotator method) (gain.annotation.score_annotator.GenomicScoreAnnotatorBase method) (gain.annotation.score_annotator.PositionScoreAnnotator method) build_score_from_resource() (in module gain.genomic_resources.genomic_scores) build_score_from_resource_id() (in module gain.genomic_resources.genomic_scores) build_score_implementation_from_resource() (in module gain.genomic_resources.implementations.genomic_scores_impl) build_serializer() (gpf.parquet.schema2.serializers.VariantsDataSerializer static method) build_simple_effect_annotator() (in module gain.annotation.simple_effect_annotator) build_statistics() (gain.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeStatistics static method) build_study_layout() (gpf.duckdb_storage.duckdb_genotype_storage.AbstractDuckDbStorage method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbParquetStorage method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3ParquetStorage method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3Storage method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbStorage method) build_summary_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor method) build_summary_schema() (in module gpf.parquet.schema2.serializers) build_summary_variants_query() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) build_summary_variants_query_runner() (gpf.duckdb_storage.duckdb2_variants.DuckDb2Variants method) (gpf.inmemory_storage.raw_variants.RawFamilyVariants method) (gpf.parquet_storage.storage.ParquetLoaderVariants method) (gpf.query_variants.base_query_variants.QueryVariants method) (gpf.query_variants.sql.schema2.base_variants.SqlSchema2Variants method) build_table() (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) build_table_name() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect method) (gpf.query_variants.sql.schema2.base_query_builder.Dialect method) build_values_categorical_distribution() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method) build_values_ordinal_distribution() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method) build_values_violinplot() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method) build_variant_row() (studies.response_transformer.ResponseTransformer method) (studies.study_wrapper.ResponseTransformerProtocol method) build_variant_types_query() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) build_vcf_allele() (gpf.variants.core.Allele static method)

C

cache() (gain.task_graph.cache.FileTaskCache method) (gain.task_graph.cache.NoTaskCache method) (gain.task_graph.cache.TaskCache method) CACHE_LOCK (gpf.pheno.registry.PhenoRegistry attribute) cache_pipeline_resources() (in module gain.annotation.annotate_utils) cache_resources() (in module gain.genomic_resources.cached_repository) CacheRecord (class in gain.task_graph.cache) CacheRecordType (class in gain.task_graph.cache) CacheResource (class in gain.genomic_resources.cached_repository) CachingProtocol (class in gain.genomic_resources.cached_repository) calc() (gpf.pheno_tool.tool.PhenoTool method) calc_alleles() (gpf.variants.family_variant.FamilyVariant static method) calc_alt_alleles() (gpf.variants.family_variant.FamilyVariant static method) calc_batched_heuristics() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) calc_bin_begin() (in module gain.utils.regions) calc_bin_end() (in module gain.utils.regions) calc_bin_index() (in module gain.utils.regions) calc_by_effect() (gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapter method) (gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapterBase method) (pheno_tool_api.adapter.PhenoToolAdapter method) calc_coding_bins() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) calc_enrichment_test() (enrichment_api.enrichment_helper.EnrichmentHelper method) (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground method) (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground method) (gpf.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground method) (gpf.enrichment_tool.samocha_background.SamochaEnrichmentBackground method) calc_expected_observed_pvalue() (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground static method) (gpf.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground static method) calc_family_bins() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) calc_frame_for_gtf_cds_feature() (in module gain.genomic_resources.gene_models.serialization) calc_frames() (gain.genomic_resources.gene_models.transcript_models.TranscriptModel method) (gain.genomic_resources.gene_models.TranscriptModel method) calc_frequency_bins() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) calc_heuristics() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) calc_info_hash() (gain.gene_scores.implementations.gene_scores_impl.GeneScoreImplementation method) (gain.gene_sets.implementations.gene_sets_impl.GeneSetCollectionImpl method) (gain.genomic_resources.implementations.annotation_pipeline_impl.AnnotationPipelineImplementation method) (gain.genomic_resources.implementations.gene_models_impl.GeneModelsImpl method) (gain.genomic_resources.implementations.genomic_scores_impl.CnvCollectionImplementation method) (gain.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation method) (gain.genomic_resources.implementations.liftover_chain_impl.LiftoverChainImplementation method) (gain.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeImplementation method) (gain.genomic_resources.resource_implementation.GenomicResourceImplementation method) (gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation method) calc_inheritance_trio() (gpf.variants.family_variant.FamilyAllele class method) calc_region_bins() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) calc_regression() (gpf.pheno.utils.lin_regress.LinearRegression method) calc_statistics_hash() (gain.gene_scores.implementations.gene_scores_impl.GeneScoreImplementation method) (gain.gene_sets.implementations.gene_sets_impl.GeneSetCollectionImpl method) (gain.genomic_resources.implementations.annotation_pipeline_impl.AnnotationPipelineImplementation method) (gain.genomic_resources.implementations.gene_models_impl.GeneModelsImpl method) (gain.genomic_resources.implementations.genomic_scores_impl.CnvCollectionImplementation method) (gain.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation method) (gain.genomic_resources.implementations.liftover_chain_impl.LiftoverChainImplementation method) (gain.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeImplementation method) (gain.genomic_resources.resource_implementation.GenomicResourceImplementation method) (gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation method) calc_variants() (gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapter method) (gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapterBase method) (pheno_tool_api.adapter.PhenoToolAdapter method) (pheno_tool_api.adapter.PhenoToolAdapterBase method) calculate_simple_best_state() (in module gpf.variants.family_variant) call_region() (gain.annotation.simple_effect_annotator.SimpleEffectAnnotator method) camelize_string() (in module gain.utils.helpers) can_extend() (gpf.pedigrees.pedigrees.Realization method) categorical (gpf.pheno.common.InferenceConfig attribute) (gpf.pheno.common.MeasureType attribute) categorical_attr() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) categorical_config (gpf.pheno.common.MeasureHistogramConfigs attribute) CategoricalHistogram (class in gain.genomic_resources.histogram) CategoricalHistogramConfig (class in gain.genomic_resources.histogram) CategoricalHistogramSchema (class in gain.gene_sets.gene_set) cds_intron_regions() (gain.annotation.simple_effect_annotator.SimpleEffectAnnotator method) cds_len() (gain.genomic_resources.gene_models.transcript_models.TranscriptModel method) (gain.genomic_resources.gene_models.TranscriptModel method) cds_regions() (gain.annotation.simple_effect_annotator.SimpleEffectAnnotator method) (gain.effect_annotation.annotation_request.BaseAnnotationRequest method) (gain.genomic_resources.gene_models.transcript_models.TranscriptModel method) (gain.genomic_resources.gene_models.TranscriptModel method) cds_to_dictlist() (genomes_api.views.GeneModels method) chain_tasks() (in module gain.task_graph.graph) change_password() (in module users_api.views) (users_api.models.WdaeUser static method) check_affected_dad_family() (in module gpf.pedigrees.family_tag_builder) check_affected_mom_family() (in module gpf.pedigrees.family_tag_builder) check_affected_prb_family() (in module gpf.pedigrees.family_tag_builder) check_affected_sib_family() (in module gpf.pedigrees.family_tag_builder) check_control_family() (in module gpf.pedigrees.family_tag_builder) check_denovo_trio() (gpf.variants.family_variant.FamilyAllele static method) CHECK_DONE_VERBOSITY (gpf.query_variants.query_runners.QueryResult attribute) check_family_tags_query() (in module gpf.pedigrees.family_tag_builder) check_female_prb_family() (in module gpf.pedigrees.family_tag_builder) check_for_repeated_attributes_in_annotator() (in module gain.annotation.annotation_factory) check_for_repeated_attributes_in_pipeline() (in module gain.annotation.annotation_factory) check_for_unused_parameters() (in module gain.annotation.annotation_factory) check_if_new_stop() (gain.effect_annotation.effect_checkers.frame_shift.FrameShiftEffectChecker method) check_inheritance_denovo_only() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) check_inheritance_query_value() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) check_male_prb_family() (in module gpf.pedigrees.family_tag_builder) check_mendelian_trio() (gpf.variants.family_variant.FamilyAllele static method) check_missing_dad_family() (in module gpf.pedigrees.family_tag_builder) check_missing_mom_family() (in module gpf.pedigrees.family_tag_builder) check_multiplex_family() (in module gpf.pedigrees.family_tag_builder) check_nuclear_family() (in module gpf.pedigrees.family_tag_builder) check_omission_trio() (gpf.variants.family_variant.FamilyAllele static method) check_quad_family() (in module gpf.pedigrees.family_tag_builder) check_roles_denovo_only() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) check_roles_query_value() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) check_simplex_family() (in module gpf.pedigrees.family_tag_builder) check_stop_codon() (gain.effect_annotation.effect_checkers.frame_shift.FrameShiftEffectChecker method) (gain.effect_annotation.effect_checkers.utr.UTREffectChecker method) check_tag() (in module gpf.pedigrees.family_tag_builder) check_trio_family() (in module gpf.pedigrees.family_tag_builder) check_unaffected_dad_family() (in module gpf.pedigrees.family_tag_builder) check_unaffected_mom_family() (in module gpf.pedigrees.family_tag_builder) check_unaffected_prb_family() (in module gpf.pedigrees.family_tag_builder) check_unaffected_sib_family() (in module gpf.pedigrees.family_tag_builder) check_update_manifest() (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) check_variant_types_value() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method) check_verif_code() (in module users_api.views) checkers (gpf.configuration.gpf_config_parser.GPFConfigValidator attribute) child (gpf.variants.attributes.Role attribute) children_set() (gpf.pedigrees.pedigrees.Individual method) (gpf.pedigrees.pedigrees.IndividualGroup method) (gpf.pedigrees.pedigrees.MatingUnit method) (gpf.pedigrees.pedigrees.SibshipUnit method) children_zygosity (gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute) ChildrenBySex (class in gpf.person_sets) (class in gpf.person_sets.person_sets) ChildrenStats (class in gpf.person_sets) (class in gpf.person_sets.person_sets) choose_bin_lin() (gain.genomic_resources.histogram.NumberHistogram method) choose_bin_log() (gain.genomic_resources.histogram.NumberHistogram method) chrom (gain.annotation.annotatable.Annotatable property) (gain.genomic_resources.genomic_position_table.Line attribute) (gain.genomic_resources.genomic_position_table.line.Line attribute) (gain.genomic_resources.genomic_position_table.line.LineBase attribute) CHROM (gain.genomic_resources.genomic_position_table.table.GenomicPositionTable attribute) (gain.genomic_resources.genomic_position_table.table_vcf.VCFGenomicPositionTable attribute) (gain.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) chrom (gain.genomic_resources.genomic_scores.CNV attribute) (gain.genomic_resources.genomic_scores.ScoreLine property) (gpf.variants.core.Allele property) (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) (gpf.variants.variant.SummaryVariant property) chrom_count (gain.genomic_resources.implementations.reference_genome_impl.GenomeStatistic property) chrom_key (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (gain.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) chrom_map (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (gain.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) chrom_order (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (gain.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) chrom_prefix (gain.genomic_resources.reference_genome.ReferenceGenome property) ChromMappingAnnotator (class in gain.annotation.chrom_mapping_annotator) chromosome (gain.annotation.annotatable.Annotatable property) (gpf.variants.core.Allele property) (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) (gpf.variants.variant.SummaryVariant property) chromosomes (gain.genomic_resources.reference_genome.ReferenceGenome property) (gpf.variants_loaders.cnv.loader.CNVLoader property) (gpf.variants_loaders.dae.loader.DaeTransmittedLoader property) (gpf.variants_loaders.dae.loader.DenovoLoader property) (gpf.variants_loaders.parquet.loader.ParquetLoader property) (gpf.variants_loaders.raw.loader.VariantsLoader property) (gpf.variants_loaders.raw.loader.VariantsLoaderDecorator property) (gpf.variants_loaders.vcf.loader.SingleVcfLoader property) (gpf.variants_loaders.vcf.loader.VcfLoader property) ChromosomeStatistic (class in gain.genomic_resources.implementations.reference_genome_impl) CHUNK_SIZE (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol attribute) clean() (users_api.forms.WdaeLoginForm method) clear() (datasets_api.models.DatasetHierarchy class method) (gain.genomic_resources.aggregators.Aggregator method) (gain.genomic_resources.genomic_position_table.line.LineBuffer method) (gain.genomic_resources.genomic_position_table.LineBuffer method) clear_registered_contexts() (in module gain.genomic_resources.genomic_context) clear_tags() (gpf.pedigrees.family_tag_builder.FamilyTagsBuilder method) cli() (in module gain.annotation.annotate_columns) (in module gain.annotation.annotate_doc) (in module gain.annotation.annotate_vcf) (in module gpf.enrichment_tool.build_coding_length_enrichment_background) (in module gpf.enrichment_tool.build_ur_synonymous_enrichment_background) (in module gpf.enrichment_tool.enrichment_cache_builder) (in module gpf.gpf_instance.adjustments.gpf_instance_adjustments) (in module gpf.parquet.schema2.annotate_schema2_parquet) (in module gpf.tools.reannotate_instance) (in module gpf_web.wgpf) cli_arguments() (gpf.variants_loaders.raw.loader.CLILoader class method) (gpf.variants_loaders.raw.loader.VariantsLoaderDecorator class method) (in module gpf.tools.simple_study_import) cli_browse() (in module gain.genomic_resources.cli) cli_cache_repo() (in module gpf.tools.grr_cache_repo) cli_columns() (in module gain.effect_annotation.cli) cli_defaults() (gpf.variants_loaders.raw.loader.CLILoader class method) (gpf.variants_loaders.raw.loader.VariantsLoaderDecorator class method) cli_export() (in module gpf.gene_profile.exporter) cli_manage() (in module gain.genomic_resources.cli) cli_vcf() (in module gain.effect_annotation.cli) CLIAnnotationContextProvider (class in gain.annotation.annotation_genomic_context_cli) CLIArgument (class in gpf.variants_loaders.raw.loader) CLIGenomicContextProvider (class in gain.genomic_resources.genomic_context_cli) CLIGenotypeStorageContextProvider (class in gpf.genotype_storage.genotype_storage_genomic_context_cli) CLILoader (class in gpf.variants_loaders.raw.loader) close() (gain.annotation.annotation_pipeline.AnnotationPipeline method) (gain.annotation.annotation_pipeline.Annotator method) (gain.annotation.annotation_pipeline.AnnotatorDecorator method) (gain.annotation.cnv_collection_annotator.CnvCollectionAnnotator method) (gain.annotation.effect_annotator.EffectAnnotatorAdapter method) (gain.annotation.liftover_annotator.AbstractLiftoverAnnotator method) (gain.annotation.normalize_allele_annotator.NormalizeAlleleAnnotator method) (gain.annotation.score_annotator.GenomicScoreAnnotatorBase method) (gain.effect_annotation.annotator.EffectAnnotator method) (gain.effect_annotation.cli.VariantColumnInputFile method) (gain.effect_annotation.cli.VariantColumnOutputFile method) (gain.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (gain.genomic_resources.gene_models.gene_models.GeneModels method) (gain.genomic_resources.gene_models.GeneModels method) (gain.genomic_resources.genomic_position_table.BigWigTable method) (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table.GenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table_bigwig.BigWigTable method) (gain.genomic_resources.genomic_position_table.table_inmemory.InmemoryGenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table_tabix.TabixGenomicPositionTable method) (gain.genomic_resources.genomic_scores.GenomicScore method) (gain.genomic_resources.liftover_chain.LiftoverChain method) (gain.genomic_resources.reference_genome.ReferenceGenome method) (gain.genomic_resources.repository.GenomicResourceProtocolRepo method) (gain.genomic_resources.repository.GenomicResourceRepo method) (gain.task_graph.dask_executor.DaskExecutor method) (gain.task_graph.executor.TaskGraphExecutor method) (gain.task_graph.logging.FsspecHandler method) (gain.task_graph.process_pool_executor.ProcessPoolTaskExecutor method) (gain.task_graph.sequential_executor.SequentialExecutor method) (gain.utils.debug_closing.closing method) (gain.utils.debug_closing.HasClose method) (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) (gpf.gpf_instance.adjustments.adjust_command.AdjustmentsCommand method) (gpf.parquet.schema2.loader.MultiReader method) (gpf.parquet.schema2.loader.Reader method) (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) (gpf.parquet.schema2.variants_parquet_writer.ContinuousParquetFileWriter method) (gpf.parquet.schema2.variants_parquet_writer.VariantsParquetWriter method) (gpf.pedigrees.families_data.FamiliesData method) (gpf.pheno.browser.PhenoBrowser method) (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.prepare_data.PreparePhenoBrowserBase method) (gpf.query_variants.query_runners.QueryResult method) (gpf.query_variants.query_runners.QueryRunner method) (gpf.studies.study.GenotypeData method) (gpf.variants_loaders.cnv.loader.CNVLoader method) (gpf.variants_loaders.dae.loader.DaeTransmittedLoader method) (gpf.variants_loaders.dae.loader.DenovoLoader method) (gpf.variants_loaders.parquet.loader.ParquetLoader method) (gpf.variants_loaders.raw.loader.VariantsLoader method) (gpf.variants_loaders.raw.loader.VariantsLoaderDecorator method) (gpf.variants_loaders.vcf.loader.SingleVcfLoader method) (gpf.variants_loaders.vcf.loader.VcfLoader method) (gpf.variants_loaders.vcf.serializer.VcfSerializer method) closing (class in gain.utils.debug_closing) CNV (class in gain.genomic_resources.genomic_scores) cnv (gpf.testing.import_helpers.StudyInputLayout attribute) (gpf.variants.core.Allele.Type attribute) CNV_FILTER_GRAMMAR (gain.annotation.cnv_collection_annotator.CnvCollectionAnnotator attribute) cnv_import() (in module gpf.testing.import_helpers) cnv_liftover_main() (in module gpf.tools.liftover_tools) cnv_study() (in module gpf.testing.import_helpers) cnv_variant_type() (in module gain.utils.cnv_utils) CNVAllele (class in gain.annotation.annotatable) CnvCollection (class in gain.genomic_resources.genomic_scores) CnvCollectionAnnotator (class in gain.annotation.cnv_collection_annotator) CnvCollectionImplementation (class in gain.genomic_resources.implementations.genomic_scores_impl) CNVLiftoverTool (class in gpf.tools.liftover_tools)

CNVLoader (class in gpf.variants_loaders.cnv.loader) coalesce() (in module gain.utils.regions) cod2aa() (gain.effect_annotation.annotation_request.BaseAnnotationRequest method) (gain.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) code_type (users_api.views.BasePasswordView attribute) (users_api.views.ResetPassword attribute) (users_api.views.SetPassword attribute) coding_bin (gpf.parquet.partition_descriptor.Partition attribute) coding_bins (gpf.query_variants.sql.schema2.sql_query_builder.QueryHeuristics attribute) coding_bins() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) CodingEffectChecker (class in gain.effect_annotation.effect_checkers.coding) CodonsAa (gain.effect_annotation.gene_codes.NuclearCode attribute) CodonsAaKeys (gain.effect_annotation.gene_codes.NuclearCode attribute) coercers (gpf.configuration.gpf_config_parser.GPFConfigValidator attribute) collapse() (in module gain.utils.regions) collapse_no_chrom() (in module gain.utils.regions) collect_all_resources() (gain.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) collect_child_configs() (gpf.pheno.prepare_data.PreparePhenoBrowserBase method) collect_denovo_events() (gpf.enrichment_tool.genotype_helper.GenotypeHelper static method) collect_directory_configs() (gpf.configuration.gpf_config_parser.GPFConfigParser class method) collect_dvc_entries() (in module gain.genomic_resources.cli) collect_expectations() (gpf.tools.gpf_validation_runner.MainRunner static method) collect_genotype_data_backgrounds() (enrichment_api.enrichment_helper.EnrichmentHelper method) collect_gtf_cds_regions() (in module gain.genomic_resources.gene_models.serialization) collect_gtf_start_codon_regions() (in module gain.genomic_resources.gene_models.serialization) collect_gtf_stop_codon_regions() (in module gain.genomic_resources.gene_models.serialization) collect_instruments() (in module gpf.pheno.pheno_import) collect_pedigree_parquet_schema() (in module gpf.parquet.parquet_writer) collect_person_collection_attributes() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) collect_resource_entries() (gain.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) collect_variant_counts() (in module gpf.gene_profile.generate_gene_profile) CollectionConfigsView (class in person_sets_api.views) CollectionDomainView (class in person_sets_api.views) collections_descriptions (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb property) (gpf.gene_sets.gene_sets_db.GeneSetsDb property) CollectionStatsView (class in person_sets_api.views) color (gpf.person_sets.person_sets.PersonSetConfig attribute) (gpf.person_sets.PersonSetConfig attribute) column (gain.annotation.annotation_config.ErrorMark attribute) column_counts() (in module gpf.pheno.graphs) column_name (gain.gene_scores.gene_scores.ScoreDef attribute) (gain.gene_scores.gene_scores.ScoreDesc attribute) (gpf.common_reports.denovo_report.EffectCell property) combine() (gpf.pedigrees.families_data.FamiliesData static method) (gpf.person_sets.person_sets.PersonSetCollection static method) (gpf.person_sets.PersonSetCollection static method) (gpf.variants.variant.VariantDesc static method) Command (class in users_api.management.commands.dataset_groups) (class in users_api.management.commands.datasets_export) (class in users_api.management.commands.datasets_restore) (class in users_api.management.commands.datasets_show) (class in users_api.management.commands.unlock_user) (class in users_api.management.commands.user_create) (class in users_api.management.commands.user_set_name) (class in users_api.management.commands.user_setpasswd) (class in users_api.management.commands.users_add) (class in users_api.management.commands.users_export) (class in users_api.management.commands.users_group_add) (class in users_api.management.commands.users_group_remove) (class in users_api.management.commands.users_remove) (class in users_api.management.commands.users_restore) (class in users_api.management.commands.users_show) common_report (gpf.pheno.common.StudyConfig attribute) common_reports_api module common_reports_api.common_reports_helper module common_reports_api.urls module common_reports_api.views module CommonReport (class in gpf.common_reports.common_report) CommonReportsHelper (class in common_reports_api.common_reports_helper) CommonStudyMixin (class in gpf.studies.study) complement() (gain.effect_annotation.annotation_request.NegativeStrandAnnotationRequest static method) (in module gain.utils.variant_utils) COMPLEX (gain.annotation.annotatable.Annotatable.Type attribute) complex (gpf.variants.core.Allele.Type attribute) compound() (gpf.query_variants.attribute_queries.AttributeQueryTransformerFunction method) (gpf.query_variants.attribute_queries.AttributeQueryTransformerSQL method) (gpf.query_variants.attribute_queries.AttributeQueryTransformerSQLLegacy method) (gpf.query_variants.attribute_queries.CompoundStripTransformer method) (gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method) CompoundStripTransformer (class in gpf.query_variants.attribute_queries) compute_md5_sum() (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) COMPUTED (gain.task_graph.cache.CacheRecordType attribute) ConcatAggregator (class in gain.genomic_resources.aggregators) config (studies.study_wrapper.WDAEAbstractStudy property) config_columns (studies.study_wrapper.WDAEAbstractStudy property) config_json() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) ConfigDumper (class in gpf.configuration.study_config_builder) ConfigurationView (class in gene_profiles_api.views) configure_argument_parser() (in module gain.annotation.annotate_doc) configure_task_logging() (in module gain.task_graph.logging) ConfigView (class in gene_view.views) confirm_login_allowed() (users_api.forms.WdaeLoginForm method) conftest module connect() (gpf.duckdb_storage.duckdb_connection_factory.DuckDbConnectionFactory method) (gpf.duckdb_storage.duckdb_genotype_storage.AbstractDuckDbStorage method) (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) connected_component() (in module gain.utils.regions) connected_components() (gpf.pedigrees.pedigrees.FamilyConnections method) construct_import_annotation_pipeline() (in module gpf.import_tools.import_tools) construct_import_annotation_pipeline_config() (in module gpf.import_tools.import_tools) containing_path() (in module gain.utils.fs_utils) contains() (gain.genomic_resources.gene_models.Exon method) (gain.genomic_resources.gene_models.transcript_models.Exon method) (gain.genomic_resources.genomic_position_table.line.LineBuffer method) (gain.genomic_resources.genomic_position_table.LineBuffer method) (gain.utils.regions.Region method) CONTENT_ID (gpf_instance.views.AboutDescriptionView attribute) (gpf_instance.views.DescriptionView attribute) (gpf_instance.views.MarkdownFileView attribute) context (gain.annotation.processing_pipeline.Annotation attribute) context_providers_add_argparser_arguments() (in module gain.genomic_resources.genomic_context) context_providers_init() (in module gain.genomic_resources.genomic_context) context_providers_init_with_argparser() (in module gain.genomic_resources.genomic_context) continuous (gpf.pheno.common.InferenceConfig attribute) (gpf.pheno.common.MeasureType attribute) ContinuousParquetFileWriter (class in gpf.parquet.schema2.parquet_io) (class in gpf.parquet.schema2.variants_parquet_writer) CONTROL (gpf.pedigrees.family.FamilyTag attribute) convert() (in module utils.streaming_response_util) convert_coordinate() (gain.genomic_resources.liftover_chain.LiftoverChain method) convert_size() (in module gain.utils.helpers) convert_to_float() (in module gpf.pheno.prepare.measure_classifier) convert_to_int() (in module gpf.pheno.prepare.measure_classifier) convert_to_numeric() (in module gpf.pheno.prepare.measure_classifier) convert_to_string() (in module gpf.pheno.prepare.measure_classifier) convert_to_tab_separated() (in module gain.genomic_resources.testing) Convertible (class in gpf.pheno.prepare.measure_classifier) copy() (gpf.pedigrees.families_data.FamiliesData method) (gpf.pedigrees.pedigrees.Realization method) (in module gain.utils.fs_utils) copy_graph() (in module gpf.pedigrees.pedigrees) copy_proto_genomic_resources() (in module gain.genomic_resources.testing) copy_resource() (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) copy_resource_file() (gain.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) count (gain.gene_sets.gene_set.GeneSet attribute) count_measures() (gpf.pheno.browser.PhenoBrowser method) (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.pheno_data.PhenotypeGroup method) (gpf.pheno.pheno_data.PhenotypeStudy method) count_total (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) count_unique_values (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) count_variant() (gpf.common_reports.denovo_report.EffectCell method) (gpf.common_reports.denovo_report.EffectRow method) (in module gpf.gene_profile.generate_gene_profile) count_with_values (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) count_without_values (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) CountAggregator (class in gain.genomic_resources.aggregators) counter() (gpf.tools.gpf_validation_runner.AbstractRunner method) (gpf.tools.gpf_validation_runner.MainRunner method) CounterAggregator (class in gain.genomic_resources.aggregators) CounterBase (class in gpf.enrichment_tool.event_counters) CountError CreatableSlugRelatedField (class in users_api.serializers) create() (gain.annotation.annotation_config.AttributeInfo static method) (gain.task_graph.cache.TaskCache static method) (groups_api.serializers.GroupCreateSerializer method) (groups_api.views.GroupsViewSet method) (users_api.models.BaseVerificationCode class method) (users_api.models.WdaeUserManager method) (users_api.serializers.DatasetSerializer method) (users_api.serializers.UserSerializer method) (users_api.views.UserViewSet method) create_aggregator() (in module gain.genomic_resources.aggregators) create_aggregator_definition() (in module gain.genomic_resources.aggregators) create_and_node() (in module gpf.query_variants.attribute_queries) create_annotation_request() (gain.effect_annotation.annotator.AnnotationRequestFactory static method) create_background() (enrichment_api.enrichment_helper.EnrichmentHelper method) create_browser() (gpf.pheno.pheno_data.PhenotypeData static method) create_browser_tables() (gpf.pheno.browser.PhenoBrowser static method) create_common_reports_helper() (in module common_reports_api.views) create_counter() (enrichment_api.enrichment_helper.EnrichmentHelper method) create_database_connection() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) (in module gpf.duckdb_storage.duckdb_storage_helpers) create_denovo_gene_set_spec() (in module gpf.gene_sets.denovo_gene_sets_config) create_df() (gpf.pheno_tool.tool.PhenoTool method) create_duckdb_tables() (in module gpf.duckdb_storage.duckdb_storage_helpers) create_effect() (gain.effect_annotation.effect.EffectFactory class method) (gain.effect_annotation.effect_checkers.frame_shift.FrameShiftEffectChecker method) (gain.effect_annotation.effect_checkers.promoter.PromoterEffectChecker method) (gain.effect_annotation.effect_checkers.utr.UTREffectChecker method) create_effect_details() (gain.effect_annotation.effect.AnnotationEffect method) create_effect_with_aa_change() (gain.effect_annotation.effect.EffectFactory class method) create_effect_with_prot_length() (gain.effect_annotation.effect.EffectFactory class method) create_effect_with_prot_pos() (gain.effect_annotation.effect.EffectFactory class method) create_effect_with_request() (gain.effect_annotation.effect.EffectFactory class method) create_effect_with_tm() (gain.effect_annotation.effect.EffectFactory class method) create_empty_collection() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection static method) create_enrichment_builder() (in module enrichment_api.views) create_enrichment_description() (enrichment_api.enrichment_builder.EnrichmentBuilder method) create_enrichment_helper() (in module enrichment_api.views) create_executor() (gain.task_graph.cli_tools.TaskGraphCli static method) create_gp_table() (gpf.gene_profile.db.GeneProfileDBWriter method) create_import_tasks() (in module gpf.pheno.pheno_import) create_intronic_effect() (gain.effect_annotation.effect.EffectFactory class method) create_intronic_non_coding_effect() (gain.effect_annotation.effect.EffectFactory class method) create_memory_connection() (in module gpf.duckdb_storage.duckdb_storage_helpers) create_negative_strand_effect() (gain.effect_annotation.effect_checkers.promoter.PromoterEffectChecker method) create_or_node() (in module gpf.query_variants.attribute_queries) create_parquet_scans_layout_from_layout() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage static method) create_parquet_scans_layout_relative() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) create_pheno_browser_helper() (in module pheno_browser_api.views) create_positive_strand_effect() (gain.effect_annotation.effect_checkers.promoter.PromoterEffectChecker method) create_reference_allele() (gpf.variants.variant.SummaryAllele static method) create_regions_from_genes() (in module gain.genomic_resources.gene_models.gene_models) create_relative_parquet_scans_layout() (in module gpf.duckdb_storage.duckdb_storage_helpers) create_runner() (gpf.genotype_storage.genotype_storage.GenotypeStorage method) create_s3_attach_db_clause() (in module gpf.duckdb_storage.duckdb_storage_helpers) create_s3_filesystem() (in module gpf.duckdb_storage.duckdb_storage_helpers) create_s3_secret_clause() (in module gpf.duckdb_storage.duckdb_storage_helpers) create_sandwich_instance() (gpf.pedigrees.pedigrees.FamilyConnections method) create_schema2_dataset_layout() (in module gpf.schema2_storage.schema2_layout) create_statistics_build_tasks() (gain.gene_scores.implementations.gene_scores_impl.GeneScoreImplementation method) (gain.gene_sets.implementations.gene_sets_impl.GeneSetCollectionImpl method) (gain.genomic_resources.implementations.annotation_pipeline_impl.AnnotationPipelineImplementation method) (gain.genomic_resources.implementations.gene_models_impl.GeneModelsImpl method) (gain.genomic_resources.implementations.genomic_scores_impl.CnvCollectionImplementation method) (gain.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation method) (gain.genomic_resources.implementations.liftover_chain_impl.LiftoverChainImplementation method) (gain.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeImplementation method) (gain.genomic_resources.resource_implementation.GenomicResourceImplementation method) (gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation method) create_study_parquet_tables_layout() (in module gpf.duckdb_storage.duckdb_storage_helpers) create_summary_runner() (gpf.genotype_storage.genotype_storage.GenotypeStorage method) create_superuser() (users_api.models.WdaeUserManager method) create_table() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) (gpf.pheno.common.ImportManifest static method) create_table_layout() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage static method) (in module gpf.duckdb_storage.duckdb_storage_helpers) create_table_partitioned() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) create_tables() (in module gpf.pheno.pheno_import) create_task() (gain.task_graph.graph.TaskGraph method) create_user() (users_api.models.WdaeUserManager method) create_utr_effect() (gain.effect_annotation.effect_checkers.utr.UTREffectChecker method) created_at (users_api.models.BaseVerificationCode attribute) (users_api.models.ResetPasswordCode attribute) (users_api.models.SetPasswordCode attribute) CriteriaFilter (class in gpf.person_filters.person_filters) criterias (gpf.gene_sets.denovo_gene_sets_config.DGSSpec attribute) cshl2cnv_variant() (in module gain.utils.cnv_utils) cshl2vcf_variant() (in module gain.utils.dae_utils) cshl_format() (in module gpf.variants.variant) cshl_location (gpf.variants.variant.SummaryAllele property) (gpf.variants.variant.SummaryVariant property) cshl_position (gpf.variants.variant.SummaryAllele property) cshl_variant (gpf.variants.variant.SummaryAllele property) (gpf.variants.variant.SummaryVariant property) cshl_variant_full (gpf.variants.variant.SummaryAllele property) (gpf.variants.variant.SummaryVariant property) CSHLAlleleRecordToAnnotatable (class in gain.annotation.record_to_annotatable) csrf_clear() (in module users_api.models) current_idx (gpf.parquet.schema2.loader.MultiReader property) (gpf.parquet.schema2.loader.Reader property) curve_p0() (gpf.pedigrees.layout.Line method) curve_p1() (gpf.pedigrees.layout.Line method) curve_p2() (gpf.pedigrees.layout.Line method) curve_p3() (gpf.pedigrees.layout.Line method) curve_y_at() (gpf.pedigrees.layout.Line method) curved (gpf.pedigrees.layout.Line property) custom_query_transformer() (in module studies.conftest) custom_response_transformer() (in module studies.conftest) custom_wgpf() (in module studies.conftest) custom_wgpf_module() (in module studies.conftest) CustomFormatter (class in gpf_web.default_settings)

D

dad (gpf.variants.attributes.Role attribute) dae (gpf.testing.import_helpers.StudyInputLayout attribute) dae2vcf_variant() (in module gain.utils.dae_utils) dae_import() (in module gpf.testing.import_helpers) dae_liftover_main() (in module gpf.tools.liftover_tools) dae_study() (in module gpf.testing.import_helpers) DaeAlleleRecordToAnnotatable (class in gain.annotation.record_to_annotatable) DaeLiftoverTool (class in gpf.tools.liftover_tools) DaeTransmittedFamiliesGenotypes (class in gpf.variants_loaders.dae.loader) DaeTransmittedLoader (class in gpf.variants_loaders.dae.loader) dangling() (gpf.pedigrees.pedigrees.Realization method) dangling_set() (gpf.pedigrees.pedigrees.Realization method) DaskExecutor (class in gain.task_graph.dask_executor) data (query_state_save.models.QueryState attribute) (users_api.models.GpUserState attribute) data_dictionary (gpf.pheno.common.PhenoImportConfig attribute) data_reset() (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) DataDictionaryConfig (class in gpf.pheno.common) Dataset (class in datasets_api.models) Dataset.DoesNotExist Dataset.MultipleObjectsReturned dataset_id (datasets_api.models.Dataset attribute) dataset_name (datasets_api.models.Dataset attribute) DatasetAccessRightsView (class in query_base.query_base) DatasetBaseMixin (class in users_api.management.commands.dataset_mixin) DatasetDescriptionView (class in datasets_api.views) DatasetHelpers (class in gpf.tools.dataset_helpers) DatasetHierarchy (class in datasets_api.models) DatasetHierarchy.DoesNotExist DatasetHierarchy.MultipleObjectsReturned DatasetHierarchyView (class in datasets_api.views) DatasetPedigreeView (class in datasets_api.views) DatasetPermissionsSingleView (class in datasets_api.views) DatasetPermissionsView (class in datasets_api.views) datasets() (in module conftest) datasets_api module datasets_api.migrations module datasets_api.migrations.0001_initial module datasets_api.migrations.0002_dataset_groups module datasets_api.migrations.0003_alter_dataset_options module datasets_api.migrations.0004_dataset_broken module datasets_api.migrations.0005_dataset_dataset_name module datasets_api.migrations.0006_datasethierarchy module datasets_api.migrations.0007_datasethierarchy_direct module datasets_api.migrations.0008_datasethierarchy_instance_id module datasets_api.models module datasets_api.permissions module datasets_api.urls module datasets_api.views module DatasetSerializer (class in users_api.serializers) DatasetView (class in datasets_api.views) date_joined (users_api.models.WdaeUser attribute) db (gpf.duckdb_storage.duckdb_storage_config.DuckDbConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (gpf.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute) Db2Layout (class in gpf.query_variants.sql.schema2.sql_query_builder) db_name (gpf.pheno.pheno_import.MeasureReport attribute) dd() (in module gain.gene_sets.gene_term) deauthenticate() (users_api.models.WdaeUser method) declared_fields (users_api.forms.WdaeLoginForm attribute) (users_api.forms.WdaePasswordForgottenForm attribute) (users_api.forms.WdaeRegisterPasswordForm attribute) (users_api.forms.WdaeResetPasswordForm attribute) decorate() (gain.annotation.annotation_pipeline.InputAnnotableAnnotatorDecorator static method) (gain.annotation.annotation_pipeline.ValueTransformAnnotatorDecorator static method) default (gain.annotation.annotation_config.AttributeInfo attribute) (gain.annotation.annotation_pipeline.AttributeDesc attribute) (gpf.person_sets.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.PersonSetCollectionConfig attribute) DEFAULT_AGGREGATOR_TYPE (gain.annotation.gene_score_annotator.GeneScoreAnnotator attribute) DEFAULT_COMPRESSION (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter attribute) (gpf.parquet.schema2.variants_parquet_writer.ContinuousParquetFileWriter attribute) default_config() (gain.genomic_resources.histogram.CategoricalHistogramConfig static method) (gain.genomic_resources.histogram.NullHistogramConfig static method) (gain.genomic_resources.histogram.NumberHistogramConfig static method) default_groups (datasets_api.models.Dataset property) default_setters (gpf.configuration.gpf_config_parser.GPFConfigValidator attribute) DefaultBox (class in gpf.configuration.gpf_config_parser) DefaultGeneModelsId (class in genomes_api.views) DefaultGenotypeStorage (class in gpf.gpf_instance.adjustments.gpf_instance_adjustments) DefaultRepositoryContextProvider (class in gain.genomic_resources.genomic_context) definition (gain.genomic_resources.repository.GenomicResourceRepo property) degree() (gpf.pedigrees.pedigrees.Realization method) del_loader_prefix() (gpf.import_tools.import_tools.ImportProject static method) delete() (users_api.views.FederationCredentials method) delete_resource_file() (gain.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) DeleteAttributesFromAWSBatchFilter (class in gain.annotation.processing_pipeline) DeleteAttributesFromAWSFilter (class in gain.annotation.processing_pipeline) DeleteAttributesFromVariantFilter (class in gpf.parquet.schema2.processing_pipeline) DeleteAttributesFromVariantsBatchFilter (class in gpf.parquet.schema2.processing_pipeline) delimiter (gpf.pheno.common.DataDictionaryConfig attribute) (gpf.pheno.common.InstrumentConfig attribute) (gpf.pheno.common.InstrumentDictionaryConfig attribute) (gpf.pheno.common.PhenoImportConfig attribute) (gpf.pheno.pheno_import.ImportInstrument attribute) denovo (gpf.testing.import_helpers.StudyInputLayout attribute) (gpf.variants.attributes.Inheritance attribute) (gpf.variants.attributes.TransmissionType attribute) denovo_gene_sets_db (gpf.gpf_instance.gpf_instance.GPFInstance property) (gpf.gpf_instance.GPFInstance property) denovo_gene_sets_types (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb property) denovo_import() (in module gpf.testing.import_helpers) denovo_liftover_main() (in module gpf.tools.liftover_tools) denovo_study() (in module gpf.testing.import_helpers) DenovoFamiliesGenotypes (class in gpf.variants_loaders.dae.loader) DenovoGeneSetCollection (class in gpf.gene_sets.denovo_gene_set_collection) DenovoGeneSetHelpers (class in gpf.gene_sets.denovo_gene_set_helpers) DenovoGeneSetsConfig (class in gpf.gene_sets.denovo_gene_sets_config) DenovoGeneSetsDb (class in gene_sets.views) (class in gpf.gene_sets.denovo_gene_sets_db) DenovoGeneSetsTypesView (class in gene_sets.views) DenovoLiftoverTool (class in gpf.tools.liftover_tools) DenovoLoader (class in gpf.variants_loaders.dae.loader) DenovoReport (class in gpf.common_reports.denovo_report) DenovoReportTable (class in gpf.common_reports.denovo_report) dependencies (datasets_api.migrations.0001_initial.Migration attribute) (datasets_api.migrations.0002_dataset_groups.Migration attribute) (datasets_api.migrations.0003_alter_dataset_options.Migration attribute) (datasets_api.migrations.0004_dataset_broken.Migration attribute) (datasets_api.migrations.0005_dataset_dataset_name.Migration attribute) (datasets_api.migrations.0006_datasethierarchy.Migration attribute) (datasets_api.migrations.0007_datasethierarchy_direct.Migration attribute) (datasets_api.migrations.0008_datasethierarchy_instance_id.Migration attribute) (query_state_save.migrations.0001_initial.Migration attribute) (query_state_save.migrations.0002_auto_20190205_0736.Migration attribute) (query_state_save.migrations.0003_querystate_origin_querystate_timestamp.Migration attribute) (user_queries.migrations.0001_initial.Migration attribute) (users_api.migrations.0001_initial.Migration attribute) (users_api.migrations.0002_auto_20190424_0751.Migration attribute) (users_api.migrations.0003_authenticationlog.Migration attribute) (users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more.Migration attribute) (users_api.migrations.0005_gpuserstate.Migration attribute)

deps (gain.task_graph.graph.TaskDesc attribute) desc (gain.gene_sets.gene_set.GeneSet attribute) (gain.genomic_resources.genomic_scores.ScoreDef attribute) descendant (datasets_api.models.Dataset attribute) (datasets_api.models.DatasetHierarchy attribute) descendant_id (datasets_api.models.DatasetHierarchy attribute) description (gain.annotation.annotation_config.AnnotationPreamble attribute) (gain.annotation.annotation_config.AttributeInfo attribute) (gain.annotation.annotation_config.RawPreamble attribute) (gain.annotation.annotation_pipeline.AttributeDesc attribute) (gain.gene_scores.gene_scores.ScoreDef attribute) (gain.gene_scores.gene_scores.ScoreDesc attribute) (gain.gene_sets.gene_set.MetaSchema attribute) (gain.gene_sets.gene_term.GeneInfo attribute) (gain.genomic_resources.statistics.base_statistic.Statistic attribute) (gpf.genomic_scores.scores.ScoreDesc attribute) (gpf.studies.study.CommonStudyMixin property) (groups_api.views.GroupsViewSet attribute) (studies.study_wrapper.WDAEAbstractStudy property) (studies.study_wrapper.WDAEStudy property) (user_queries.models.UserQuery attribute) (users_api.views.UserViewSet attribute) description_column (gpf.pheno.common.DataDictionaryConfig attribute) (gpf.pheno.common.InstrumentDictionaryConfig attribute) DescriptionView (class in gpf_instance.views) deselected_family_tags (gpf.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute) deserialize() (gain.genomic_resources.histogram.CategoricalHistogram static method) (gain.genomic_resources.histogram.NullHistogram static method) (gain.genomic_resources.histogram.NumberHistogram static method) (gain.genomic_resources.implementations.gene_models_impl.GeneModelsStatistics static method) (gain.genomic_resources.implementations.reference_genome_impl.ChromosomeStatistic static method) (gain.genomic_resources.implementations.reference_genome_impl.GenomeStatistic static method) (gain.genomic_resources.statistics.base_statistic.Statistic static method) (gain.genomic_resources.statistics.min_max.MinMaxValue static method) deserialize_family_record() (gpf.parquet.schema2.serializers.JsonVariantsDataSerializer method) (gpf.parquet.schema2.serializers.VariantsDataSerializer method) deserialize_family_variant() (gpf.query_variants.base_query_variants.QueryVariantsBase method) deserialize_summary_record() (gpf.parquet.schema2.serializers.JsonVariantsDataSerializer method) (gpf.parquet.schema2.serializers.VariantsDataSerializer method) deserialize_summary_variant() (gpf.query_variants.base_query_variants.QueryVariantsBase method) destination (gpf.pheno.common.PhenoImportConfig attribute) DestinationConfig (class in gpf.pheno.common) destroy() (users_api.views.UserViewSet method) detail (groups_api.views.GroupsViewSet attribute) (users_api.views.UserViewSet attribute) details (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.variant.SummaryAllele property) (gpf.variants.variant.SummaryVariant property) determine_destination() (in module gpf.pheno.pheno_import) determine_histogram_type() (in module gpf.pheno.prepare.measure_classifier) DGSCQuery (class in gpf.gene_sets.denovo_gene_sets_config) DGSSpec (class in gpf.gene_sets.denovo_gene_sets_config) Dialect (class in gpf.query_variants.sql.schema2.base_query_builder) DictAggregator (class in gain.genomic_resources.aggregators) dictionary (gpf.pheno.common.InstrumentDescriptionsConfig attribute) (gpf.pheno.common.MeasureDescriptionsConfig attribute) diff() (gpf.pedigrees.family.Person method) difference() (in module gain.utils.regions) direct (datasets_api.models.DatasetHierarchy attribute) directory (gain.gene_sets.gene_set.GeneSetResourceSchema attribute) disable_study_config() (gpf.tools.dataset_helpers.DatasetHelpers method) display_name (gpf.pheno.common.RegressionMeasure attribute) (gpf.variants.attributes.Role property) DISPLAY_NAME_TYPE (gpf.variants.core.Allele attribute) display_values (gain.genomic_resources.histogram.CategoricalHistogram property) displayed_values_count (gain.gene_sets.gene_set.CategoricalHistogramSchema attribute) (gain.gene_sets.gene_set.NumericHistogramSchema attribute) (gain.genomic_resources.histogram.CategoricalHistogramConfig attribute) displayed_values_percent (gain.gene_sets.gene_set.CategoricalHistogramSchema attribute) (gain.genomic_resources.histogram.CategoricalHistogramConfig attribute) do_annotate_variant() (gain.effect_annotation.annotator.EffectAnnotator method) do_measure_build() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method) do_study_config() (gpf.duckdb_storage.duckdb_import_storage.AbstractDuckDbImportStorage class method) DockerAnnotator (class in gain.annotation.docker_annotator) documentation (gain.annotation.annotation_config.AnnotatorInfo attribute) (gain.annotation.annotation_config.AttributeInfo property) domain (gpf.person_sets.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.PersonSetCollectionConfig attribute) (gpf.pheno.pheno_data.Measure property) domain_json() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) DOWNLOAD_LIMIT (gene_view.views.DownloadSummaryVariantsView attribute) (genotype_browser.views.GenotypeBrowserQueryDownloadView attribute) DownloadSummaryVariantsView (class in gene_view.views) draw() (gpf.pedigrees.drawing.OffsetLayoutDrawer method) draw_categorical_violin_distribution() (in module gpf.pheno.graphs) draw_families() (in module gpf.tools.draw_pedigree) draw_families_report() (in module gpf.tools.draw_pedigree) draw_linregres() (in module gpf.pheno.graphs) draw_measure_violinplot() (in module gpf.pheno.graphs) draw_ordinal_violin_distribution() (in module gpf.pheno.graphs) draw_pedigree() (in module gpf.tools.draw_pedigree) drop_gp_table() (gpf.gene_profile.db.GeneProfileDBWriter method) DuckDb2Runner (class in gpf.duckdb_storage.duckdb2_variants) DuckDb2Variants (class in gpf.duckdb_storage.duckdb2_variants) duckdb_connect() (in module gpf.duckdb_storage.duckdb_legacy_genotype_storage) duckdb_parquet_storage_factory() (in module gpf.duckdb_storage.duckdb_genotype_storage) duckdb_s3_parquet_storage_factory() (in module gpf.duckdb_storage.duckdb_genotype_storage) duckdb_s3_storage_factory() (in module gpf.duckdb_storage.duckdb_genotype_storage) duckdb_storage_factory() (in module gpf.duckdb_storage.duckdb_genotype_storage) DuckDbBaseConf (class in gpf.duckdb_storage.duckdb_storage_config) DuckDbConf (class in gpf.duckdb_storage.duckdb_storage_config) DuckDbConnectionFactory (class in gpf.duckdb_storage.duckdb_connection_factory) DuckDbImportStorage (class in gpf.duckdb_storage.duckdb_import_storage) DuckDbLegacyImportStorage (class in gpf.duckdb_storage.duckdb_import_storage) DuckDbLegacyStorage (class in gpf.duckdb_storage.duckdb_legacy_genotype_storage) DuckDbParquetConf (class in gpf.duckdb_storage.duckdb_storage_config) DuckDbParquetImportStorage (class in gpf.duckdb_storage.duckdb_import_storage) DuckDbParquetStorage (class in gpf.duckdb_storage.duckdb_genotype_storage) DuckDbQueryDialect (class in gpf.duckdb_storage.duckdb_variants) DuckDbRunner (class in gpf.duckdb_storage.duckdb_variants) DuckDbS3Conf (class in gpf.duckdb_storage.duckdb_storage_config) DuckDbS3ImportStorage (class in gpf.duckdb_storage.duckdb_import_storage) DuckDbS3ParquetConf (class in gpf.duckdb_storage.duckdb_storage_config) DuckDbS3ParquetImportStorage (class in gpf.duckdb_storage.duckdb_import_storage) DuckDbS3ParquetStorage (class in gpf.duckdb_storage.duckdb_genotype_storage) DuckDbS3Storage (class in gpf.duckdb_storage.duckdb_genotype_storage) DuckDbStorage (class in gpf.duckdb_storage.duckdb_genotype_storage) DuckDbVariants (class in gpf.duckdb_storage.duckdb_variants)

E

effect (gpf.enrichment_tool.genotype_helper.GeneEffect attribute) effect_gene_symbols (gpf.variants.variant.SummaryAllele property) (gpf.variants.variant.SummaryVariant property) effect_genes (gpf.enrichment_tool.genotype_helper.AlleleEvent attribute) (gpf.variants.variant.SummaryAllele property) EFFECT_GROUPS (gain.effect_annotation.effect.EffectTypesMixin attribute) effect_severity() (gain.effect_annotation.effect.AnnotationEffect class method) effect_type (gain.annotation.simple_effect_annotator.SimpleEffect attribute) EFFECT_TYPES (gain.effect_annotation.effect.EffectTypesMixin attribute) effect_types (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) (gpf.variants.variant.SummaryAllele property) (gpf.variants.variant.SummaryVariant property) effect_types() (gain.annotation.simple_effect_annotator.SimpleEffectAnnotator static method) (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) EFFECT_TYPES_MAPPING (gain.effect_annotation.effect.EffectTypesMixin attribute) EFFECT_TYPES_UI_NAMING (gain.effect_annotation.effect.EffectTypesMixin attribute) EffectAnnotator (class in gain.effect_annotation.annotator) EffectAnnotatorAdapter (class in gain.annotation.effect_annotator) EffectAnnotatorBuilder (class in gain.effect_annotation.cli) EffectCell (class in gpf.common_reports.denovo_report) EffectChecker (class in gain.effect_annotation.effect_checkers.effect_checker) EffectFactory (class in gain.effect_annotation.effect) EffectGene (class in gain.effect_annotation.effect) EffectRow (class in gpf.common_reports.denovo_report) effects (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (gpf.gene_sets.denovo_gene_sets_config.EffectsCriteria attribute) (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.variant.SummaryAllele property) (gpf.variants.variant.SummaryVariant property) effects_description() (gain.effect_annotation.effect.AnnotationEffect class method) EffectsCriteria (class in gpf.gene_sets.denovo_gene_sets_config) EffectTranscript (class in gain.effect_annotation.effect) EffectTypesMixin (class in gain.effect_annotation.effect) email (users_api.models.AuthenticationLog attribute) (users_api.models.WdaeUser attribute) email_user() (users_api.models.WdaeUser method) empty() (gain.task_graph.graph.TaskGraph method) enabled (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) EnableDisableStudies (class in gpf.gpf_instance.adjustments.gpf_instance_adjustments) end (gain.utils.regions.BedRegion property) (gain.utils.regions.Region property) (gpf.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.SingleCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.TripleCriteria attribute) end_position (gain.annotation.annotatable.Annotatable property) (gpf.variants.core.Allele property) (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) (gpf.variants.variant.SummaryVariant property) endpoint_url (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute) enforce_csrf() (utils.authentication.SessionAuthenticationWithoutCSRF method) enforce_type (gain.gene_sets.gene_set.CategoricalHistogramSchema attribute) (gain.genomic_resources.histogram.CategoricalHistogramConfig attribute) enrichment_api module enrichment_api.enrichment_builder module enrichment_api.enrichment_helper module enrichment_api.enrichment_serializer module

enrichment_api.urls module enrichment_api.views module enrichment_cache_path (studies.study_wrapper.WDAEAbstractStudy property) enrichment_config (studies.study_wrapper.WDAEAbstractStudy property) enrichment_grr() (in module conftest) enrichment_test() (enrichment_api.enrichment_builder.BaseEnrichmentBuilder method) (enrichment_api.enrichment_builder.EnrichmentBuilder method) EnrichmentBackgroundResourceImplementation (class in gpf.enrichment_tool.resource_implementations.enrichment_resource_impl) EnrichmentBuilder (class in enrichment_api.enrichment_builder) EnrichmentHelper (class in enrichment_api.enrichment_helper) EnrichmentModelsView (class in enrichment_api.views) EnrichmentResult (class in gpf.enrichment_tool.event_counters) EnrichmentSerializer (class in enrichment_api.enrichment_serializer) EnrichmentSingleResult (class in gpf.enrichment_tool.event_counters) EnrichmentTestView (class in enrichment_api.views) ensure_log_dir() (in module gain.task_graph.logging) entries_to_delete (gain.genomic_resources.repository.ManifestUpdate attribute) entries_to_update (gain.genomic_resources.repository.ManifestUpdate attribute) error (gain.task_graph.cache.CacheRecord property) ERROR (gain.task_graph.cache.CacheRecordType attribute) (gpf.tools.gpf_validation_runner.TestStatus attribute) error_case_count (gpf.tools.gpf_validation_runner.AbstractRunner property) error_mark (gain.annotation.annotation_config.AnnotationConfigurationError attribute) error_messages (users_api.forms.WdaeLoginForm attribute) (users_api.forms.WdaeResetPasswordForm attribute) ErrorMark (class in gain.annotation.annotation_config) errors_case_count (gpf.tools.gpf_validation_runner.MainRunner property) escape_char() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method) (gpf.query_variants.sql.schema2.base_query_builder.Dialect static method) escape_quote_char() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method) (gpf.query_variants.sql.schema2.base_query_builder.Dialect static method) event_counts() (gpf.enrichment_tool.event_counters.CounterBase method) EventCountersResult (class in gpf.enrichment_tool.event_counters) events() (gpf.enrichment_tool.event_counters.CounterBase method) (gpf.enrichment_tool.event_counters.EventsCounter method) (gpf.enrichment_tool.event_counters.GeneEventsCounter method) EventsCounter (class in gpf.enrichment_tool.event_counters) EventsResult (class in gpf.enrichment_tool.event_counters) execute() (gain.task_graph.base_executor.TaskGraphExecutorBase method) (gain.task_graph.executor.TaskGraphExecutor method) (gpf.gpf_instance.adjustments.adjust_command.AdjustmentsCommand method) (gpf.gpf_instance.adjustments.adjust_duckdb_storage.AdjustDuckDbStorageCommand method) (gpf.gpf_instance.adjustments.adjust_impala_storage.AdjustImpalaStorageCommand method) (gpf.gpf_instance.adjustments.gpf_instance_adjustments.DefaultGenotypeStorage method) (gpf.gpf_instance.adjustments.gpf_instance_adjustments.EnableDisableStudies method) (gpf.gpf_instance.adjustments.gpf_instance_adjustments.InstanceIdCommand method) execute_grr_search() (in module gain.genomic_resources.explore_grr_search) exists() (in module gain.utils.fs_utils) Exon (class in gain.genomic_resources.gene_models) (class in gain.genomic_resources.gene_models.transcript_models) exon_to_dict() (genomes_api.views.GeneModels method) expand_effect_types() (in module gain.effect_annotation.effect) expand_gene_set() (in module utils.expand_gene_set) expand_gene_syms() (in module utils.expand_gene_set) ExportUsersBase (class in users_api.management.commands.export_base) extend() (gpf.pedigrees.pedigrees.Realization method) extract_person_set_collection_query() (studies.query_transformer.QueryTransformer method) (studies.study_wrapper.QueryTransformerProtocol method) extract_tasks() (gain.task_graph.graph.TaskGraph method)

F

F (gpf.variants.attributes.Sex attribute) FAIL (gpf.tools.gpf_validation_runner.TestStatus attribute) failed_attempt (users_api.models.AuthenticationLog attribute) failed_case_count (gpf.tools.gpf_validation_runner.AbstractRunner property) (gpf.tools.gpf_validation_runner.MainRunner property) families (gpf.pheno.pheno_data.PhenotypeData property) (gpf.pheno.pheno_data.PhenotypeGroup property) (gpf.pheno.pheno_data.PhenotypeStudy property) (gpf.query_variants.base_query_variants.QueryVariants property) (gpf.studies.study.GenotypeData property) (gpf.studies.study.GenotypeDataGroup property) (gpf.studies.study.GenotypeDataStudy property) (studies.study_wrapper.WDAEAbstractStudy property) families_of_persons() (gpf.pedigrees.families_data.FamiliesData method) FamiliesData (class in gpf.pedigrees.families_data) FamiliesDataDownloadView (class in common_reports_api.views) FamiliesGenotypes (class in gpf.variants_loaders.raw.loader) FamiliesGroupCounters (class in gpf.common_reports.family_counter) FamiliesLoader (class in gpf.pedigrees.loader) FamiliesReport (class in gpf.common_reports.family_report) Family (class in gpf.pedigrees.family) family (gpf.common_reports.family_counter.FamilyCounter property) (gpf.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute) (gpf.schema2_storage.schema2_layout.Schema2DatasetLayout attribute) family_allele_indexes (gpf.variants.family_variant.FamilyVariant property) family_alleles (gpf.variants.family_variant.FamilyVariant property) family_alt_alleles (gpf.variants.family_variant.FamilyVariant property) family_api module family_api.urls module family_api.views module family_attributes (gpf.variants.family_variant.FamilyAllele property) family_base() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) family_best_state (gpf.variants.family_variant.FamilyVariant property) family_bin (gpf.parquet.partition_descriptor.Partition attribute) (gpf.pedigrees.family.Person property) FAMILY_BIN_HEURISTIC_CUTOFF (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase attribute) family_bins (gpf.query_variants.sql.schema2.sql_query_builder.QueryHeuristics attribute) family_bins() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) FAMILY_COLUMNS (gpf.parquet.schema2.loader.ParquetLoader attribute) family_genotype (gpf.variants.family_variant.FamilyVariant property) family_genotype_iterator() (gpf.variants_loaders.dae.loader.DaeTransmittedFamiliesGenotypes method) (gpf.variants_loaders.dae.loader.DenovoFamiliesGenotypes method) (gpf.variants_loaders.raw.loader.FamiliesGenotypes method) (gpf.variants_loaders.vcf.loader.VcfFamiliesGenotypes method) family_id (gpf.enrichment_tool.genotype_helper.VariantEvent attribute) (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) family_ids() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) family_index (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) family_partition() (gpf.parquet.partition_descriptor.PartitionDescriptor method) family_partition_schema() (gpf.parquet.partition_descriptor.PartitionDescriptor method) family_query() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) family_variant_filter_function() (gpf.inmemory_storage.raw_variants.RawFamilyVariants class method) family_variants (gpf.variants_loaders.raw.loader.FullVariant attribute) family_variants() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) family_variants_iterator() (gpf.inmemory_storage.raw_variants.RawFamilyVariants method) (gpf.variants_loaders.raw.loader.VariantsLoader method) FamilyAllele (class in gpf.variants.family_variant) FamilyAlleleParquetSerializer (class in gpf.parquet.schema2.serializers) FamilyConnections (class in gpf.pedigrees.pedigrees) FamilyCounter (class in gpf.common_reports.family_counter) FamilyCounterDownloadView (class in common_reports_api.views) FamilyCounterListView (class in common_reports_api.views) FamilyDetailsView (class in family_api.views) FamilyFilter (class in gpf.person_filters) (class in gpf.person_filters.person_filters) FamilyQueryBuilder (class in gpf.query_variants.sql.schema2.family_builder) FamilyRoleBuilder (class in gpf.pedigrees.family_role_builder) FamilyTag (class in gpf.pedigrees.family) FamilyTagsBuilder (class in gpf.pedigrees.family_tag_builder) FamilyVariant (class in gpf.variants.family_variant) favicon() (in module gpfjs.views) fchrom (gain.genomic_resources.genomic_position_table.Line attribute) (gain.genomic_resources.genomic_position_table.line.Line attribute) (gain.genomic_resources.genomic_position_table.line.LineBase attribute) FederationCredentials (class in users_api.views) FederationDatasetsView (class in datasets_api.views) female (gpf.enrichment_tool.event_counters.EnrichmentResult attribute) (gpf.enrichment_tool.event_counters.EventCountersResult attribute) (gpf.enrichment_tool.event_counters.EventsResult attribute) (gpf.enrichment_tool.event_counters.VariantEventsResult attribute) (gpf.person_sets.ChildrenBySex attribute) (gpf.person_sets.ChildrenStats attribute) (gpf.person_sets.person_sets.ChildrenBySex attribute) (gpf.person_sets.person_sets.ChildrenStats attribute) (gpf.variants.attributes.Sex attribute) FEMALE_PRB (gpf.pedigrees.family.FamilyTag attribute) females_count() (gpf.pheno.graphs.GraphColumn method) fetch() (gain.genomic_resources.genomic_position_table.line.LineBuffer method) (gain.genomic_resources.genomic_position_table.LineBuffer method) (gain.genomic_resources.reference_genome.ReferenceGenome method) (gain.utils.processing_pipeline.Source method) (gpf.parquet.schema2.processing_pipeline.Schema2SummaryVariantsBatchSource method) (gpf.parquet.schema2.processing_pipeline.Schema2SummaryVariantsSource method) (gpf.parquet.schema2.processing_pipeline.VariantsLoaderBatchSource method) (gpf.parquet.schema2.processing_pipeline.VariantsLoaderSource method) (gpf.variants_loaders.raw.loader.VariantsLoader method) fetch_annotation() (gpf.duckdb_storage.duckdb2_variants.DuckDb2Variants method) fetch_cnvs() (gain.genomic_resources.genomic_scores.CnvCollection method) fetch_family_variants() (gpf.parquet.schema2.loader.ParquetLoader method) (gpf.variants_loaders.raw.loader.VariantsLoader method) fetch_region() (gain.genomic_resources.genomic_scores.AlleleScore method) (gain.genomic_resources.genomic_scores.PositionScore method) fetch_region_values() (gain.genomic_resources.genomic_scores.AlleleScore method) (gain.genomic_resources.genomic_scores.CnvCollection method) (gain.genomic_resources.genomic_scores.GenomicScore method) (gain.genomic_resources.genomic_scores.PositionScore method) fetch_scores() (gain.genomic_resources.genomic_scores.AlleleScore method) (gain.genomic_resources.genomic_scores.PositionScore method) fetch_scores_agg() (gain.genomic_resources.genomic_scores.AlleleScore method) (gain.genomic_resources.genomic_scores.PositionScore method) fetch_summary_variants() (gpf.parquet.schema2.loader.ParquetLoader method) (gpf.variants_loaders.raw.loader.VariantsLoader method) fetch_variants() (gpf.parquet.schema2.loader.ParquetLoader method) fgt2str() (in module gpf.utils.variant_utils) fields (groups_api.serializers.GroupCreateSerializer.Meta attribute) (groups_api.serializers.GroupRetrieveSerializer.Meta attribute) (groups_api.serializers.GroupSerializer.Meta attribute) (query_state_save.serializers.QueryStateSerializer.Meta attribute) (users_api.serializers.UserSerializer.Meta attribute) (users_api.serializers.UserWithoutEmailSerializer.Meta attribute) figure_filepath() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method) file_exists() (gain.genomic_resources.cached_repository.CachingProtocol method) (gain.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (gain.genomic_resources.repository.GenomicResource method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) filename (gain.gene_sets.gene_set.GeneSetResourceSchema attribute) (gain.genomic_resources.repository.ResourceFileState attribute) (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentResourceBackground property) (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property) files (gain.gene_scores.gene_scores.GeneScore property) (gain.gene_sets.gene_set.GeneSetCollection property) (gain.genomic_resources.implementations.annotation_pipeline_impl.AnnotationPipelineImplementation property) (gain.genomic_resources.implementations.gene_models_impl.GeneModelsImpl property) (gain.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation property) (gain.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeImplementation property) (gain.genomic_resources.liftover_chain.LiftoverChain property) (gain.genomic_resources.resource_implementation.GenomicResourceImplementation property) (gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation property) (gpf.pheno.common.InstrumentDescriptionsConfig attribute) (gpf.pheno.common.MeasureDescriptionsConfig attribute) (gpf.pheno.pheno_import.ImportInstrument attribute) FileTaskCache (class in gain.task_graph.cache) filetype_parsers (gpf.configuration.gpf_config_parser.GPFConfigParser attribute) fill_family_bins() (in module gpf.parquet.parquet_writer) fill_query_parameters() (in module gain.utils.sql_utils) Filter (class in gain.utils.processing_pipeline) filter() (gain.annotation.processing_pipeline.AnnotationsWithSourceBatchFilter method) (gain.annotation.processing_pipeline.AnnotationsWithSourceFilter method) (gain.annotation.processing_pipeline.DeleteAttributesFromAWSBatchFilter method) (gain.annotation.processing_pipeline.DeleteAttributesFromAWSFilter method) (gain.utils.processing_pipeline.Filter method) (gpf.parquet.schema2.processing_pipeline.AnnotationPipelineVariantsBatchFilter method) (gpf.parquet.schema2.processing_pipeline.AnnotationPipelineVariantsFilter method) (gpf.parquet.schema2.processing_pipeline.DeleteAttributesFromVariantFilter method) (gpf.parquet.schema2.processing_pipeline.DeleteAttributesFromVariantsBatchFilter method) (gpf.parquet.schema2.variants_parquet_writer.Schema2SummaryVariantBatchConsumer method) (gpf.parquet.schema2.variants_parquet_writer.Schema2SummaryVariantConsumer method) (gpf.parquet.schema2.variants_parquet_writer.Schema2VariantBatchConsumer method) (gpf.parquet.schema2.variants_parquet_writer.Schema2VariantConsumer method)

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

G

gain module gain.annotation module gain.annotation.annotatable module gain.annotation.annotate_columns module gain.annotation.annotate_doc module gain.annotation.annotate_utils module gain.annotation.annotate_vcf module gain.annotation.annotation_config module gain.annotation.annotation_factory module gain.annotation.annotation_genomic_context_cli module gain.annotation.annotation_pipeline module gain.annotation.annotator_base module gain.annotation.chrom_mapping_annotator module gain.annotation.cnv_collection_annotator module gain.annotation.debug_annotator module gain.annotation.docker_annotator module gain.annotation.effect_annotator module gain.annotation.gene_score_annotator module gain.annotation.gene_set_annotator module gain.annotation.liftover_annotator module gain.annotation.normalize_allele_annotator module gain.annotation.processing_pipeline module gain.annotation.record_to_annotatable module gain.annotation.score_annotator module gain.annotation.simple_effect_annotator module gain.annotation.utils module gain.dask module gain.dask.config module gain.dask.named_cluster module gain.effect_annotation module gain.effect_annotation.annotation_effects module gain.effect_annotation.annotation_request module gain.effect_annotation.annotator module gain.effect_annotation.cli module gain.effect_annotation.effect module gain.effect_annotation.effect_checkers module gain.effect_annotation.effect_checkers.coding module gain.effect_annotation.effect_checkers.effect_checker module gain.effect_annotation.effect_checkers.frame_shift module gain.effect_annotation.effect_checkers.intron module gain.effect_annotation.effect_checkers.promoter module gain.effect_annotation.effect_checkers.protein_change module gain.effect_annotation.effect_checkers.splice_site module gain.effect_annotation.effect_checkers.start_loss module gain.effect_annotation.effect_checkers.stop_loss module gain.effect_annotation.effect_checkers.utr module gain.effect_annotation.gene_codes module gain.effect_annotation.variant module gain.gene_scores module gain.gene_scores.gene_scores module gain.gene_scores.implementations module gain.gene_scores.implementations.gene_scores_impl module gain.gene_sets module gain.gene_sets.gene_set module gain.gene_sets.gene_term module gain.gene_sets.implementations module gain.gene_sets.implementations.gene_sets_impl module gain.genomic_resources module gain.genomic_resources.aggregators module gain.genomic_resources.cached_repository module gain.genomic_resources.cli module gain.genomic_resources.draw_score_histograms module gain.genomic_resources.explore_grr_search module gain.genomic_resources.fsspec_protocol module gain.genomic_resources.gene_models module gain.genomic_resources.gene_models.gene_models module gain.genomic_resources.gene_models.gene_models_factory module gain.genomic_resources.gene_models.parsers module gain.genomic_resources.gene_models.serialization module gain.genomic_resources.gene_models.transcript_models module gain.genomic_resources.genomic_context module gain.genomic_resources.genomic_context_base module gain.genomic_resources.genomic_context_cli module gain.genomic_resources.genomic_position_table module gain.genomic_resources.genomic_position_table.line module gain.genomic_resources.genomic_position_table.table module gain.genomic_resources.genomic_position_table.table_bigwig module gain.genomic_resources.genomic_position_table.table_inmemory module gain.genomic_resources.genomic_position_table.table_tabix module gain.genomic_resources.genomic_position_table.table_vcf module gain.genomic_resources.genomic_position_table.utils module gain.genomic_resources.genomic_scores module gain.genomic_resources.group_repository module gain.genomic_resources.histogram module gain.genomic_resources.implementations module gain.genomic_resources.implementations.annotation_pipeline_impl module gain.genomic_resources.implementations.gene_models_impl module gain.genomic_resources.implementations.genomic_scores_impl module gain.genomic_resources.implementations.liftover_chain_impl module gain.genomic_resources.implementations.reference_genome_impl module gain.genomic_resources.liftover_chain module gain.genomic_resources.reference_genome module gain.genomic_resources.repository module gain.genomic_resources.repository_factory module gain.genomic_resources.resource_implementation module gain.genomic_resources.statistics module gain.genomic_resources.statistics.base_statistic module gain.genomic_resources.statistics.min_max module gain.genomic_resources.testing module gain.genomic_resources.utils module gain.genomic_resources.variant_utils module gain.task_graph module gain.task_graph.base_executor module gain.task_graph.cache module gain.task_graph.cli_tools module gain.task_graph.dask_executor module gain.task_graph.demo_graphs_cli module gain.task_graph.executor module gain.task_graph.graph module gain.task_graph.logging module gain.task_graph.process_pool_executor module gain.task_graph.sequential_executor module gain.testing module gain.testing.acgt_import module gain.testing.alla_import module gain.testing.foobar_import module gain.testing.t4c8_import module gain.utils module gain.utils.cnv_utils module gain.utils.dae_utils module gain.utils.debug_closing module gain.utils.dict_utils module gain.utils.fs_utils module gain.utils.helpers module gain.utils.processing_pipeline module gain.utils.regions module gain.utils.sql_utils module gain.utils.stats_collection module gain.utils.variant_utils module gain.utils.verbosity_configuration module GAP (gpf.pedigrees.drawing.OffsetLayoutDrawer attribute) gd2str() (in module gain.effect_annotation.effect) ge2str() (in module gain.effect_annotation.effect) gender_palette() (in module gpf.pheno.graphs) gender_palette_light() (in module gpf.pheno.graphs) gene (gain.annotation.simple_effect_annotator.SimpleEffect attribute) (gpf.enrichment_tool.genotype_helper.GeneEffect attribute) gene_effect_get_genes() (in module gain.effect_annotation.effect) gene_effect_get_genes_worst() (in module gain.effect_annotation.effect) gene_effect_get_worst_effect() (in module gain.effect_annotation.effect) gene_effects() (gain.effect_annotation.effect.AnnotationEffect class method) gene_id (gain.gene_sets.gene_term.GeneInfo attribute) gene_models (gpf.gpf_instance.gpf_instance.GPFInstance property) (gpf.gpf_instance.GPFInstance property) gene_models_by_gene_name() (gain.genomic_resources.gene_models.gene_models.GeneModels method) (gain.genomic_resources.gene_models.GeneModels method) gene_models_by_location() (gain.genomic_resources.gene_models.gene_models.GeneModels method) (gain.genomic_resources.gene_models.GeneModels method) gene_models_to_gtf() (in module gain.genomic_resources.gene_models.serialization) gene_names() (gain.genomic_resources.gene_models.gene_models.GeneModels method) (gain.genomic_resources.gene_models.GeneModels method) gene_number (gain.genomic_resources.implementations.gene_models_impl.StatisticsData attribute) gene_profiles_api module gene_profiles_api.table_views module gene_profiles_api.urls module gene_profiles_api.views module GENE_REGIONS_HEURISTIC_CUTOFF (gpf.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute) (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase attribute) GENE_REGIONS_HEURISTIC_EXTEND (gpf.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute) (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase attribute) gene_scores module gene_scores.urls module gene_scores.views module gene_scores_db (gpf.gpf_instance.gpf_instance.GPFInstance property) (gpf.gpf_instance.GPFInstance property) gene_set_id (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (gpf.gene_sets.denovo_gene_sets_config.DGSSpec attribute) gene_sets module gene_sets.urls module gene_sets.views module gene_sets_db (gpf.gpf_instance.gpf_instance.GPFInstance property) (gpf.gpf_instance.GPFInstance property) gene_sets_ids (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) gene_sym (gain.gene_sets.gene_term.GeneInfo attribute) gene_view module gene_view.urls module gene_view.views module GeneEffect (class in gpf.enrichment_tool.genotype_helper) GeneEventsCounter (class in gpf.enrichment_tool.event_counters) GeneInfo (class in gain.gene_sets.gene_term) GeneModels (class in gain.genomic_resources.gene_models) (class in gain.genomic_resources.gene_models.gene_models) (class in genomes_api.views) GeneModelsImpl (class in gain.genomic_resources.implementations.gene_models_impl) GeneModelsStatistics (class in gain.genomic_resources.implementations.gene_models_impl) GeneProfileDB (class in gpf.gene_profile.db) GeneProfileDBWriter (class in gpf.gene_profile.db) generate_gp() (in module gpf.gene_profile.generate_gene_profile) generate_import_manifests() (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.pheno_data.PhenotypeGroup method) (gpf.pheno.pheno_data.PhenotypeStudy method) generate_import_task_graph() (gpf.duckdb_storage.duckdb_import_storage.AbstractDuckDbImportStorage method) (gpf.import_tools.import_tools.ImportStorage method) (gpf.inmemory_storage.inmemory_import_storage.InmemoryImportStorage method) (gpf.parquet_storage.storage.ParquetImportStorage method) (gpf.schema2_storage.schema2_import_storage.Schema2ImportStorage method) generate_instrument_table_name() (in module gpf.pheno.db) generate_phenotype_data_config() (in module gpf.pheno.pheno_import) generate_reannotate_task_graph() (gpf.schema2_storage.schema2_import_storage.Schema2ImportStorage static method) generate_variants() (gene_view.views.DownloadSummaryVariantsView method) generated (gpf.pedigrees.family.Person property) generation_ranks() (gpf.pedigrees.pedigrees.IndividualGroup method) genes (gain.gene_sets.gene_term.NCBIGeneInfo attribute) genes() (gain.effect_annotation.effect.AnnotationEffect class method) (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) genes_prob() (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground method) (gpf.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground method) genes_weight() (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground method) (gpf.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground method) GeneScore (class in gain.gene_scores.gene_scores) GeneScoreAnnotator (class in gain.annotation.gene_score_annotator) GeneScoreEnrichmentBackground (class in gpf.enrichment_tool.gene_weights_background) GeneScoreImplementation (class in gain.gene_scores.implementations.gene_scores_impl) GeneScoresDb (class in gain.gene_scores.gene_scores) GeneScoresDownloadView (class in gene_scores.views) GeneScoresListView (class in gene_scores.views) GeneScoresPartitionsView (class in gene_scores.views) GeneSet (class in gain.gene_sets.gene_set) GeneSetAnnotator (class in gain.annotation.gene_set_annotator) GeneSetCollection (class in gain.gene_sets.gene_set) GeneSetCollectionImpl (class in gain.gene_sets.implementations.gene_sets_impl) GeneSetDownloadView (class in gene_sets.views) GeneSetResourceSchema (class in gain.gene_sets.gene_set) GeneSetsCollectionsView (class in gene_sets.views) GeneSetsDb (class in gpf.gene_sets.gene_sets_db) GeneSetsHasDenovoView (class in gene_sets.views) GeneSetsView (class in gene_sets.views) GeneSymbolsSearch (class in genomes_api.views) GeneSymbolsValidate (class in genomes_api.views) GeneSymbolsView (class in gene_profiles_api.table_views) GeneTerms (class in gain.gene_sets.gene_term) genetic_model (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) GeneticModel (class in gpf.variants.attributes) GeneWeightsEnrichmentBackground (class in gpf.enrichment_tool.gene_weights_background) genomes_api module genomes_api.urls module genomes_api.views module GenomeStatistic (class in gain.genomic_resources.implementations.reference_genome_impl) GenomeStatisticsMixin (class in gain.genomic_resources.implementations.reference_genome_impl) GenomeView (class in gpf_instance.views) GENOMIC_SCORE_HELP (gain.annotation.score_annotator.GenomicScoreAnnotatorBase attribute) genomic_scores (gpf.gpf_instance.gpf_instance.GPFInstance property) (gpf.gpf_instance.GPFInstance property) genomic_scores_api module genomic_scores_api.urls module genomic_scores_api.views module GenomicContext (class in gain.genomic_resources.genomic_context_base) GenomicContextProvider (class in gain.genomic_resources.genomic_context_base) GenomicPositionTable (class in gain.genomic_resources.genomic_position_table.table) GenomicResource (class in gain.genomic_resources.repository) GenomicResourceCachedRepo (class in gain.genomic_resources.cached_repository) GenomicResourceGroupRepo (class in gain.genomic_resources.group_repository) GenomicResourceImplementation (class in gain.genomic_resources.resource_implementation) GenomicResourceProtocolRepo (class in gain.genomic_resources.repository) GenomicResourceRepo (class in gain.genomic_resources.repository) GenomicScore (class in gain.genomic_resources.genomic_scores) GenomicScoreAnnotatorBase (class in gain.annotation.score_annotator) GenomicScoreDescsView (class in genomic_scores_api.views) GenomicScoreImplementation (class in gain.genomic_resources.implementations.genomic_scores_impl) GenomicScoresRegistry (class in gpf.genomic_scores.scores) GenomicScoresView (class in genomic_scores_api.views) genotype (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) genotype_browser module genotype_browser.urls module genotype_browser.views module genotype_data (studies.study_wrapper.WDAEAbstractStudy property) genotype_data_persons() (gpf.pheno_tool.tool.PhenoToolHelper method) genotype_data_variants() (gpf.pheno_tool.tool.PhenoToolHelper method) genotype_storages (gpf.gpf_instance.gpf_instance.GPFInstance property) (gpf.gpf_instance.GPFInstance property) GenotypeBrowserQueryDownloadView (class in genotype_browser.views) GenotypeBrowserQueryView (class in genotype_browser.views) GenotypeBrowserRunner (class in gpf.tools.gpf_validation_runner) GenotypeData (class in gpf.studies.study) GenotypeDataGroup (class in gpf.studies.study) GenotypeDataStudy (class in gpf.studies.study) GenotypeHelper (class in gpf.enrichment_tool.genotype_helper) GenotypeStorage (class in gpf.genotype_storage.genotype_storage) GenotypeStorageRegistry (class in gpf.genotype_storage.genotype_storage_registry) get() (common_reports_api.views.FamiliesDataDownloadView method) (common_reports_api.views.VariantReportsFullView method) (common_reports_api.views.VariantReportsView method) (datasets_api.views.DatasetDescriptionView method) (datasets_api.views.DatasetHierarchyView method) (datasets_api.views.DatasetPedigreeView method) (datasets_api.views.DatasetPermissionsSingleView method) (datasets_api.views.DatasetPermissionsView method) (datasets_api.views.DatasetView method) (datasets_api.views.FederationDatasetsView method) (datasets_api.views.VisibleDatasetsView method) (enrichment_api.views.EnrichmentModelsView method) (family_api.views.AllMemberDetailsView method) (family_api.views.FamilyDetailsView method) (family_api.views.ListAllDetailsView method) (family_api.views.ListFamiliesView method) (family_api.views.ListMembersView method) (family_api.views.MemberDetailsView method) (family_api.views.TagsView method) (gain.genomic_resources.genomic_position_table.BigWigLine method) (gain.genomic_resources.genomic_position_table.Line method) (gain.genomic_resources.genomic_position_table.line.BigWigLine method) (gain.genomic_resources.genomic_position_table.line.Line method) (gain.genomic_resources.genomic_position_table.line.LineBase method) (gain.genomic_resources.genomic_position_table.line.VCFLine method) (gain.genomic_resources.genomic_position_table.VCFLine method) (gene_profiles_api.table_views.GeneSymbolsView method) (gene_profiles_api.table_views.TableRowsView method) (gene_profiles_api.views.ConfigurationView method) (gene_profiles_api.views.ProfileView method) (gene_scores.views.GeneScoresDownloadView method) (gene_scores.views.GeneScoresListView method) (gene_scores.views.HistogramView method) (gene_sets.views.DenovoGeneSetsDb method) (gene_sets.views.DenovoGeneSetsTypesView method) (gene_sets.views.GeneSetDownloadView method) (gene_sets.views.GeneSetsCollectionsView method) (gene_sets.views.GeneSetsHasDenovoView method) (gene_view.views.ConfigView method) (genomes_api.views.DefaultGeneModelsId method) (genomes_api.views.GeneModels method) (genomes_api.views.GeneSymbolsSearch method) (genomic_scores_api.views.GenomicScoreDescsView method) (genomic_scores_api.views.GenomicScoresView method) (gpf.pedigrees.families_data.FamiliesData method) (gpf.studies.variants_db.VariantsDb method) (gpf_instance.views.AboutDescriptionView method) (gpf_instance.views.DescriptionView method) (gpf_instance.views.GenomeView method) (gpf_instance.views.MarkdownFileView method) (measures_api.views.PhenoMeasureListView method) (measures_api.views.PhenoMeasureRegressionsView method) (measures_api.views.PhenoMeasuresView method) (person_sets_api.views.CollectionConfigsView method) (person_sets_api.views.CollectionDomainView method) (person_sets_api.views.CollectionStatsView method) (pheno_browser_api.views.PhenoImagesView method) (pheno_browser_api.views.PhenoInstrumentsView method) (pheno_browser_api.views.PhenoMeasureDescriptionView method) (pheno_browser_api.views.PhenoMeasuresCount method) (pheno_browser_api.views.PhenoMeasuresDownload method) (pheno_browser_api.views.PhenoMeasuresInfoView method) (pheno_browser_api.views.PhenoMeasuresView method) (pheno_tool_api.views.PhenoToolInstruments method) (pheno_tool_api.views.PhenoToolMeasure method) (pheno_tool_api.views.PhenoToolMeasures method) (user_queries.views.UserQueryCollectView method) (users_api.views.BasePasswordView method) (users_api.views.FederationCredentials method) (users_api.views.ForgotPassword method) (users_api.views.UserGpStateView method) (users_api.views.WdaeLoginView method) get_about_etag() (in module gpf_instance.views) get_active_vertex_edges() (gpf.pedigrees.pedigrees.Realization method) get_active_vertices() (gpf.pedigrees.pedigrees.Realization method) get_aggregator_class() (in module gain.genomic_resources.aggregators) get_all_attribute_descriptions() (gain.annotation.annotation_pipeline.Annotator method) (gain.annotation.annotation_pipeline.AnnotatorDecorator method) (gain.annotation.chrom_mapping_annotator.ChromMappingAnnotator method) (gain.annotation.cnv_collection_annotator.CnvCollectionAnnotator method) (gain.annotation.debug_annotator.HelloWorldAnnotator method) (gain.annotation.effect_annotator.EffectAnnotatorAdapter method) (gain.annotation.gene_score_annotator.GeneScoreAnnotator method) (gain.annotation.gene_set_annotator.GeneSetAnnotator method) (gain.annotation.liftover_annotator.AbstractLiftoverAnnotator method) (gain.annotation.normalize_allele_annotator.NormalizeAlleleAnnotator method) (gain.annotation.score_annotator.GenomicScoreAnnotatorBase method) (gain.annotation.simple_effect_annotator.SimpleEffectAnnotator method) get_all_chrom_lengths() (gain.genomic_resources.reference_genome.ReferenceGenome method) get_all_chromosomes() (gain.genomic_resources.genomic_scores.GenomicScore method) get_all_gene_score_descs() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_all_gene_scores() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_all_gene_sets() (gain.gene_sets.gene_set.BaseGeneSetCollection method) (gain.gene_sets.gene_set.GeneSetCollection method) (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection class method) (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) (gpf.gene_sets.gene_sets_db.GeneSetsDb method) get_all_genotype_data() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) (gpf.studies.variants_db.VariantsDb method) get_all_genotype_group_ids() (gpf.studies.variants_db.VariantsDb method) get_all_genotype_groups() (gpf.studies.variants_db.VariantsDb method) get_all_genotype_storage_ids() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) get_all_genotype_storages() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) get_all_genotype_studies() (gpf.studies.variants_db.VariantsDb method) get_all_genotype_study_ids() (gpf.studies.variants_db.VariantsDb method) get_all_phenotype_data() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) (gpf.pheno.registry.PhenoRegistry method) get_all_phenotype_storage_ids() (gpf.pheno.storage.PhenotypeStorageRegistry method) get_all_phenotype_storages() (gpf.pheno.storage.PhenotypeStorageRegistry method) get_all_records() (gain.genomic_resources.genomic_position_table.BigWigTable method) (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table.GenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table_bigwig.BigWigTable method) (gain.genomic_resources.genomic_position_table.table_inmemory.InmemoryGenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table_tabix.TabixGenomicPositionTable method) get_all_resources() (gain.genomic_resources.cached_repository.CachingProtocol method) (gain.genomic_resources.cached_repository.GenomicResourceCachedRepo method) (gain.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (gain.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (gain.genomic_resources.group_repository.GenomicResourceGroupRepo method) (gain.genomic_resources.repository.GenomicResourceProtocolRepo method) (gain.genomic_resources.repository.GenomicResourceRepo method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) get_all_resources_dict() (gain.genomic_resources.cached_repository.CachingProtocol method) (gain.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (gain.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) get_all_scores() (gain.gene_scores.gene_scores.GeneScore method) (gain.genomic_resources.genomic_scores.GenomicScore method) get_allowed_genotype_studies() (in module datasets_api.permissions) get_amino_acids() (gain.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) (gain.effect_annotation.annotation_request.PositiveStrandAnnotationRequest method) get_annotatable() (gpf.variants.core.Allele method) get_annotation_pipeline() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_annotation_pipeline_config() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) (gpf.import_tools.import_tools.ImportProject method) get_annotator_by_attribute_info() (gain.annotation.annotation_pipeline.AnnotationPipeline method) get_annotator_factory() (in module gain.annotation.annotation_factory) get_argument_parser() (gpf.tools.reannotate_instance.ReannotateInstanceTool method) get_attr() (gpf.pedigrees.family.Person method) get_attribute() (gpf.variants.family_variant.FamilyAllele method) (gpf.variants.variant.SummaryAllele method) (gpf.variants.variant.SummaryVariant method) (gpf.variants_loaders.raw.loader.VariantsLoader method) (gpf.variants_loaders.raw.loader.VariantsLoaderDecorator method) get_attribute_info() (gain.annotation.annotation_pipeline.AnnotationPipeline method) get_attributes() (gain.annotation.annotation_pipeline.AnnotationPipeline method) (gain.annotation.annotation_pipeline.ReannotationPipeline method) get_attributes_by_type() (gain.annotation.annotation_pipeline.AnnotationPipeline method) get_available_annotator_types() (in module gain.annotation.annotation_factory) get_available_scores() (gain.genomic_resources.genomic_scores.ScoreLine method) get_base_dir() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) get_base_resource_schema() (in module gain.genomic_resources.resource_implementation) get_bbox() (gpf.pedigrees.layout.Layout method) get_cache_path() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_children() (datasets_api.models.DatasetHierarchy class method) (gpf.person_sets.person_sets.PersonSet method) (gpf.person_sets.PersonSet method) get_children_by_sex() (gpf.person_sets.person_sets.PersonSet method) (gpf.person_sets.PersonSet method) get_children_count() (gpf.person_sets.person_sets.PersonSet method) (gpf.person_sets.PersonSet method) get_children_ids() (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.pheno_data.PhenotypeGroup method) (gpf.pheno.pheno_data.PhenotypeStudy method) (gpf.studies.study.GenotypeData method) (gpf.studies.study.GenotypeDataGroup method) (gpf.studies.study.GenotypeDataStudy method) (studies.study_wrapper.WDAEAbstractStudy method) (studies.study_wrapper.WDAEStudyGroup method) get_children_stats() (gpf.person_sets.person_sets.PersonSet method) (gpf.person_sets.PersonSet method) get_chrom_file() (gain.genomic_resources.implementations.reference_genome_impl.GenomeStatisticsMixin static method) get_chrom_length() (gain.genomic_resources.reference_genome.ReferenceGenome method) get_chromosome_length() (gain.genomic_resources.genomic_position_table.BigWigTable method) (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table.GenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table_bigwig.BigWigTable method) (gain.genomic_resources.genomic_position_table.table_inmemory.InmemoryGenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table_tabix.TabixGenomicPositionTable method) get_chromosome_length_tabix() (in module gain.utils.regions) get_chromosomes() (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table.GenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table_tabix.TabixGenomicPositionTable method) get_clean_config() (in module studies.study_wrapper) get_clean_gene_id() (in module gain.gene_sets.gene_term) get_code() (users_api.models.BaseVerificationCode class method) get_coding_left() (gain.effect_annotation.annotation_request.BaseAnnotationRequest method) get_coding_region_for_pos() (gain.effect_annotation.annotation_request.BaseAnnotationRequest method) get_coding_right() (gain.effect_annotation.annotation_request.BaseAnnotationRequest method) get_codons() (gain.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) (gain.effect_annotation.annotation_request.PositiveStrandAnnotationRequest method) get_codons_left() (gain.effect_annotation.annotation_request.BaseAnnotationRequest method) get_codons_right() (gain.effect_annotation.annotation_request.BaseAnnotationRequest method) get_collection_types_legend() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) get_column_key() (gain.genomic_resources.genomic_position_table.table.GenomicPositionTable method) get_column_sources() (studies.study_wrapper.WDAEStudy method) get_columns() (gpf.pedigrees.family.Family method) get_columns_as_sources() (studies.study_wrapper.WDAEStudy static method) get_columns_to_draw() (in module gpf.pheno.graphs) get_common_report() (common_reports_api.common_reports_helper.BaseCommonReportsHelper method) (common_reports_api.common_reports_helper.CommonReportsHelper method) (gpf.pheno.pheno_data.PhenotypeData method) (gpf.studies.study.GenotypeData method) get_completed_tasks() (gain.task_graph.base_executor.TaskGraphExecutorBase method) (gain.task_graph.executor.TaskGraphExecutor method) get_config() (gain.genomic_resources.genomic_scores.GenomicScore method) (gain.genomic_resources.repository.GenomicResource method) (gain.genomic_resources.resource_implementation.GenomicResourceImplementation method) get_config_histograms() (gain.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation method) get_content_file_path() (gain.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) get_context_genotype_storages() (in module gpf.genotype_storage.genotype_storage_genomic_context_cli) get_context_keys() (gain.genomic_resources.genomic_context_base.GenomicContext method) (gain.genomic_resources.genomic_context_base.PriorityGenomicContext method) (gain.genomic_resources.genomic_context_base.SimpleGenomicContext method) (gpf.gpf_instance_plugin.gpf_instance_context_plugin.GPFInstanceGenomicContext method) get_context_object() (gain.genomic_resources.genomic_context_base.GenomicContext method) (gain.genomic_resources.genomic_context_base.PriorityGenomicContext method) (gain.genomic_resources.genomic_context_base.SimpleGenomicContext method) (gpf.gpf_instance_plugin.gpf_instance_context_plugin.GPFInstanceGenomicContext method) get_context_pipeline() (in module gain.annotation.annotation_genomic_context_cli) get_context_provider_priority() (gain.genomic_resources.genomic_context_base.GenomicContextProvider method) get_context_provider_type() (gain.genomic_resources.genomic_context_base.GenomicContextProvider method) get_count() (pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method) (pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method) get_data_dir() (gpf.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage method) get_dataset() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) (users_api.management.commands.dataset_mixin.DatasetBaseMixin method) get_dataset_groups() (in module datasets_api.permissions) get_dataset_info() (in module datasets_api.permissions) get_datasets() (groups_api.serializers.GroupRetrieveSerializer method) get_db() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) get_db_filename() (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3Storage method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbStorage method) (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) get_default_annotation_attribute() (gain.genomic_resources.genomic_scores.GenomicScore method) get_default_annotation_attributes() (gain.genomic_resources.genomic_scores.GenomicScore method) get_default_application() (in module users_api.models) get_default_background_model() (enrichment_api.enrichment_helper.EnrichmentHelper method) get_default_counting_model() (enrichment_api.enrichment_helper.EnrichmentHelper method) get_default_genotype_storage() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) get_default_grr_definition() (in module gain.genomic_resources.repository_factory) get_default_grr_definition_path() (in module gain.genomic_resources.repository_factory) get_default_phenotype_storage() (gpf.pheno.storage.PhenotypeStorageRegistry method) get_denovo_events() (gpf.enrichment_tool.genotype_helper.GenotypeHelper method) get_denovo_gene_set_spec() (in module utils.gene_sets) get_description() (gain.genomic_resources.repository.GenomicResource method) get_description_etag() (in module datasets_api.views) (in module gpf_instance.views) get_direct_datasets_parents() (datasets_api.models.DatasetHierarchy class method) get_directly_allowed_genotype_data() (in module datasets_api.permissions) get_effect() (gain.effect_annotation.effect_checkers.coding.CodingEffectChecker method) (gain.effect_annotation.effect_checkers.effect_checker.EffectChecker method) (gain.effect_annotation.effect_checkers.frame_shift.FrameShiftEffectChecker method) (gain.effect_annotation.effect_checkers.intron.IntronicEffectChecker method) (gain.effect_annotation.effect_checkers.promoter.PromoterEffectChecker method) (gain.effect_annotation.effect_checkers.protein_change.ProteinChangeEffectChecker method) (gain.effect_annotation.effect_checkers.splice_site.SpliceSiteEffectChecker method) (gain.effect_annotation.effect_checkers.start_loss.StartLossEffectChecker method) (gain.effect_annotation.effect_checkers.stop_loss.StopLossEffectChecker method) (gain.effect_annotation.effect_checkers.utr.UTREffectChecker method) get_effect_for_transcript() (gain.effect_annotation.annotator.EffectAnnotator method) get_effect_types() (gain.effect_annotation.effect.EffectTypesMixin class method) (in module gain.effect_annotation.annotation_effects) get_effect_types_set() (in module gain.effect_annotation.annotation_effects) get_empty() (gpf.common_reports.denovo_report.EffectRow method) get_enrichment_cache_path() (in module gpf.enrichment_tool.enrichment_utils) get_enrichment_config() (in module gpf.enrichment_tool.enrichment_utils) get_enrichment_models() (enrichment_api.enrichment_helper.BaseEnrichmentHelper method) (enrichment_api.enrichment_helper.EnrichmentHelper method) get_exon_number_for() (in module gain.genomic_resources.gene_models.serialization) get_exonic_distance() (gain.effect_annotation.annotation_request.BaseAnnotationRequest method) get_exonic_length() (gain.effect_annotation.annotation_request.BaseAnnotationRequest method) get_exonic_position() (gain.effect_annotation.annotation_request.BaseAnnotationRequest method) get_family_counter_list() (common_reports_api.common_reports_helper.BaseCommonReportsHelper method) (common_reports_api.common_reports_helper.CommonReportsHelper method) get_family_counter_tsv() (common_reports_api.common_reports_helper.BaseCommonReportsHelper method) (common_reports_api.common_reports_helper.CommonReportsHelper method) get_family_data_tsv() (common_reports_api.common_reports_helper.BaseCommonReportsHelper method) (common_reports_api.common_reports_helper.CommonReportsHelper method) get_family_pedigree() (in module gpf.common_reports.family_counter) get_family_pq_filepaths() (gpf.parquet.schema2.loader.ParquetLoader method) get_family_read_counts() (gpf.variants_loaders.dae.loader.DaeTransmittedFamiliesGenotypes method) get_family_type() (in module gpf.common_reports.family_counter) get_file_chromosomes() (gain.genomic_resources.genomic_position_table.BigWigTable method) (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table.GenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table_bigwig.BigWigTable method) (gain.genomic_resources.genomic_position_table.table_inmemory.InmemoryGenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table_tabix.TabixGenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table_vcf.VCFGenomicPositionTable method) (gain.genomic_resources.genomic_position_table.VCFGenomicPositionTable method) get_file_content() (gain.genomic_resources.repository.GenomicResource method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) get_file_url() (gain.genomic_resources.repository.GenomicResource method) get_files() (gain.genomic_resources.repository.Manifest method) get_filtered_family_data_tsv() (common_reports_api.common_reports_helper.BaseCommonReportsHelper method) (common_reports_api.common_reports_helper.CommonReportsHelper method) get_final() (gain.genomic_resources.aggregators.Aggregator method) (gain.genomic_resources.aggregators.ConcatAggregator method) (gain.genomic_resources.aggregators.CountAggregator method) (gain.genomic_resources.aggregators.CounterAggregator method) (gain.genomic_resources.aggregators.DictAggregator method) (gain.genomic_resources.aggregators.JoinAggregator method) (gain.genomic_resources.aggregators.ListAggregator method) (gain.genomic_resources.aggregators.MaxAggregator method) (gain.genomic_resources.aggregators.MeanAggregator method) (gain.genomic_resources.aggregators.MedianAggregator method) (gain.genomic_resources.aggregators.MinAggregator method) (gain.genomic_resources.aggregators.ModeAggregator method) get_frame() (gain.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) (gain.effect_annotation.annotation_request.PositiveStrandAnnotationRequest method) get_full_common_report() (common_reports_api.common_reports_helper.BaseCommonReportsHelper method) (common_reports_api.common_reports_helper.CommonReportsHelper method) get_full_id() (gain.genomic_resources.repository.GenomicResource method) get_gene_collection_count_statistics() (gain.gene_sets.gene_set.GeneSetCollection method) get_gene_models() (gain.effect_annotation.cli.EffectAnnotatorBuilder method) (gain.genomic_resources.genomic_context_base.GenomicContext method) get_gene_score() (gain.gene_scores.gene_scores.GeneScoresDb method) (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_gene_score_desc() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_gene_score_ids() (gain.gene_scores.gene_scores.GeneScoresDb method) get_gene_scores() (gain.gene_scores.gene_scores.GeneScoresDb method) get_gene_set() (gain.gene_sets.gene_set.BaseGeneSetCollection method) (gain.gene_sets.gene_set.GeneSetCollection method) (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) (gpf.gene_sets.gene_sets_db.GeneSetsDb method) get_gene_set_collection_ids() (gpf.gene_sets.gene_sets_db.GeneSetsDb method) get_gene_set_from_collections() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection class method) get_gene_set_ids() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) (gpf.gene_sets.gene_sets_db.GeneSetsDb method) get_gene_sets_list_statistics() (gain.gene_sets.gene_set.GeneSetCollection method) get_gene_sets_per_gene_hist() (gain.gene_sets.gene_set.GeneSetCollection method) get_gene_sets_per_gene_hist_filename() (gain.gene_sets.gene_set.GeneSetCollection method) get_gene_sets_per_gene_hist_image_filename() (gain.gene_sets.gene_set.GeneSetCollection method) get_gene_sets_types_legend() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) get_gene_value() (gain.gene_scores.gene_scores.GeneScore method) get_gene_view_summary_variants() (studies.study_wrapper.WDAEAbstractStudy method) (studies.study_wrapper.WDAEStudy method) get_gene_view_summary_variants_download() (studies.study_wrapper.WDAEAbstractStudy method) (studies.study_wrapper.WDAEStudy method) get_genes() (gain.gene_scores.gene_scores.GeneScore method) get_genes_per_gene_set_hist() (gain.gene_sets.gene_set.GeneSetCollection method) get_genes_per_gene_set_hist_filename() (gain.gene_sets.gene_set.GeneSetCollection method) get_genes_per_gene_set_hist_image_filename() (gain.gene_sets.gene_set.GeneSetCollection method) get_genomic_context() (gain.effect_annotation.cli.EffectAnnotatorBuilder method) (in module gain.genomic_resources.genomic_context) get_genomic_resource() (in module gain.annotation.score_annotator) get_genomic_resource_id_version() (gain.genomic_resources.repository.GenomicResource method) get_genomic_resources_repository() (gain.genomic_resources.genomic_context_base.GenomicContext method) get_genotype_data() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_genotype_data_config() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_genotype_data_ids() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_genotype_group() (gpf.studies.variants_db.VariantsDb method) get_genotype_group_config() (gpf.studies.variants_db.VariantsDb method) get_genotype_storage() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) (gpf.import_tools.import_tools.ImportProject method) (gpf.tools.dataset_helpers.DatasetHelpers method) get_genotype_storage_factory() (in module gpf.genotype_storage.genotype_storage_registry) get_genotype_storage_types() (in module gpf.genotype_storage.genotype_storage_registry)

get_genotype_study() (gpf.studies.variants_db.VariantsDb method) get_genotype_study_config() (gpf.studies.variants_db.VariantsDb method) get_global_statistic_file() (gain.genomic_resources.implementations.reference_genome_impl.GenomeStatisticsMixin static method) get_gp() (gpf.gene_profile.db.GeneProfileDB method) get_gp_configuration() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_gp_statistic() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_gpf_instance() (gpf.import_tools.import_tools.ImportProject method) (in module gpf.pheno.pheno_import) get_graph() (gpf.pedigrees.pedigrees.FamilyConnections method) get_grr() (gain.effect_annotation.cli.EffectAnnotatorBuilder method) get_grr_from_context() (in module gain.annotation.annotate_utils) get_header() (gain.effect_annotation.cli.VariantColumnInputFile method) get_histogram_file() (gain.genomic_resources.histogram.HistogramStatisticMixin static method) get_histogram_filename() (gain.gene_scores.gene_scores.GeneScore method) (gain.genomic_resources.genomic_scores.GenomicScore method) get_histogram_image_file() (gain.genomic_resources.histogram.HistogramStatisticMixin static method) get_histogram_image_filename() (gain.gene_scores.gene_scores.GeneScore method) (gain.genomic_resources.genomic_scores.GenomicScore method) get_histogram_image_url() (gain.gene_scores.gene_scores.GeneScore method) (gain.genomic_resources.genomic_scores.GenomicScore method) get_id() (gain.genomic_resources.repository.GenomicResource method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) get_idx() (in module gain.genomic_resources.genomic_position_table.table) get_image() (gpf.pheno.pheno_data.PhenotypeData method) (pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method) (pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method) get_import_storage() (gpf.import_tools.import_tools.ImportProject method) get_import_storage_factory() (in module gpf.import_tools.import_tools) get_import_storage_types() (in module gpf.import_tools.import_tools) get_import_variants_buckets() (gpf.import_tools.import_tools.ImportProject method) get_individual() (gpf.pedigrees.pedigrees.FamilyConnections method) get_individuals() (gpf.pedigrees.pedigrees.FamilyConnections method) get_individuals_with_rank() (gpf.pedigrees.pedigrees.FamilyConnections method) get_info() (gain.annotation.annotation_pipeline.AnnotationPipeline method) (gain.annotation.annotation_pipeline.Annotator method) (gain.gene_scores.implementations.gene_scores_impl.GeneScoreImplementation method) (gain.gene_sets.implementations.gene_sets_impl.GeneSetCollectionImpl method) (gain.genomic_resources.implementations.annotation_pipeline_impl.AnnotationPipelineImplementation method) (gain.genomic_resources.implementations.gene_models_impl.GeneModelsImpl method) (gain.genomic_resources.implementations.genomic_scores_impl.CnvCollectionImplementation method) (gain.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation method) (gain.genomic_resources.implementations.liftover_chain_impl.LiftoverChainImplementation method) (gain.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeImplementation method) (gain.genomic_resources.resource_implementation.GenomicResourceImplementation method) (gain.genomic_resources.resource_implementation.InfoImplementationMixin method) (gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation method) get_input_filenames() (gpf.import_tools.import_tools.ImportProject method) get_instance_timestamp_etag() (in module datasets_api.permissions) get_instrument_measures() (gpf.pheno.pheno_data.PhenotypeData method) get_instruments() (gpf.pheno.pheno_data.PhenotypeData method) (pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method) (pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method) get_interval() (gpf.pedigrees.pedigrees.Realization method) get_interval_locus_ploidy() (in module gpf.utils.variant_utils) get_labels() (gain.genomic_resources.repository.GenomicResource method) get_last_login_for() (users_api.models.AuthenticationLog static method) get_leaf_children() (gpf.studies.study.GenotypeData method) get_leaves() (gpf.pheno.pheno_data.PhenotypeGroup method) get_line_iterator() (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table_tabix.TabixGenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table_vcf.VCFGenomicPositionTable method) (gain.genomic_resources.genomic_position_table.VCFGenomicPositionTable method) get_lines() (gain.effect_annotation.cli.VariantColumnInputFile method) get_locked_out_error() (users_api.models.AuthenticationLog static method) get_locus_ploidy() (in module gpf.utils.variant_utils) get_manifest() (gain.genomic_resources.repository.GenomicResource method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) get_mating_units() (gpf.pedigrees.pedigrees.FamilyConnections method) get_max() (gain.gene_scores.gene_scores.GeneScore method) get_maximal_set() (gpf.pedigrees.pedigrees.Realization method) get_measure() (gpf.pheno.pheno_data.PhenotypeData method) get_measure_description() (gpf.pheno.pheno_data.PhenotypeData method) (pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method) (pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method) get_measure_ids() (pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method) (pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method) get_measures() (gpf.pheno.pheno_data.PhenotypeData method) (studies.study_wrapper.WDAEAbstractStudy method) get_measures_df() (gpf.pheno.db.PhenoDb method) get_measures_info() (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.pheno_data.PhenotypeGroup method) (gpf.pheno.pheno_data.PhenotypeStudy method) (pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method) (pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method) get_measures_json() (studies.study_wrapper.WDAEAbstractStudy method) (studies.study_wrapper.WDAEStudy method) get_member() (gpf.pedigrees.family.Family method) get_members_with_roles() (gpf.pedigrees.family.Family method) get_members_with_statuses() (gpf.pedigrees.family.Family method) get_memory_limit() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) get_min() (gain.gene_scores.gene_scores.GeneScore method) get_min_max_file() (gain.genomic_resources.statistics.min_max.MinMaxValueStatisticMixin static method) get_next_by_created_at() (users_api.models.BaseVerificationCode method) (users_api.models.ResetPasswordCode method) (users_api.models.SetPasswordCode method) get_next_by_time() (users_api.models.AuthenticationLog method) get_normalize_measure_id() (gpf.pheno_tool.tool.PhenoTool method) get_nucleotides_count_to_full_codon() (gain.effect_annotation.annotation_request.BaseAnnotationRequest static method) get_or_create() (users_api.models.WdaeUserManager method) get_or_create_query_transformer() (in module studies.query_transformer) get_or_create_resource() (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) get_or_create_response_transformer() (in module studies.response_transformer) get_origin_display() (query_state_save.models.QueryState method) get_out_attributes() (gain.effect_annotation.cli.AnnotationAttributes method) get_output_parquet_files_dir() (in module gpf.pheno.pheno_import) get_page_display() (query_state_save.models.QueryState method) get_paginated_response() (utils.pagination.WdaePageNumberPagination method) get_parents() (datasets_api.models.DatasetHierarchy class method) get_parquet_dataset_dir() (gpf.import_tools.import_tools.ImportProject method) get_parser() (in module gain.genomic_resources.gene_models.parsers) get_partition_descriptor() (gpf.import_tools.import_tools.ImportProject method) get_pedigree() (gpf.import_tools.import_tools.ImportProject method) get_pedigree_column_names() (in module gpf.pedigrees.family) get_pedigree_df() (gpf.pheno.db.PhenoDb method) (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.pheno_data.PhenotypeGroup method) (gpf.pheno.pheno_data.PhenotypeStudy method) get_pedigree_filename() (gpf.import_tools.import_tools.ImportProject method) get_pedigree_loader() (gpf.import_tools.import_tools.ImportProject method) get_pedigree_params() (gpf.import_tools.import_tools.ImportProject method) get_people_measure_values() (gpf.pheno.db.PhenoDb method) (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.pheno_data.PhenotypeGroup method) (gpf.pheno.pheno_data.PhenotypeStudy method) get_people_measure_values_df() (gpf.pheno.db.PhenoDb method) (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.pheno_data.PhenotypeGroup method) (gpf.pheno.pheno_data.PhenotypeStudy method) get_permissions_etag() (in module datasets_api.permissions) get_permitted_datasets() (query_base.query_base.QueryBaseView method) get_person_color() (gpf.person_sets.person_sets.PersonSetCollection static method) (gpf.person_sets.PersonSetCollection static method) get_person_roles() (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.pheno_data.PhenotypeGroup method) get_person_set() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) get_person_set_collection() (gpf.pheno.pheno_data.PhenotypeData method) (gpf.studies.study.GenotypeData method) (studies.study_wrapper.WDAEAbstractStudy method) get_person_set_collection_legend() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) get_person_set_of_person() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) get_persons() (gpf.pheno.pheno_data.PhenotypeData method) get_persons_df() (gpf.pheno.db.PhenoDb method) (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.pheno_data.PhenotypeGroup method) (gpf.pheno.pheno_data.PhenotypeStudy method) get_pheno_browser_images_dir() (in module gpf.pheno.pheno_data) get_pheno_cache_path() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_pheno_db_dir() (in module gpf.pheno.pheno_data) get_phenotype_data() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) (gpf.pheno.registry.PhenoRegistry method) get_phenotype_data_config() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) (gpf.pheno.registry.PhenoRegistry method) get_phenotype_data_ids() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) (gpf.pheno.registry.PhenoRegistry method) get_phenotype_storage() (gpf.pheno.storage.PhenotypeStorageRegistry method) get_pipeline_from_context() (in module gain.annotation.annotate_utils) get_previous_by_created_at() (users_api.models.BaseVerificationCode method) (users_api.models.ResetPasswordCode method) (users_api.models.SetPasswordCode method) get_previous_by_time() (users_api.models.AuthenticationLog method) get_processing_annotation_batch_size() (gpf.import_tools.import_tools.ImportProject method) get_processing_parquet_dataset_dir() (gpf.import_tools.import_tools.ImportProject method) get_protein_length() (gain.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) (gain.effect_annotation.annotation_request.PositiveStrandAnnotationRequest method) get_protein_position() (gain.effect_annotation.annotation_request.BaseAnnotationRequest method) (gain.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) (gain.effect_annotation.annotation_request.PositiveStrandAnnotationRequest method) get_protein_position_for_pos() (gain.effect_annotation.annotation_request.BaseAnnotationRequest method) get_public_url() (gain.genomic_resources.cached_repository.CachingProtocol method) (gain.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (gain.genomic_resources.repository.GenomicResource method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) get_query_leaf_studies() (gpf.studies.study.GenotypeData method) get_query_person_set_ids() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) get_queryset() (groups_api.views.GroupsViewSet method) get_record() (gain.task_graph.cache.FileTaskCache method) (gain.task_graph.cache.NoTaskCache method) (gain.task_graph.cache.TaskCache method) get_records_in_region() (gain.genomic_resources.genomic_position_table.BigWigTable method) (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table.GenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table_bigwig.BigWigTable method) (gain.genomic_resources.genomic_position_table.table_inmemory.InmemoryGenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table_tabix.TabixGenomicPositionTable method) get_reference_genome() (gain.genomic_resources.genomic_context_base.GenomicContext method) get_refernce_genome() (gain.effect_annotation.cli.EffectAnnotatorBuilder method) get_region_scores() (gain.genomic_resources.genomic_scores.PositionScore method) get_regression_measures() (gpf.pheno.prepare_data.PreparePhenoBrowserBase method) get_regressions() (gpf.pheno.pheno_data.PhenotypeData method) (gpf.pheno.pheno_data.PhenotypeGroup method) (gpf.pheno.pheno_data.PhenotypeStudy method) get_remaining_lockout_time() (users_api.models.AuthenticationLog static method) get_repo_public_url() (gain.genomic_resources.repository.GenomicResource method) get_repo_url() (gain.genomic_resources.repository.GenomicResource method) get_resource() (gain.genomic_resources.cached_repository.GenomicResourceCachedRepo method) (gain.genomic_resources.group_repository.GenomicResourceGroupRepo method) (gain.genomic_resources.repository.GenomicResourceProtocolRepo method) (gain.genomic_resources.repository.GenomicResourceRepo method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) get_resource_cached_files() (gain.genomic_resources.cached_repository.GenomicResourceCachedRepo method) get_resource_file_size() (gain.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) get_resource_file_timestamp() (gain.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) get_resource_file_url() (gain.genomic_resources.cached_repository.CachingProtocol method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) get_resource_ids() (gain.annotation.annotation_pipeline.AnnotationPipeline method) get_resource_implementation_builder() (in module gain.genomic_resources) get_resource_url() (gain.genomic_resources.cached_repository.CachingProtocol method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) get_result_by_sex() (gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapter method) (pheno_tool_api.adapter.PhenoToolAdapter method) (pheno_tool_api.views.PhenoToolView static method) get_row_group_size() (gpf.import_tools.import_tools.ImportProject method) get_schema() (gain.gene_scores.gene_scores.GeneScore static method) (gain.gene_sets.implementations.gene_sets_impl.GeneSetCollectionImpl static method) (gain.genomic_resources.gene_models.gene_models.GeneModels static method) (gain.genomic_resources.gene_models.GeneModels static method) (gain.genomic_resources.genomic_scores.AlleleScore static method) (gain.genomic_resources.genomic_scores.CnvCollection static method) (gain.genomic_resources.genomic_scores.GenomicScore static method) (gain.genomic_resources.genomic_scores.PositionScore static method) (gain.genomic_resources.liftover_chain.LiftoverChain static method) (gain.genomic_resources.reference_genome.ReferenceGenome static method) (gain.genomic_resources.resource_implementation.ResourceConfigValidationMixin static method) (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentResourceBackground static method) (gpf.enrichment_tool.samocha_background.SamochaEnrichmentBackground static method) get_score() (gain.genomic_resources.genomic_scores.ScoreLine method) get_score_definition() (gain.genomic_resources.genomic_scores.GenomicScore method) get_score_desc() (gain.gene_scores.gene_scores.GeneScoresDb method) get_score_df() (gain.gene_scores.gene_scores.GeneScore method) get_score_histogram() (gain.gene_scores.gene_scores.GeneScore method) (gain.genomic_resources.genomic_scores.GenomicScore method) get_score_ids() (gain.gene_scores.gene_scores.GeneScoresDb method) get_score_range() (gain.gene_scores.gene_scores.GeneScore method) (gain.genomic_resources.genomic_scores.GenomicScore method) get_scores() (gain.gene_scores.gene_scores.GeneScore method) (gain.gene_scores.gene_scores.GeneScoresDb method) (gpf.genomic_scores.scores.GenomicScoresRegistry method) get_scripts_for_template() (in module gain.genomic_resources.cli) get_selected_counting_models() (enrichment_api.enrichment_helper.EnrichmentHelper method) get_selected_person_set_collections() (enrichment_api.enrichment_helper.EnrichmentHelper method) get_sequence() (gain.genomic_resources.reference_genome.ReferenceGenome method) get_serializer_class() (groups_api.views.GroupsViewSet method) (users_api.views.UserViewSet method) get_sibship_units() (gpf.pedigrees.pedigrees.FamilyConnections method) get_source() (gain.genomic_resources.genomic_context_base.GenomicContext method) (gain.genomic_resources.genomic_context_base.PriorityGenomicContext method) (gain.genomic_resources.genomic_context_base.SimpleGenomicContext method) (gpf.gpf_instance_plugin.gpf_instance_context_plugin.GPFInstanceGenomicContext method) get_source_attributes() (gain.effect_annotation.cli.AnnotationAttributes method) get_statistics() (gain.genomic_resources.implementations.gene_models_impl.GeneModelsImpl method) (gain.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeImplementation method) (gain.genomic_resources.resource_implementation.GenomicResourceImplementation method) get_statistics_folder() (gain.genomic_resources.resource_implementation.ResourceStatistics static method) get_statistics_info() (gain.gene_scores.implementations.gene_scores_impl.GeneScoreImplementation method) (gain.gene_sets.implementations.gene_sets_impl.GeneSetCollectionImpl method) (gain.genomic_resources.implementations.annotation_pipeline_impl.AnnotationPipelineImplementation method) (gain.genomic_resources.implementations.gene_models_impl.GeneModelsImpl method) (gain.genomic_resources.implementations.genomic_scores_impl.CnvCollectionImplementation method) (gain.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation method) (gain.genomic_resources.implementations.liftover_chain_impl.LiftoverChainImplementation method) (gain.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeImplementation method) (gain.genomic_resources.resource_implementation.GenomicResourceImplementation method) (gain.genomic_resources.resource_implementation.InfoImplementationMixin method) (gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation method) get_statistics_template_data() (gain.genomic_resources.resource_implementation.InfoImplementationMixin method) get_stats() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) get_status_code() (users_api.forms.WdaeLoginForm method) get_storage_types() (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbParquetStorage class method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3ParquetStorage class method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3Storage class method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbStorage class method) (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage class method) (gpf.genotype_storage.genotype_storage.GenotypeStorage class method) (gpf.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage class method) (gpf.parquet_storage.storage.ParquetGenotypeStorage class method) get_studies() (gpf_instance.extension.GPFExtensionBase method) get_studies_ids() (gpf.studies.study.GenotypeData method) (gpf.studies.study.GenotypeDataGroup method) (gpf.studies.study.GenotypeDataStudy method) (gpf_instance.extension.GPFExtensionBase method) (studies.study_wrapper.WDAEAbstractStudy method) (studies.study_wrapper.WDAEStudyGroup method) get_study_config_tables() (in module gpf.duckdb_storage.duckdb_storage_helpers) get_summary() (gain.genomic_resources.repository.GenomicResource method) get_summary_pq_filepaths() (gpf.parquet.schema2.loader.ParquetLoader method) get_sym_2_fn() (in module gpf.enrichment_tool.event_counters) get_task_deps() (gain.task_graph.graph.TaskGraph method) get_task_desc() (gain.task_graph.graph.TaskGraph method) get_template() (gain.gene_scores.implementations.gene_scores_impl.GeneScoreImplementation method) (gain.gene_sets.implementations.gene_sets_impl.GeneSetCollectionImpl method) (gain.genomic_resources.implementations.annotation_pipeline_impl.AnnotationPipelineImplementation method) (gain.genomic_resources.implementations.gene_models_impl.GeneModelsImpl method) (gain.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation method) (gain.genomic_resources.implementations.liftover_chain_impl.LiftoverChainImplementation method) (gain.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeImplementation method) (gain.genomic_resources.resource_implementation.InfoImplementationMixin method) get_template_data() (gain.genomic_resources.resource_implementation.InfoImplementationMixin method) get_tool() (gpf_instance.extension.GPFExtensionBase method) get_total_count() (gain.genomic_resources.aggregators.Aggregator method) get_transcript_models() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) get_type() (gain.genomic_resources.repository.GenomicResource method) get_unique_family_variants() (studies.query_transformer.QueryTransformer method) (studies.study_wrapper.QueryTransformerProtocol method) get_unused_keys() (gain.annotation.annotation_config.ParamsUsageMonitor method) get_url() (gain.genomic_resources.cached_repository.CachingProtocol method) (gain.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (gain.genomic_resources.repository.GenomicResource method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) get_used_count() (gain.genomic_resources.aggregators.Aggregator method) get_used_keys() (gain.annotation.annotation_config.ParamsUsageMonitor method) get_user_groups() (in module datasets_api.permissions) get_user_info() (in module users_api.views) get_values() (gain.effect_annotation.cli.AnnotationAttributes method) (gain.gene_scores.gene_scores.GeneScore method) get_variant_loader() (gpf.import_tools.import_tools.ImportProject method) get_variant_loader_chrom_lens() (gpf.import_tools.import_tools.ImportProject method) get_variant_loader_chromosomes() (gpf.import_tools.import_tools.ImportProject method) get_variant_loader_types() (gpf.import_tools.import_tools.ImportProject method) get_variant_params() (gpf.import_tools.import_tools.ImportProject method) get_variant_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor method) get_version_str() (gain.genomic_resources.repository.GenomicResource method) get_visible_groups() (users_api.management.commands.export_base.ExportUsersBase method) get_wdae_children() (in module datasets_api.permissions) get_wdae_dataset() (in module datasets_api.permissions) get_wdae_parents() (in module datasets_api.permissions) get_wgpf_instance() (in module gpf_instance.gpf_instance) get_work_dir() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) get_x_scale() (gain.gene_scores.gene_scores.GeneScore method) get_y_scale() (gain.gene_scores.gene_scores.GeneScore method) glob() (in module gain.utils.fs_utils) glot_and() (in module gain.utils.sql_utils) gp_from_table_row() (gpf.gene_profile.db.GeneProfileDB method) gp_from_table_row_single_view() (gpf.gene_profile.db.GeneProfileDB method) gpf module gpf.common_reports module gpf.common_reports.common_report module gpf.common_reports.denovo_report module gpf.common_reports.family_counter module gpf.common_reports.family_report module gpf.common_reports.people_counter module gpf.configuration module gpf.configuration.gpf_config_parser module gpf.configuration.schemas module gpf.configuration.schemas.dae_conf module gpf.configuration.schemas.gene_profile module gpf.configuration.schemas.gene_weights_db module gpf.configuration.schemas.person_sets module gpf.configuration.schemas.phenotype_data module gpf.configuration.schemas.study_config module gpf.configuration.schemas.wdae_study_config module gpf.configuration.study_config_builder module gpf.configuration.utils module gpf.duckdb_storage module gpf.duckdb_storage.duckdb2_variants module gpf.duckdb_storage.duckdb_connection_factory module gpf.duckdb_storage.duckdb_genotype_storage module gpf.duckdb_storage.duckdb_import_storage module gpf.duckdb_storage.duckdb_legacy_genotype_storage module gpf.duckdb_storage.duckdb_storage_config module gpf.duckdb_storage.duckdb_storage_helpers module gpf.duckdb_storage.duckdb_variants module gpf.enrichment_tool module gpf.enrichment_tool.base_enrichment_background module gpf.enrichment_tool.build_coding_length_enrichment_background module gpf.enrichment_tool.build_ur_synonymous_enrichment_background module gpf.enrichment_tool.enrichment_cache_builder module gpf.enrichment_tool.enrichment_utils module gpf.enrichment_tool.event_counters module gpf.enrichment_tool.gene_weights_background module gpf.enrichment_tool.genotype_helper module gpf.enrichment_tool.resource_implementations module gpf.enrichment_tool.resource_implementations.enrichment_resource_impl module gpf.enrichment_tool.samocha_background module gpf.gene_profile module gpf.gene_profile.convert_gene_profile_to_duckdb module gpf.gene_profile.db module gpf.gene_profile.exporter module gpf.gene_profile.generate_gene_profile module gpf.gene_profile.statistic module gpf.gene_sets module gpf.gene_sets.denovo_gene_set_collection module gpf.gene_sets.denovo_gene_set_helpers module gpf.gene_sets.denovo_gene_sets_config module gpf.gene_sets.denovo_gene_sets_db module gpf.gene_sets.gene_sets_db module gpf.genomic_scores module gpf.genomic_scores.scores module gpf.genotype_storage module gpf.genotype_storage.genotype_storage module gpf.genotype_storage.genotype_storage_genomic_context_cli module gpf.genotype_storage.genotype_storage_registry module gpf.gpf_instance module gpf.gpf_instance.adjustments module gpf.gpf_instance.adjustments.adjust_command module gpf.gpf_instance.adjustments.adjust_duckdb_storage module gpf.gpf_instance.adjustments.adjust_impala_storage module gpf.gpf_instance.adjustments.gpf_instance_adjustments module gpf.gpf_instance.gpf_instance module gpf.gpf_instance_plugin module gpf.gpf_instance_plugin.gpf_instance_context_plugin module gpf.import_tools module gpf.import_tools.cli module gpf.import_tools.import_config module gpf.import_tools.import_tools module gpf.inmemory_storage module gpf.inmemory_storage.annotation_serialization module gpf.inmemory_storage.inmemory_genotype_storage module gpf.inmemory_storage.inmemory_import_storage module gpf.inmemory_storage.raw_variants module gpf.parquet module gpf.parquet.helpers module gpf.parquet.parquet_writer module gpf.parquet.partition_descriptor module gpf.parquet.schema2 module gpf.parquet.schema2.annotate_schema2_parquet module gpf.parquet.schema2.loader module gpf.parquet.schema2.merge_parquet module gpf.parquet.schema2.parquet_io module gpf.parquet.schema2.processing_pipeline module gpf.parquet.schema2.serializers module gpf.parquet.schema2.variants_parquet_writer module gpf.parquet_storage module gpf.parquet_storage.storage module gpf.pedigrees module gpf.pedigrees.drawing module gpf.pedigrees.families_data module gpf.pedigrees.family module gpf.pedigrees.family_role_builder module gpf.pedigrees.family_tag_builder module gpf.pedigrees.layout module gpf.pedigrees.loader module gpf.pedigrees.pedigrees module gpf.pedigrees.testing module gpf.person_filters module gpf.person_filters.person_filters module gpf.person_sets module gpf.person_sets.person_sets module gpf.pheno module gpf.pheno.browser module gpf.pheno.build_pheno_browser module gpf.pheno.common module gpf.pheno.db module gpf.pheno.graphs module gpf.pheno.import_tools module gpf.pheno.pheno_data module gpf.pheno.pheno_import module gpf.pheno.prepare module gpf.pheno.prepare.measure_classifier module gpf.pheno.prepare_data module gpf.pheno.registry module gpf.pheno.storage module gpf.pheno.update_pheno_descriptions module gpf.pheno.utils module gpf.pheno.utils.commons module gpf.pheno.utils.lin_regress module gpf.pheno_tool module gpf.pheno_tool.pheno_tool_adapter module gpf.pheno_tool.tool module gpf.query_variants module gpf.query_variants.attribute_queries module gpf.query_variants.base_query_variants module gpf.query_variants.query_runners module gpf.query_variants.sql module gpf.query_variants.sql.schema2 module gpf.query_variants.sql.schema2.base_query_builder module gpf.query_variants.sql.schema2.base_variants module gpf.query_variants.sql.schema2.family_builder module gpf.query_variants.sql.schema2.sql_query_builder module gpf.query_variants.sql.schema2.summary_builder module gpf.schema2_storage module gpf.schema2_storage.schema2_import_storage module gpf.schema2_storage.schema2_layout module gpf.studies module gpf.studies.study module gpf.studies.variants_db module gpf.testing module gpf.testing.acgt_import module gpf.testing.alla_import module gpf.testing.foobar_import module gpf.testing.import_helpers module gpf.testing.setup_helpers module gpf.testing.t4c8_import module gpf.tools module gpf.tools.dae2vcf module gpf.tools.dataset_helpers module gpf.tools.denovo2vcf module gpf.tools.draw_pedigree module gpf.tools.generate_common_report module gpf.tools.generate_denovo_gene_sets module gpf.tools.gpf_convert_study_config module gpf.tools.gpf_validation_runner module gpf.tools.grr_cache_repo module gpf.tools.liftover_tools module gpf.tools.ped2ped module gpf.tools.reannotate_instance module gpf.tools.simple_study_import module gpf.tools.to_gpf_gene_models_format module gpf.tools.vcf2tsv module gpf.utils module gpf.utils.testing module gpf.utils.variant_utils module gpf.variants module gpf.variants.attributes module gpf.variants.core module gpf.variants.family_variant module gpf.variants.variant module gpf.variants_loaders module gpf.variants_loaders.cnv module gpf.variants_loaders.cnv.flexible_cnv_loader module gpf.variants_loaders.cnv.loader module gpf.variants_loaders.dae module gpf.variants_loaders.dae.loader module gpf.variants_loaders.parquet module gpf.variants_loaders.parquet.loader module gpf.variants_loaders.raw module gpf.variants_loaders.raw.flexible_variant_loader module gpf.variants_loaders.raw.loader module gpf.variants_loaders.vcf module gpf.variants_loaders.vcf.loader module gpf.variants_loaders.vcf.serializer module gpf_instance module gpf_instance (gpf.pheno.common.PhenoImportConfig attribute) gpf_instance.apps module gpf_instance.extension module gpf_instance.gpf_instance module gpf_instance.urls module gpf_instance.views module gpf_web module gpf_web.default_settings module gpf_web.eager_settings module gpf_web.gunicorn_settings module gpf_web.mypy_settings module gpf_web.remote_settings module gpf_web.settings module gpf_web.silk_settings module gpf_web.urls module gpf_web.wdaemanage module gpf_web.wgpf module gpf_web.wgpf_settings module GPFConfigParser (class in gpf.configuration.gpf_config_parser) GPFConfigValidator (class in gpf.configuration.gpf_config_parser) GPFExtensionBase (class in gpf_instance.extension) GPFInstance (class in gpf.gpf_instance) (class in gpf.gpf_instance.gpf_instance) GPFInstanceConfig (class in gpf.pheno.common) GPFInstanceContextProvider (class in gpf.gpf_instance_plugin.gpf_instance_context_plugin) GPFInstanceGenomicContext (class in gpf.gpf_instance_plugin.gpf_instance_context_plugin) gpfjs module gpfjs.views module GPFOAuth2Authentication (class in utils.authentication) GPFTool (class in gpf_instance.extension) GPStatistic (class in gpf.gene_profile.statistic) GpUserState (class in users_api.models) gpuserstate (users_api.models.WdaeUser attribute) GpUserState.DoesNotExist GpUserState.MultipleObjectsReturned GraphColumn (class in gpf.pheno.graphs) grey (gpf_web.default_settings.CustomFormatter attribute) group_post_delete() (in module users_api.models) group_pre_delete() (in module users_api.models) GroupCreateSerializer (class in groups_api.serializers) GroupCreateSerializer.Meta (class in groups_api.serializers) grouping() (gpf.query_variants.attribute_queries.AttributeQueryTransformerFunction method) (gpf.query_variants.attribute_queries.AttributeQueryTransformerSQL method) (gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method) GroupRetrieveSerializer (class in groups_api.serializers) GroupRetrieveSerializer.Meta (class in groups_api.serializers) groups (datasets_api.models.Dataset attribute) (users_api.models.WdaeUser attribute) groups_api module groups_api.migrations module groups_api.serializers module groups_api.urls module groups_api.views module GroupSerializer (class in groups_api.serializers) GroupSerializer.Meta (class in groups_api.serializers) GroupsViewSet (class in groups_api.views) grr (gpf.gpf_instance.gpf_instance.GPFInstance property) (gpf.gpf_instance.GPFInstance property) gt2str() (in module gpf.utils.variant_utils) gt_flatten() (gpf.variants.family_variant.FamilyAllele method) (gpf.variants.family_variant.FamilyVariant method) gtf_canonical_index() (in module gain.genomic_resources.gene_models.serialization)

H

half_sibling (gpf.variants.attributes.Role attribute) handle() (users_api.management.commands.dataset_groups.Command method) (users_api.management.commands.datasets_export.Command method) (users_api.management.commands.datasets_restore.Command method) (users_api.management.commands.datasets_show.Command method) (users_api.management.commands.unlock_user.Command method) (users_api.management.commands.user_create.Command method) (users_api.management.commands.user_set_name.Command method) (users_api.management.commands.user_setpasswd.Command method) (users_api.management.commands.users_add.Command method) (users_api.management.commands.users_export.Command method) (users_api.management.commands.users_group_add.Command method) (users_api.management.commands.users_group_remove.Command method) (users_api.management.commands.users_remove.Command method) (users_api.management.commands.users_restore.Command method) (users_api.management.commands.users_show.Command method) handle_dataset() (users_api.management.commands.datasets_restore.Command method) handle_default_args() (in module gain.annotation.annotate_utils) handle_measure_inference_tasks() (in module gpf.pheno.pheno_import) handle_partial_permissions() (in module datasets_api.permissions) handle_user() (users_api.management.commands.import_base.ImportUsersBase method) (users_api.management.commands.users_export.Command method) has_affected_status_queries() (gpf.inmemory_storage.raw_variants.RawMemoryVariants method) (gpf.parquet_storage.storage.ParquetLoaderVariants method) (gpf.query_variants.base_query_variants.QueryVariants method) (gpf.query_variants.base_query_variants.QueryVariantsBase method) has_attr() (gpf.pedigrees.family.Person method) has_attribute() (gpf.variants.family_variant.FamilyAllele method) (gpf.variants.variant.SummaryAllele method) (gpf.variants.variant.SummaryVariant method) has_chromosome() (gain.genomic_resources.gene_models.gene_models.GeneModels method) (gain.genomic_resources.gene_models.GeneModels method) has_cnv (gpf.studies.study.GenotypeData property) has_coding_bins() (gpf.parquet.partition_descriptor.PartitionDescriptor method) has_complex (gpf.studies.study.GenotypeData property) has_denovo (gpf.studies.study.GenotypeData property) (gpf.studies.study.GenotypeDataGroup property) has_denovo_variants() (gpf.import_tools.import_tools.ImportProject method) has_family_bins() (gpf.parquet.partition_descriptor.PartitionDescriptor method) has_family_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor method) has_frequency_bins() (gpf.parquet.partition_descriptor.PartitionDescriptor method) has_gene_score() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) has_gene_set_collection() (gpf.gene_sets.gene_sets_db.GeneSetsDb method) has_gene_sets() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) has_genotype_data (studies.study_wrapper.WDAEAbstractStudy property) has_genotype_storage() (gpf.import_tools.import_tools.ImportProject method) has_instrument_descriptions (gpf.pheno.browser.PhenoBrowser property) has_measure() (gpf.pheno.pheno_data.PhenotypeData method) has_measure_descriptions (gpf.pheno.browser.PhenoBrowser property) has_members() (gpf.pedigrees.family.Family method) has_object_permission() (datasets_api.permissions.IsDatasetAllowed method) has_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor method) has_permission() (datasets_api.permissions.IsDatasetAllowed method) has_pheno_data (studies.study_wrapper.WDAEAbstractStudy property)

has_phenotype_data() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) (gpf.pheno.registry.PhenoRegistry method) has_region_bins() (gpf.parquet.partition_descriptor.PartitionDescriptor method) has_summary_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor method) has_tag() (gpf.pedigrees.family.Person method) has_task() (gain.task_graph.graph.TaskGraph method) has_transmitted (gpf.studies.study.GenotypeData property) (gpf.studies.study.GenotypeDataGroup property) has_unlimited_download (users_api.models.WdaeUser property) has_utr3_region() (gain.effect_annotation.annotation_request.BaseAnnotationRequest method) (gain.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) has_utr5_region() (gain.effect_annotation.annotation_request.BaseAnnotationRequest method) (gain.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) has_variants() (gpf.import_tools.import_tools.ImportProject method) (gpf.schema2_storage.schema2_layout.Schema2DatasetLayout method) has_view_range() (gain.genomic_resources.histogram.NumberHistogramConfig method) has_wildcard() (gain.annotation.annotation_config.AnnotationConfigParser static method) has_zygosity (gpf.studies.study.GenotypeData property) HasClose (class in gain.utils.debug_closing) head() (pheno_browser_api.views.PhenoMeasuresDownload method) header (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (gain.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) HelloWorldAnnotator (class in gain.annotation.debug_annotator) help (gain.gene_scores.gene_scores.ScoreDesc attribute) (gpf.genomic_scores.scores.ScoreDesc attribute) (users_api.management.commands.dataset_groups.Command attribute) (users_api.management.commands.datasets_export.Command attribute) (users_api.management.commands.datasets_restore.Command attribute) (users_api.management.commands.datasets_show.Command attribute) (users_api.management.commands.unlock_user.Command attribute) (users_api.management.commands.user_create.Command attribute) (users_api.management.commands.user_set_name.Command attribute) (users_api.management.commands.user_setpasswd.Command attribute) (users_api.management.commands.users_add.Command attribute) (users_api.management.commands.users_export.Command attribute) (users_api.management.commands.users_group_add.Command attribute) (users_api.management.commands.users_group_remove.Command attribute) (users_api.management.commands.users_remove.Command attribute) (users_api.management.commands.users_restore.Command attribute) (users_api.management.commands.users_show.Command attribute) heterozygous (gpf.variants.attributes.Zygosity attribute) hist (gain.gene_scores.gene_scores.ScoreDesc attribute) (gpf.genomic_scores.scores.ScoreDesc attribute) hist_conf (gain.gene_scores.gene_scores.ScoreDef attribute) (gain.genomic_resources.genomic_scores.ScoreDef attribute) histogram_configs (gpf.pheno.common.PhenoImportConfig attribute) histogram_type (gpf.pheno.common.InferenceConfig attribute) (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) HistogramError histograms (gain.gene_sets.gene_set.GeneSetResourceSchema attribute) HistogramStatisticMixin (class in gain.genomic_resources.histogram) HistogramView (class in gene_scores.views) homozygous (gpf.variants.attributes.Zygosity attribute) hundred_groups() (in module conftest) hundred_users() (in module conftest)

I

id (datasets_api.models.Dataset attribute) (datasets_api.models.DatasetHierarchy attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbBaseConf attribute) (gpf.person_sets.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.person_sets.PersonSetConfig attribute) (gpf.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.PersonSetConfig attribute) (gpf.pheno.common.PhenoImportConfig attribute) (query_state_save.models.QueryState attribute) (user_queries.models.UserQuery attribute) (users_api.models.AuthenticationLog attribute) (users_api.models.GpUserState attribute) (users_api.models.ResetPasswordCode attribute) (users_api.models.SetPasswordCode attribute) (users_api.models.WdaeUser attribute) id_to_position (gpf.pedigrees.layout.Layout property) import_config (gpf.pheno.common.ImportManifest attribute) import_dataset() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) (gpf.parquet_storage.storage.ParquetGenotypeStorage method) import_pheno_data() (in module gpf.pheno.pheno_import) ImportConfigNormalizer (class in gpf.import_tools.import_tools) ImportInstrument (class in gpf.pheno.pheno_import) ImportManifest (class in gpf.pheno.common) ImportProject (class in gpf.import_tools.import_tools) ImportStorage (class in gpf.import_tools.import_tools) ImportUsersBase (class in users_api.management.commands.import_base) in_start_codons() (gain.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) (gain.effect_annotation.annotation_request.PositiveStrandAnnotationRequest method) inc() (gain.utils.stats_collection.StatsCollection method) include_reference (gpf.import_tools.import_tools.ImportProject property) increase_indent() (gpf.configuration.study_config_builder.ConfigDumper method) indel (gpf.variants.core.Allele.Type attribute) index (gpf.import_tools.import_tools.Bucket attribute) index() (in module gpfjs.views) Individual (class in gpf.pedigrees.pedigrees) individual_set() (gpf.pedigrees.pedigrees.Individual method) (gpf.pedigrees.pedigrees.IndividualGroup method) (gpf.pedigrees.pedigrees.MatingUnit method) (gpf.pedigrees.pedigrees.SibshipUnit method) IndividualGroup (class in gpf.pedigrees.pedigrees) individuals_by_rank (gpf.pedigrees.layout.Layout property) IndividualWithCoordinates (class in gpf.pedigrees.layout) infer_gene_model_parser() (in module gain.genomic_resources.gene_models.parsers) infer_measures() (in module gpf.pheno.pheno_import) inference_config (gpf.pheno.common.PhenoImportConfig attribute) inference_reference_impl() (in module gpf.pheno.prepare.measure_classifier) inference_report (gpf.pheno.pheno_import.MeasureReport attribute) InferenceConfig (class in gpf.pheno.common) InferenceReport (class in gpf.pheno.prepare.measure_classifier) InfoImplementationMixin (class in gain.genomic_resources.resource_implementation) InfoImplementationMixin.FileEntry (class in gain.genomic_resources.resource_implementation) Inheritance (class in gpf.variants.attributes) inheritance() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) inheritance_in_members (gpf.variants.family_variant.FamilyAllele property) init() (gain.annotation.annotation_genomic_context_cli.CLIAnnotationContextProvider method) (gain.genomic_resources.genomic_context.DefaultRepositoryContextProvider method) (gain.genomic_resources.genomic_context_base.GenomicContextProvider method) (gain.genomic_resources.genomic_context_cli.CLIGenomicContextProvider method) (gpf.genotype_storage.genotype_storage_genomic_context_cli.CLIGenotypeStorageContextProvider method) (gpf.gpf_instance_plugin.gpf_instance_context_plugin.GPFInstanceContextProvider method) init_normalize_measures() (gpf.pheno_tool.tool.PhenoTool method) init_vcf_loaders() (gpf.variants_loaders.vcf.loader.VcfLoader method) initial (datasets_api.migrations.0001_initial.Migration attribute) (user_queries.migrations.0001_initial.Migration attribute) (users_api.migrations.0001_initial.Migration attribute) InmemoryGenomicPositionTable (class in gain.genomic_resources.genomic_position_table.table_inmemory) InmemoryGenotypeStorage (class in gpf.inmemory_storage.inmemory_genotype_storage) InmemoryImportStorage (class in gpf.inmemory_storage.inmemory_import_storage) input_dir (gpf.import_tools.import_tools.ImportProject property) (gpf.pheno.common.PhenoImportConfig attribute) input_files (gain.task_graph.graph.TaskDesc attribute) input_reference_genome (gain.annotation.annotation_config.AnnotationPreamble attribute) (gain.annotation.annotation_config.RawPreamble attribute) input_reference_genome_res (gain.annotation.annotation_config.AnnotationPreamble attribute) InputAnnotableAnnotatorDecorator (class in gain.annotation.annotation_pipeline) insert_gp() (gpf.gene_profile.db.GeneProfileDBWriter method) insert_gps() (gpf.gene_profile.db.GeneProfileDBWriter method) instance_id (datasets_api.models.DatasetHierarchy attribute) InstanceIdCommand (class in gpf.gpf_instance.adjustments.gpf_instance_adjustments) Instrument (class in gpf.pheno.pheno_data) instrument (gpf.pheno.common.DataDictionaryConfig attribute) (gpf.pheno.common.InstrumentConfig attribute) (gpf.pheno.common.InstrumentDictionaryConfig attribute) instrument_column (gpf.pheno.common.DataDictionaryConfig attribute) (gpf.pheno.common.InstrumentDictionaryConfig attribute) instrument_dictionary (gpf.pheno.common.PhenoImportConfig attribute) instrument_files (gpf.pheno.common.PhenoImportConfig attribute) instrument_name (gpf.pheno.common.RegressionMeasure attribute) (gpf.pheno.pheno_import.MeasureReport attribute) InstrumentConfig (class in gpf.pheno.common) InstrumentDescriptionsConfig (class in gpf.pheno.common) InstrumentDictionaryConfig (class in gpf.pheno.common) instruments (gpf.pheno.pheno_data.PhenotypeData property) int_type() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method) (gpf.query_variants.sql.schema2.base_query_builder.Dialect static method) intermediate_output_files (gain.task_graph.graph.TaskDesc attribute) internal (gain.annotation.annotation_config.AttributeInfo attribute) (gain.annotation.annotation_pipeline.AttributeDesc attribute) intersection() (gain.utils.regions.Region method) (gpf.pedigrees.pedigrees.Interval method) (in module gain.utils.regions)

intersects() (gain.utils.regions.Region method) Interval (class in gpf.pedigrees.pedigrees) IntervalForVertex (class in gpf.pedigrees.pedigrees) IntronicEffectChecker (class in gain.effect_annotation.effect_checkers.intron) invalidate() (gain.genomic_resources.cached_repository.CachingProtocol method) (gain.genomic_resources.cached_repository.GenomicResourceCachedRepo method) (gain.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (gain.genomic_resources.group_repository.GenomicResourceGroupRepo method) (gain.genomic_resources.repository.GenomicResource method) (gain.genomic_resources.repository.GenomicResourceProtocolRepo method) (gain.genomic_resources.repository.GenomicResourceRepo method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) (gain.task_graph.cache.CacheRecord method) inverse_curve_p1() (gpf.pedigrees.layout.Line method) inverse_curve_p2() (gpf.pedigrees.layout.Line method) inverse_curve_y_at() (gpf.pedigrees.layout.Line method) is_active (users_api.models.WdaeUser attribute) is_active_vertex() (gpf.pedigrees.pedigrees.Realization method) is_all_reference_genotype() (in module gpf.utils.variant_utils) is_all_unknown_genotype() (in module gpf.utils.variant_utils) is_browser_outdated() (gpf.pheno.pheno_data.PhenotypeData method) is_cached() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) is_closed() (gpf.query_variants.query_runners.QueryRunner method) is_cnv() (gpf.variants.core.Allele.Type class method) is_coding() (gain.genomic_resources.gene_models.transcript_models.TranscriptModel method) (gain.genomic_resources.gene_models.TranscriptModel method) is_compressed_filename() (in module gain.utils.fs_utils) is_connected() (gpf.pedigrees.pedigrees.FamilyConnections method) is_convertible_to_numeric() (in module gpf.pheno.prepare.measure_classifier) is_done() (gpf.query_variants.query_runners.QueryResult method) (gpf.query_variants.query_runners.QueryRunner method) is_email_valid() (in module utils.email_regex) is_empty() (gpf.common_reports.denovo_report.DenovoReport method) (gpf.common_reports.denovo_report.DenovoReportTable method) (gpf.common_reports.denovo_report.EffectCell method) (gpf.common_reports.people_counter.PeopleCounter method) (gpf.parquet.partition_descriptor.Partition method) (gpf.query_variants.sql.schema2.sql_query_builder.QueryHeuristics method) is_empty_field() (gpf.common_reports.people_counter.PeopleCounter method) is_genotype (studies.study_wrapper.WDAEAbstractStudy property) is_gr_id_token() (in module gain.genomic_resources.repository) is_group (gpf.pheno.pheno_data.PhenotypeData property) (gpf.pheno.pheno_data.PhenotypeGroup property) (gpf.studies.study.GenotypeData property) (gpf.studies.study.GenotypeDataGroup property) (gpf.studies.study.GenotypeDataStudy property) (studies.study_wrapper.WDAEAbstractStudy property) is_in_interval_order() (gpf.pedigrees.pedigrees.Realization method) is_individual() (gpf.pedigrees.pedigrees.Individual method) (gpf.pedigrees.pedigrees.IndividualGroup method) is_loaded() (gain.gene_sets.gene_set.GeneSetCollection method) (gain.genomic_resources.gene_models.gene_models.GeneModels method) (gain.genomic_resources.gene_models.GeneModels method) (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground method) (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground method) (gpf.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground method) (gpf.enrichment_tool.samocha_background.SamochaEnrichmentBackground method) is_maximal() (gpf.pedigrees.pedigrees.Realization method) is_nan() (in module gpf.pheno.prepare.measure_classifier) is_numeric() (gpf.pheno.common.MeasureType static method) is_older_than() (gpf.pheno.common.ImportManifest method) is_open() (gain.annotation.annotation_pipeline.Annotator method) (gain.annotation.annotation_pipeline.AnnotatorDecorator method) (gain.annotation.score_annotator.GenomicScoreAnnotatorBase method) (gain.genomic_resources.genomic_scores.GenomicScore method) (gain.genomic_resources.liftover_chain.LiftoverChain method) (gain.genomic_resources.reference_genome.ReferenceGenome method) is_password_valid() (in module utils.password_requirements) is_pedigree_only() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) is_phenotype (studies.study_wrapper.WDAEAbstractStudy property) is_pseudoautosomal() (gain.genomic_resources.reference_genome.ReferenceGenome method) is_read_only() (gpf.duckdb_storage.duckdb_genotype_storage.AbstractDuckDbStorage method) (gpf.genotype_storage.genotype_storage.GenotypeStorage method) is_reference() (gpf.variants.family_variant.FamilyVariant method) is_reference_allele (gpf.variants.variant.SummaryAllele property) is_reference_genotype() (in module gpf.utils.variant_utils) is_row_empty() (gpf.common_reports.denovo_report.EffectRow method) is_s3url() (in module gain.utils.fs_utils) is_staff (users_api.models.WdaeUser attribute) is_start_codon_affected() (gain.effect_annotation.annotation_request.BaseAnnotationRequest method) (gain.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) is_started() (gpf.query_variants.query_runners.QueryRunner method) is_stop_codon_affected() (gain.effect_annotation.annotation_request.BaseAnnotationRequest method) (gain.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) is_study() (datasets_api.models.DatasetHierarchy class method) is_superuser (users_api.models.WdaeUser attribute) is_text() (gpf.pheno.common.MeasureType static method) is_tr() (gpf.variants.core.Allele.Type class method) is_unknown() (gpf.variants.family_variant.FamilyVariant method) is_unknown_genotype() (in module gpf.utils.variant_utils) is_user_locked_out() (users_api.models.AuthenticationLog static method) is_valid_family() (gpf.pedigrees.pedigrees.FamilyConnections static method) is_version_constraint_satisfied() (in module gain.genomic_resources.repository) IsDatasetAllowed (class in datasets_api.permissions) isin() (gain.utils.regions.Region method) isnan() (in module gain.utils.helpers) items() (gpf.pedigrees.families_data.FamiliesData method) iterator_to_json() (in module users_api.views) (in module utils.streaming_response_util)

J

jitter (gpf.pheno.common.RegressionMeasure attribute) join() (in module gain.utils.fs_utils) join_base_url_and_parquet_scan() (in module gpf.duckdb_storage.duckdb_storage_helpers) join_gene_models() (gain.genomic_resources.gene_models.gene_models.GeneModels static method) (gain.genomic_resources.gene_models.GeneModels static method)

join_line() (in module gain.utils.dae_utils) join_pheno_df_with_variants() (gpf.pheno_tool.tool.PhenoTool static method) JoinAggregator (class in gain.genomic_resources.aggregators) JsonVariantsDataSerializer (class in gpf.parquet.schema2.serializers) jump_threshold (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (gain.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute)

K

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

kwargs (gain.task_graph.graph.TaskDesc attribute)

L

label (gpf.pedigrees.family.FamilyTag property) (gpf.pheno.graphs.GraphColumn property) label_rotation (gain.gene_sets.gene_set.CategoricalHistogramSchema attribute) (gain.genomic_resources.histogram.CategoricalHistogramConfig attribute) labels (gain.gene_sets.gene_set.MetaSchema attribute) LARGE_DELETION (gain.annotation.annotatable.Annotatable.Type attribute) large_deletion (gpf.variants.core.Allele.Type attribute) LARGE_DPI (gpf.pheno.prepare_data.PreparePhenoBrowserBase attribute) LARGE_DUPLICATION (gain.annotation.annotatable.Annotatable.Type attribute) large_duplication (gpf.variants.core.Allele.Type attribute) large_values_desc (gain.gene_scores.gene_scores.ScoreDef attribute) (gain.gene_scores.gene_scores.ScoreDesc attribute) (gain.genomic_resources.genomic_scores.ScoreDef attribute) (gpf.genomic_scores.scores.ScoreDesc attribute) last_login (users_api.models.WdaeUser attribute) Layout (class in gpf.pedigrees.layout) layout (gpf.pedigrees.family.Person property) Layout.BBox (class in gpf.pedigrees.layout) layout_parser() (in module gpf.pedigrees.layout) legend_json() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) liftover_allele() (gain.annotation.liftover_annotator.AbstractLiftoverAnnotator method) liftover_cnv() (gain.annotation.liftover_annotator.AbstractLiftoverAnnotator method) liftover_position() (gain.annotation.liftover_annotator.AbstractLiftoverAnnotator method) liftover_region() (gain.annotation.liftover_annotator.AbstractLiftoverAnnotator method) liftover_variants() (gpf.tools.liftover_tools.CNVLiftoverTool method) (gpf.tools.liftover_tools.DaeLiftoverTool method) (gpf.tools.liftover_tools.DenovoLiftoverTool method) (gpf.tools.liftover_tools.LiftoverTool method) (gpf.tools.liftover_tools.VCFLiftoverTool method) LiftoverChain (class in gain.genomic_resources.liftover_chain) LiftoverChainImplementation (class in gain.genomic_resources.implementations.liftover_chain_impl) LiftoverFunction (class in gain.annotation.liftover_annotator) LiftoverTool (class in gpf.tools.liftover_tools) Line (class in gain.genomic_resources.genomic_position_table) (class in gain.genomic_resources.genomic_position_table.line) (class in gpf.pedigrees.layout) line_iterator (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (gain.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) LinearRegression (class in gpf.pheno.utils.lin_regress) LineBase (class in gain.genomic_resources.genomic_position_table.line) LineBuffer (class in gain.genomic_resources.genomic_position_table) (class in gain.genomic_resources.genomic_position_table.line) list() (users_api.views.UserViewSet method) list_gp_gene_symbols() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) list_symbols() (gpf.gene_profile.db.GeneProfileDB method) ListAggregator (class in gain.genomic_resources.aggregators) ListAllDetailsView (class in family_api.views) ListFamiliesView (class in family_api.views) ListMembersView (class in family_api.views) literal() (gpf.query_variants.attribute_queries.AttributeQueryTransformerFunction method) (gpf.query_variants.attribute_queries.AttributeQueryTransformerSQL method) (gpf.query_variants.attribute_queries.AttributeQueryTransformerSQLLegacy method) (gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method)

load() (gain.gene_sets.gene_set.BaseGeneSetCollection method) (gain.gene_sets.gene_set.GeneSetCollection method) (gain.genomic_resources.gene_models.gene_models.GeneModels method) (gain.genomic_resources.gene_models.GeneModels method) (gpf.common_reports.common_report.CommonReport static method) (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground method) (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground method) (gpf.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground method) (gpf.enrichment_tool.samocha_background.SamochaEnrichmentBackground method) (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) (gpf.pedigrees.loader.FamiliesLoader method) load_collection() (gpf.gene_sets.denovo_gene_set_helpers.DenovoGeneSetHelpers class method) load_collection_from_dict() (gpf.gene_sets.denovo_gene_set_helpers.DenovoGeneSetHelpers class method) load_config() (gpf.configuration.gpf_config_parser.GPFConfigParser class method) load_config_dict() (gpf.configuration.gpf_config_parser.GPFConfigParser class method) load_config_raw() (gpf.configuration.gpf_config_parser.GPFConfigParser class method) load_contents() (gain.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) load_definition_file() (in module gain.genomic_resources.repository_factory) load_directory_configs() (gpf.configuration.gpf_config_parser.GPFConfigParser class method) load_from_dir() (gpf.parquet.schema2.loader.ParquetLoader static method) load_gene_mapping() (in module gain.genomic_resources.gene_models.parsers) load_gene_sets() (gain.gene_sets.gene_set.GeneSetCollection method) load_gene_terms() (in module gain.gene_sets.gene_term) load_histogram() (in module gain.genomic_resources.histogram) load_histogram_configs() (in module gpf.pheno.pheno_import) load_inference_configs() (in module gpf.pheno.pheno_import) load_instrument_description_file() (in module gpf.pheno.pheno_import) load_instrument_descriptions() (in module gpf.pheno.pheno_import) load_manifest() (gain.genomic_resources.cached_repository.CachingProtocol method) (gain.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) load_measure_description_file() (in module gpf.pheno.pheno_import) load_measure_descriptions() (in module gpf.pheno.pheno_import) load_meta() (gpf.schema2_storage.schema2_import_storage.Schema2ImportStorage static method) load_ncbi_gene_info() (in module gain.gene_sets.gene_term) load_pedigree_file() (gpf.pedigrees.loader.FamiliesLoader static method) load_pipeline_from_file() (in module gain.annotation.annotation_factory) load_pipeline_from_grr() (in module gain.annotation.annotation_factory) load_pipeline_from_yaml() (in module gain.annotation.annotation_factory) load_resource_file_state() (gain.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) load_schema2_dataset_layout() (in module gpf.schema2_storage.schema2_layout) load_simple_families_file() (gpf.pedigrees.loader.FamiliesLoader static method) load_study_config() (in module gpf.tools.gpf_convert_study_config) load_transcript_models() (in module gain.genomic_resources.gene_models.parsers) load_yaml() (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) loaded_variants (gpf.genotype_storage.genotype_storage.GenotypeStorage property) location (gpf.variants.variant.SummaryVariant property) location_variant_to_vcf_transformer() (in module gpf.variants_loaders.raw.flexible_variant_loader) log_authentication_attempt() (users_api.models.AuthenticationLog static method) log_filter() (in module utils.logger) logout() (in module users_api.views) lookup_field (groups_api.views.GroupsViewSet attribute)

M

M (gpf.variants.attributes.Sex attribute) main() (gpf.tools.gpf_validation_runner.MainRunner method) (in module gain.genomic_resources.draw_score_histograms) (in module gain.genomic_resources.explore_grr_search) (in module gain.task_graph.demo_graphs_cli) (in module gpf.gene_profile.convert_gene_profile_to_duckdb) (in module gpf.gene_profile.generate_gene_profile) (in module gpf.import_tools.cli) (in module gpf.pheno.build_pheno_browser) (in module gpf.pheno.import_tools) (in module gpf.pheno.pheno_import) (in module gpf.pheno.update_pheno_descriptions) (in module gpf.tools.dae2vcf) (in module gpf.tools.denovo2vcf) (in module gpf.tools.draw_pedigree) (in module gpf.tools.generate_common_report) (in module gpf.tools.generate_denovo_gene_sets) (in module gpf.tools.gpf_convert_study_config) (in module gpf.tools.gpf_validation_runner) (in module gpf.tools.ped2ped) (in module gpf.tools.simple_study_import) (in module gpf.tools.to_gpf_gene_models_format) (in module gpf.tools.vcf2tsv) (in module gpf_web.wdaemanage) MainRunner (class in gpf.tools.gpf_validation_runner) make_all_region_bins() (gpf.parquet.partition_descriptor.PartitionDescriptor method) make_coding_bin() (gpf.parquet.partition_descriptor.PartitionDescriptor method) make_config() (studies.study_wrapper.WDAEAbstractStudy static method) make_family_bin() (gpf.parquet.partition_descriptor.PartitionDescriptor method) make_frequency_bin() (gpf.parquet.partition_descriptor.PartitionDescriptor method) make_pedigree_filter() (in module gpf.person_filters) (in module gpf.person_filters.person_filters) make_pheno_filter() (in module gpf.person_filters) (in module gpf.person_filters.person_filters) make_pheno_filter_beta() (in module gpf.person_filters) (in module gpf.person_filters.person_filters) make_query_transformer() (in module studies.query_transformer) make_region_bin() (gpf.parquet.partition_descriptor.PartitionDescriptor method) make_region_bins_regions() (gpf.parquet.partition_descriptor.PartitionDescriptor method) make_response_transformer() (in module studies.response_transformer) make_task() (gain.task_graph.graph.TaskGraph static method) make_tool() (common_reports_api.common_reports_helper.CommonReportsHelper static method) (enrichment_api.enrichment_builder.EnrichmentBuilder static method) (enrichment_api.enrichment_helper.EnrichmentHelper static method) (gpf_instance.extension.GPFTool static method) (pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper static method) (pheno_tool_api.adapter.PhenoToolAdapter static method) make_validation_runner() (gpf.tools.gpf_validation_runner.MainRunner method) male (gpf.enrichment_tool.event_counters.EnrichmentResult attribute) (gpf.enrichment_tool.event_counters.EventCountersResult attribute) (gpf.enrichment_tool.event_counters.EventsResult attribute) (gpf.enrichment_tool.event_counters.VariantEventsResult attribute) (gpf.person_sets.ChildrenBySex attribute) (gpf.person_sets.ChildrenStats attribute) (gpf.person_sets.person_sets.ChildrenBySex attribute) (gpf.person_sets.person_sets.ChildrenStats attribute) (gpf.variants.attributes.Sex attribute) male_female_legend() (in module gpf.pheno.graphs) MALE_PRB (gpf.pedigrees.family.FamilyTag attribute) males_count() (gpf.pheno.graphs.GraphColumn method) Manifest (class in gain.genomic_resources.repository) manifest (gain.genomic_resources.repository.ManifestUpdate attribute) ManifestEntry (class in gain.genomic_resources.repository) ManifestUpdate (class in gain.genomic_resources.repository) map_chromosome() (gain.genomic_resources.genomic_position_table.table.GenomicPositionTable method) (gain.genomic_resources.liftover_chain.LiftoverChain static method) MarkdownFileView (class in gpf_instance.views) mat2str() (in module gpf.utils.variant_utils) match_labels_query() (gain.annotation.annotation_config.AnnotationConfigParser static method) matched_alleles (gpf.variants.variant.SummaryVariant property) matched_alleles_indexes (gpf.variants.variant.SummaryVariant property) matched_gene_effects (gpf.variants.variant.SummaryVariant property) Matcher (class in gpf.query_variants.attribute_queries) maternal_aunt (gpf.variants.attributes.Role attribute) maternal_cousin (gpf.variants.attributes.Role attribute) maternal_grandfather (gpf.variants.attributes.Role attribute) maternal_grandmother (gpf.variants.attributes.Role attribute) maternal_half_sibling (gpf.variants.attributes.Role attribute) maternal_uncle (gpf.variants.attributes.Role attribute) Mating (class in gpf.pedigrees.family_role_builder) MatingUnit (class in gpf.pedigrees.pedigrees) max (gain.gene_sets.gene_set.ViewRangeSchema attribute) MAX_CHILD_NUMBER (gpf.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute) max_rank (gpf.pheno.common.RankRange attribute) max_rank() (gpf.pedigrees.pedigrees.FamilyConnections method) MAX_RUNNING_TASKS (gain.task_graph.dask_executor.DaskExecutor attribute) MAX_SHOWN_VARIANTS (genotype_browser.views.GenotypeBrowserQueryDownloadView attribute) (genotype_browser.views.GenotypeBrowserQueryView attribute) max_value (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) max_x (gpf.pedigrees.layout.Layout.BBox attribute) max_y (gpf.pedigrees.layout.Layout.BBox attribute) MaxAggregator (class in gain.genomic_resources.aggregators) maximally_extend_variant() (in module gain.genomic_resources.variant_utils) md5 (gain.genomic_resources.repository.ManifestEntry attribute) (gain.genomic_resources.repository.ResourceFileState attribute) (gain.genomic_resources.resource_implementation.InfoImplementationMixin.FileEntry attribute) md5_contents() (gain.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) MeanAggregator (class in gain.genomic_resources.aggregators) Measure (class in gpf.pheno.pheno_data) measure_column (gpf.pheno.common.DataDictionaryConfig attribute) measure_name (gpf.pheno.pheno_import.MeasureReport attribute) measure_names (gpf.pheno.common.RegressionMeasure attribute) measure_to_json() (pheno_tool_api.views.PhenoToolInstruments method) measure_type (gpf.pheno.pheno_import.MeasureReport attribute) MeasureDescriptionsConfig (class in gpf.pheno.common) MeasureHistogramConfigs (class in gpf.pheno.common) MeasureReport (class in gpf.pheno.pheno_import) measures (gpf.pheno.pheno_data.PhenotypeData property) measures_api module measures_api.urls module measures_api.views module measures_count_status() (pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method) (pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method) MeasureType (class in gpf.pheno.common) media (users_api.forms.WdaeLoginForm property) (users_api.forms.WdaePasswordForgottenForm property) (users_api.forms.WdaeRegisterPasswordForm property) (users_api.forms.WdaeResetPasswordForm property) media_type (sentry.views.PlainTextParser attribute) MedianAggregator (class in gain.genomic_resources.aggregators) member_fpids (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) member_has_both_parents() (gpf.pedigrees.family.Family method) member_has_dad() (gpf.pedigrees.family.Family method) member_has_mom() (gpf.pedigrees.family.Family method) member_has_parent() (gpf.pedigrees.family.Family method) member_ids (gpf.pedigrees.family.Family property) (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) member_index (gpf.pedigrees.family.Person property) member_is_child() (gpf.pedigrees.family.Family method) member_is_parent() (gpf.pedigrees.family.Family method) MemberDetailsView (class in family_api.views) members (gpf.pedigrees.pedigrees.FamilyConnections property) members_in_order (gpf.pedigrees.family.Family property) members_in_order_get_family_structure() (in module studies.response_transformer) members_index() (gpf.pedigrees.family.Family method) memory_limit (gpf.duckdb_storage.duckdb_storage_config.DuckDbBaseConf attribute) mendelian (gpf.variants.attributes.Inheritance attribute) merge() (gain.genomic_resources.histogram.CategoricalHistogram method) (gain.genomic_resources.histogram.NullHistogram method) (gain.genomic_resources.histogram.NumberHistogram method) (gain.genomic_resources.implementations.reference_genome_impl.ChromosomeStatistic method) (gain.genomic_resources.implementations.reference_genome_impl.GenomeStatistic method) (gain.genomic_resources.statistics.base_statistic.Statistic method) (gain.genomic_resources.statistics.min_max.MinMaxValue method) merge_config() (gpf.configuration.gpf_config_parser.GPFConfigParser static method) merge_configs() (gpf.person_sets.person_sets.PersonSetCollection static method) (gpf.person_sets.PersonSetCollection static method) merge_families() (in module gpf.pedigrees.families_data) merge_histogram_configs() (in module gpf.pheno.pheno_import) merge_inference_configs() (in module gpf.pheno.pheno_import) merge_parquet_directory() (in module gpf.parquet.schema2.merge_parquet) merge_parquets() (in module gpf.parquet.helpers) (in module gpf.parquet.schema2.merge_parquet) merge_partitions() (in module gpf.parquet.schema2.annotate_schema2_parquet) merge_variants_parquets() (in module gpf.parquet.parquet_writer) (in module gpf.parquet.schema2.merge_parquet) message (gain.annotation.annotation_config.AnnotationConfigurationError attribute) meta (gain.gene_sets.gene_set.BaseResourceSchema attribute) (gpf.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute) (gpf.schema2_storage.schema2_layout.Schema2DatasetLayout attribute) metadata (gain.annotation.annotation_config.AnnotationPreamble attribute) (gain.annotation.annotation_config.RawPreamble attribute) MetaSchema (class in gain.gene_sets.gene_set) Migration (class in datasets_api.migrations.0001_initial) (class in datasets_api.migrations.0002_dataset_groups) (class in datasets_api.migrations.0003_alter_dataset_options) (class in datasets_api.migrations.0004_dataset_broken) (class in datasets_api.migrations.0005_dataset_dataset_name) (class in datasets_api.migrations.0006_datasethierarchy) (class in datasets_api.migrations.0007_datasethierarchy_direct) (class in datasets_api.migrations.0008_datasethierarchy_instance_id) (class in query_state_save.migrations.0001_initial) (class in query_state_save.migrations.0002_auto_20190205_0736) (class in query_state_save.migrations.0003_querystate_origin_querystate_timestamp) (class in user_queries.migrations.0001_initial) (class in users_api.migrations.0001_initial) (class in users_api.migrations.0002_auto_20190424_0751) (class in users_api.migrations.0003_authenticationlog) (class in users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more) (class in users_api.migrations.0005_gpuserstate) min (gain.gene_sets.gene_set.ViewRangeSchema attribute) min_individuals (gpf.pheno.common.InferenceConfig attribute) (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) min_rank (gpf.pheno.common.RankRange attribute) min_value (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) min_x (gpf.pedigrees.layout.Layout.BBox attribute) min_y (gpf.pedigrees.layout.Layout.BBox attribute) MinAggregator (class in gain.genomic_resources.aggregators) MinMaxValue (class in gain.genomic_resources.statistics.min_max) MinMaxValueStatisticMixin (class in gain.genomic_resources.statistics.min_max) missing (gpf.pedigrees.family.Person property) (gpf.variants.attributes.Inheritance attribute) MISSING_DAD (gpf.pedigrees.family.FamilyTag attribute) MISSING_MOM (gpf.pedigrees.family.FamilyTag attribute) Mode (class in gain.genomic_resources.repository) mode() (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) ModeAggregator (class in gain.genomic_resources.aggregators) model (groups_api.serializers.GroupCreateSerializer.Meta attribute) (groups_api.serializers.GroupRetrieveSerializer.Meta attribute) (groups_api.serializers.GroupSerializer.Meta attribute) (query_state_save.serializers.QueryStateSerializer.Meta attribute) (users_api.serializers.UserSerializer.Meta attribute) (users_api.serializers.UserWithoutEmailSerializer.Meta attribute) model_computed_fields (gain.gene_sets.gene_set.BaseResourceSchema attribute) (gain.gene_sets.gene_set.CategoricalHistogramSchema attribute) (gain.gene_sets.gene_set.GeneSetResourceSchema attribute) (gain.gene_sets.gene_set.MetaSchema attribute) (gain.gene_sets.gene_set.NumericHistogramSchema attribute) (gain.gene_sets.gene_set.ViewRangeSchema attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbBaseConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbParquetConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute) (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (gpf.gene_sets.denovo_gene_sets_config.DGSSpec attribute) (gpf.gene_sets.denovo_gene_sets_config.EffectsCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.SexesCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.SingleCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.TripleCriteria attribute) (gpf.person_sets.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.person_sets.PersonSetConfig attribute) (gpf.person_sets.person_sets.SourceConfig attribute) (gpf.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.PersonSetConfig attribute) (gpf.person_sets.SourceConfig attribute) (gpf.pheno.common.DataDictionaryConfig attribute) (gpf.pheno.common.DestinationConfig attribute) (gpf.pheno.common.GPFInstanceConfig attribute) (gpf.pheno.common.ImportManifest attribute) (gpf.pheno.common.InferenceConfig attribute) (gpf.pheno.common.InstrumentConfig attribute) (gpf.pheno.common.InstrumentDescriptionsConfig attribute) (gpf.pheno.common.InstrumentDictionaryConfig attribute) (gpf.pheno.common.MeasureDescriptionsConfig attribute) (gpf.pheno.common.MeasureHistogramConfigs attribute) (gpf.pheno.common.PhenoImportConfig attribute) (gpf.pheno.common.RankRange attribute) (gpf.pheno.common.RegressionMeasure attribute) (gpf.pheno.common.StudyConfig attribute) (gpf.pheno.pheno_import.MeasureReport attribute) (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) (gpf.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute) (gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute) model_config (gain.gene_sets.gene_set.BaseResourceSchema attribute) (gain.gene_sets.gene_set.CategoricalHistogramSchema attribute) (gain.gene_sets.gene_set.GeneSetResourceSchema attribute) (gain.gene_sets.gene_set.MetaSchema attribute) (gain.gene_sets.gene_set.NumericHistogramSchema attribute) (gain.gene_sets.gene_set.ViewRangeSchema attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbBaseConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbParquetConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute) (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (gpf.gene_sets.denovo_gene_sets_config.DGSSpec attribute) (gpf.gene_sets.denovo_gene_sets_config.EffectsCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.SexesCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.SingleCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.TripleCriteria attribute) (gpf.person_sets.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.person_sets.PersonSetConfig attribute) (gpf.person_sets.person_sets.SourceConfig attribute) (gpf.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.PersonSetConfig attribute) (gpf.person_sets.SourceConfig attribute) (gpf.pheno.common.DataDictionaryConfig attribute) (gpf.pheno.common.DestinationConfig attribute) (gpf.pheno.common.GPFInstanceConfig attribute) (gpf.pheno.common.ImportManifest attribute) (gpf.pheno.common.InferenceConfig attribute) (gpf.pheno.common.InstrumentConfig attribute) (gpf.pheno.common.InstrumentDescriptionsConfig attribute) (gpf.pheno.common.InstrumentDictionaryConfig attribute) (gpf.pheno.common.MeasureDescriptionsConfig attribute) (gpf.pheno.common.MeasureHistogramConfigs attribute) (gpf.pheno.common.PhenoImportConfig attribute) (gpf.pheno.common.RankRange attribute) (gpf.pheno.common.RegressionMeasure attribute) (gpf.pheno.common.StudyConfig attribute) (gpf.pheno.pheno_import.MeasureReport attribute) (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) (gpf.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute) (gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute) model_fields (gain.gene_sets.gene_set.BaseResourceSchema attribute) (gain.gene_sets.gene_set.CategoricalHistogramSchema attribute) (gain.gene_sets.gene_set.GeneSetResourceSchema attribute) (gain.gene_sets.gene_set.MetaSchema attribute) (gain.gene_sets.gene_set.NumericHistogramSchema attribute) (gain.gene_sets.gene_set.ViewRangeSchema attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbBaseConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbParquetConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute) (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (gpf.gene_sets.denovo_gene_sets_config.DGSSpec attribute) (gpf.gene_sets.denovo_gene_sets_config.EffectsCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.SexesCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.SingleCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.TripleCriteria attribute) (gpf.person_sets.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.person_sets.PersonSetConfig attribute) (gpf.person_sets.person_sets.SourceConfig attribute) (gpf.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.PersonSetConfig attribute) (gpf.person_sets.SourceConfig attribute) (gpf.pheno.common.DataDictionaryConfig attribute) (gpf.pheno.common.DestinationConfig attribute) (gpf.pheno.common.GPFInstanceConfig attribute) (gpf.pheno.common.ImportManifest attribute) (gpf.pheno.common.InferenceConfig attribute) (gpf.pheno.common.InstrumentConfig attribute) (gpf.pheno.common.InstrumentDescriptionsConfig attribute) (gpf.pheno.common.InstrumentDictionaryConfig attribute) (gpf.pheno.common.MeasureDescriptionsConfig attribute) (gpf.pheno.common.MeasureHistogramConfigs attribute) (gpf.pheno.common.PhenoImportConfig attribute) (gpf.pheno.common.RankRange attribute) (gpf.pheno.common.RegressionMeasure attribute) (gpf.pheno.common.StudyConfig attribute) (gpf.pheno.pheno_import.MeasureReport attribute) (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) (gpf.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute) (gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute) modified() (in module gain.utils.fs_utils) modify_tuple() (gpf.configuration.gpf_config_parser.GPFConfigParser class method) module common_reports_api common_reports_api.common_reports_helper common_reports_api.urls common_reports_api.views conftest datasets_api datasets_api.migrations datasets_api.migrations.0001_initial datasets_api.migrations.0002_dataset_groups datasets_api.migrations.0003_alter_dataset_options datasets_api.migrations.0004_dataset_broken datasets_api.migrations.0005_dataset_dataset_name datasets_api.migrations.0006_datasethierarchy datasets_api.migrations.0007_datasethierarchy_direct datasets_api.migrations.0008_datasethierarchy_instance_id datasets_api.models datasets_api.permissions datasets_api.urls datasets_api.views enrichment_api enrichment_api.enrichment_builder enrichment_api.enrichment_helper enrichment_api.enrichment_serializer enrichment_api.urls enrichment_api.views family_api family_api.urls family_api.views gain gain.annotation gain.annotation.annotatable gain.annotation.annotate_columns gain.annotation.annotate_doc gain.annotation.annotate_utils gain.annotation.annotate_vcf gain.annotation.annotation_config gain.annotation.annotation_factory gain.annotation.annotation_genomic_context_cli gain.annotation.annotation_pipeline gain.annotation.annotator_base gain.annotation.chrom_mapping_annotator gain.annotation.cnv_collection_annotator gain.annotation.debug_annotator gain.annotation.docker_annotator gain.annotation.effect_annotator gain.annotation.gene_score_annotator gain.annotation.gene_set_annotator gain.annotation.liftover_annotator gain.annotation.normalize_allele_annotator gain.annotation.processing_pipeline gain.annotation.record_to_annotatable gain.annotation.score_annotator gain.annotation.simple_effect_annotator gain.annotation.utils gain.dask gain.dask.config gain.dask.named_cluster gain.effect_annotation gain.effect_annotation.annotation_effects gain.effect_annotation.annotation_request gain.effect_annotation.annotator gain.effect_annotation.cli gain.effect_annotation.effect gain.effect_annotation.effect_checkers gain.effect_annotation.effect_checkers.coding gain.effect_annotation.effect_checkers.effect_checker gain.effect_annotation.effect_checkers.frame_shift gain.effect_annotation.effect_checkers.intron gain.effect_annotation.effect_checkers.promoter gain.effect_annotation.effect_checkers.protein_change gain.effect_annotation.effect_checkers.splice_site gain.effect_annotation.effect_checkers.start_loss gain.effect_annotation.effect_checkers.stop_loss gain.effect_annotation.effect_checkers.utr gain.effect_annotation.gene_codes gain.effect_annotation.variant gain.gene_scores gain.gene_scores.gene_scores gain.gene_scores.implementations gain.gene_scores.implementations.gene_scores_impl gain.gene_sets gain.gene_sets.gene_set gain.gene_sets.gene_term gain.gene_sets.implementations gain.gene_sets.implementations.gene_sets_impl gain.genomic_resources gain.genomic_resources.aggregators gain.genomic_resources.cached_repository gain.genomic_resources.cli gain.genomic_resources.draw_score_histograms gain.genomic_resources.explore_grr_search gain.genomic_resources.fsspec_protocol gain.genomic_resources.gene_models gain.genomic_resources.gene_models.gene_models gain.genomic_resources.gene_models.gene_models_factory gain.genomic_resources.gene_models.parsers gain.genomic_resources.gene_models.serialization gain.genomic_resources.gene_models.transcript_models gain.genomic_resources.genomic_context gain.genomic_resources.genomic_context_base gain.genomic_resources.genomic_context_cli gain.genomic_resources.genomic_position_table gain.genomic_resources.genomic_position_table.line gain.genomic_resources.genomic_position_table.table gain.genomic_resources.genomic_position_table.table_bigwig gain.genomic_resources.genomic_position_table.table_inmemory gain.genomic_resources.genomic_position_table.table_tabix gain.genomic_resources.genomic_position_table.table_vcf gain.genomic_resources.genomic_position_table.utils gain.genomic_resources.genomic_scores gain.genomic_resources.group_repository gain.genomic_resources.histogram gain.genomic_resources.implementations gain.genomic_resources.implementations.annotation_pipeline_impl gain.genomic_resources.implementations.gene_models_impl gain.genomic_resources.implementations.genomic_scores_impl gain.genomic_resources.implementations.liftover_chain_impl gain.genomic_resources.implementations.reference_genome_impl gain.genomic_resources.liftover_chain gain.genomic_resources.reference_genome gain.genomic_resources.repository gain.genomic_resources.repository_factory gain.genomic_resources.resource_implementation gain.genomic_resources.statistics gain.genomic_resources.statistics.base_statistic gain.genomic_resources.statistics.min_max gain.genomic_resources.testing gain.genomic_resources.utils gain.genomic_resources.variant_utils gain.task_graph gain.task_graph.base_executor gain.task_graph.cache gain.task_graph.cli_tools gain.task_graph.dask_executor gain.task_graph.demo_graphs_cli gain.task_graph.executor gain.task_graph.graph gain.task_graph.logging gain.task_graph.process_pool_executor gain.task_graph.sequential_executor gain.testing gain.testing.acgt_import gain.testing.alla_import gain.testing.foobar_import gain.testing.t4c8_import gain.utils gain.utils.cnv_utils gain.utils.dae_utils gain.utils.debug_closing gain.utils.dict_utils gain.utils.fs_utils gain.utils.helpers gain.utils.processing_pipeline gain.utils.regions gain.utils.sql_utils gain.utils.stats_collection gain.utils.variant_utils gain.utils.verbosity_configuration gene_profiles_api gene_profiles_api.table_views gene_profiles_api.urls gene_profiles_api.views gene_scores gene_scores.urls gene_scores.views gene_sets gene_sets.urls gene_sets.views gene_view gene_view.urls gene_view.views genomes_api genomes_api.urls genomes_api.views genomic_scores_api genomic_scores_api.urls genomic_scores_api.views genotype_browser genotype_browser.urls genotype_browser.views gpf gpf.common_reports gpf.common_reports.common_report gpf.common_reports.denovo_report gpf.common_reports.family_counter gpf.common_reports.family_report gpf.common_reports.people_counter gpf.configuration gpf.configuration.gpf_config_parser gpf.configuration.schemas gpf.configuration.schemas.dae_conf gpf.configuration.schemas.gene_profile gpf.configuration.schemas.gene_weights_db gpf.configuration.schemas.person_sets gpf.configuration.schemas.phenotype_data gpf.configuration.schemas.study_config gpf.configuration.schemas.wdae_study_config gpf.configuration.study_config_builder gpf.configuration.utils gpf.duckdb_storage gpf.duckdb_storage.duckdb2_variants gpf.duckdb_storage.duckdb_connection_factory gpf.duckdb_storage.duckdb_genotype_storage gpf.duckdb_storage.duckdb_import_storage gpf.duckdb_storage.duckdb_legacy_genotype_storage gpf.duckdb_storage.duckdb_storage_config gpf.duckdb_storage.duckdb_storage_helpers gpf.duckdb_storage.duckdb_variants gpf.enrichment_tool gpf.enrichment_tool.base_enrichment_background gpf.enrichment_tool.build_coding_length_enrichment_background gpf.enrichment_tool.build_ur_synonymous_enrichment_background gpf.enrichment_tool.enrichment_cache_builder gpf.enrichment_tool.enrichment_utils gpf.enrichment_tool.event_counters gpf.enrichment_tool.gene_weights_background gpf.enrichment_tool.genotype_helper gpf.enrichment_tool.resource_implementations gpf.enrichment_tool.resource_implementations.enrichment_resource_impl gpf.enrichment_tool.samocha_background gpf.gene_profile gpf.gene_profile.convert_gene_profile_to_duckdb gpf.gene_profile.db gpf.gene_profile.exporter gpf.gene_profile.generate_gene_profile gpf.gene_profile.statistic gpf.gene_sets gpf.gene_sets.denovo_gene_set_collection gpf.gene_sets.denovo_gene_set_helpers gpf.gene_sets.denovo_gene_sets_config gpf.gene_sets.denovo_gene_sets_db gpf.gene_sets.gene_sets_db gpf.genomic_scores gpf.genomic_scores.scores gpf.genotype_storage gpf.genotype_storage.genotype_storage gpf.genotype_storage.genotype_storage_genomic_context_cli gpf.genotype_storage.genotype_storage_registry gpf.gpf_instance gpf.gpf_instance.adjustments gpf.gpf_instance.adjustments.adjust_command gpf.gpf_instance.adjustments.adjust_duckdb_storage gpf.gpf_instance.adjustments.adjust_impala_storage gpf.gpf_instance.adjustments.gpf_instance_adjustments gpf.gpf_instance.gpf_instance gpf.gpf_instance_plugin gpf.gpf_instance_plugin.gpf_instance_context_plugin gpf.import_tools gpf.import_tools.cli gpf.import_tools.import_config gpf.import_tools.import_tools gpf.inmemory_storage gpf.inmemory_storage.annotation_serialization gpf.inmemory_storage.inmemory_genotype_storage gpf.inmemory_storage.inmemory_import_storage gpf.inmemory_storage.raw_variants gpf.parquet gpf.parquet.helpers gpf.parquet.parquet_writer gpf.parquet.partition_descriptor gpf.parquet.schema2 gpf.parquet.schema2.annotate_schema2_parquet gpf.parquet.schema2.loader gpf.parquet.schema2.merge_parquet gpf.parquet.schema2.parquet_io gpf.parquet.schema2.processing_pipeline gpf.parquet.schema2.serializers gpf.parquet.schema2.variants_parquet_writer gpf.parquet_storage gpf.parquet_storage.storage gpf.pedigrees gpf.pedigrees.drawing gpf.pedigrees.families_data gpf.pedigrees.family gpf.pedigrees.family_role_builder gpf.pedigrees.family_tag_builder gpf.pedigrees.layout gpf.pedigrees.loader gpf.pedigrees.pedigrees gpf.pedigrees.testing gpf.person_filters gpf.person_filters.person_filters gpf.person_sets gpf.person_sets.person_sets gpf.pheno gpf.pheno.browser gpf.pheno.build_pheno_browser gpf.pheno.common gpf.pheno.db gpf.pheno.graphs gpf.pheno.import_tools gpf.pheno.pheno_data gpf.pheno.pheno_import gpf.pheno.prepare gpf.pheno.prepare.measure_classifier gpf.pheno.prepare_data gpf.pheno.registry gpf.pheno.storage gpf.pheno.update_pheno_descriptions gpf.pheno.utils gpf.pheno.utils.commons gpf.pheno.utils.lin_regress gpf.pheno_tool gpf.pheno_tool.pheno_tool_adapter gpf.pheno_tool.tool gpf.query_variants gpf.query_variants.attribute_queries gpf.query_variants.base_query_variants gpf.query_variants.query_runners gpf.query_variants.sql gpf.query_variants.sql.schema2 gpf.query_variants.sql.schema2.base_query_builder gpf.query_variants.sql.schema2.base_variants gpf.query_variants.sql.schema2.family_builder gpf.query_variants.sql.schema2.sql_query_builder gpf.query_variants.sql.schema2.summary_builder gpf.schema2_storage gpf.schema2_storage.schema2_import_storage gpf.schema2_storage.schema2_layout gpf.studies gpf.studies.study gpf.studies.variants_db gpf.testing gpf.testing.acgt_import gpf.testing.alla_import gpf.testing.foobar_import gpf.testing.import_helpers gpf.testing.setup_helpers gpf.testing.t4c8_import gpf.tools gpf.tools.dae2vcf gpf.tools.dataset_helpers gpf.tools.denovo2vcf gpf.tools.draw_pedigree gpf.tools.generate_common_report gpf.tools.generate_denovo_gene_sets gpf.tools.gpf_convert_study_config gpf.tools.gpf_validation_runner gpf.tools.grr_cache_repo gpf.tools.liftover_tools gpf.tools.ped2ped gpf.tools.reannotate_instance gpf.tools.simple_study_import gpf.tools.to_gpf_gene_models_format gpf.tools.vcf2tsv gpf.utils gpf.utils.testing gpf.utils.variant_utils gpf.variants gpf.variants.attributes gpf.variants.core gpf.variants.family_variant gpf.variants.variant gpf.variants_loaders gpf.variants_loaders.cnv gpf.variants_loaders.cnv.flexible_cnv_loader gpf.variants_loaders.cnv.loader gpf.variants_loaders.dae gpf.variants_loaders.dae.loader gpf.variants_loaders.parquet gpf.variants_loaders.parquet.loader gpf.variants_loaders.raw gpf.variants_loaders.raw.flexible_variant_loader gpf.variants_loaders.raw.loader gpf.variants_loaders.vcf gpf.variants_loaders.vcf.loader gpf.variants_loaders.vcf.serializer gpf_instance gpf_instance.apps gpf_instance.extension gpf_instance.gpf_instance gpf_instance.urls gpf_instance.views gpf_web gpf_web.default_settings gpf_web.eager_settings gpf_web.gunicorn_settings gpf_web.mypy_settings gpf_web.remote_settings gpf_web.settings gpf_web.silk_settings gpf_web.urls gpf_web.wdaemanage gpf_web.wgpf gpf_web.wgpf_settings gpfjs gpfjs.views groups_api groups_api.migrations groups_api.serializers groups_api.urls groups_api.views measures_api measures_api.urls measures_api.views person_sets_api person_sets_api.urls person_sets_api.views pheno_browser_api pheno_browser_api.pheno_browser_helper pheno_browser_api.urls pheno_browser_api.views pheno_tool_api pheno_tool_api.adapter pheno_tool_api.urls pheno_tool_api.views query_base query_base.query_base query_state_save query_state_save.migrations query_state_save.migrations.0001_initial query_state_save.migrations.0002_auto_20190205_0736 query_state_save.migrations.0003_querystate_origin_querystate_timestamp query_state_save.models query_state_save.serializers query_state_save.urls query_state_save.views sentry sentry.urls sentry.views studies studies.conftest studies.query_transformer studies.response_transformer studies.study_wrapper user_queries user_queries.migrations user_queries.migrations.0001_initial user_queries.models user_queries.urls user_queries.views users_api users_api.forms users_api.management users_api.management.commands users_api.management.commands.dataset_groups users_api.management.commands.dataset_mixin users_api.management.commands.datasets_export users_api.management.commands.datasets_restore users_api.management.commands.datasets_show users_api.management.commands.export_base users_api.management.commands.import_base users_api.management.commands.unlock_user users_api.management.commands.user_create users_api.management.commands.user_set_name users_api.management.commands.user_setpasswd users_api.management.commands.users_add users_api.management.commands.users_export users_api.management.commands.users_group_add users_api.management.commands.users_group_remove users_api.management.commands.users_remove users_api.management.commands.users_restore users_api.management.commands.users_show users_api.migrations users_api.migrations.0001_initial users_api.migrations.0002_auto_20190424_0751 users_api.migrations.0003_authenticationlog users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more users_api.migrations.0005_gpuserstate users_api.models users_api.serializers users_api.urls users_api.validators users_api.views utils utils.authentication utils.datasets utils.email_regex utils.expand_gene_set utils.gene_sets utils.logger utils.pagination utils.password_requirements utils.query_params utils.streaming_response_util utils.testing

mom (gpf.variants.attributes.Role attribute) MULTIPLEX (gpf.pedigrees.family.FamilyTag attribute) MultiReader (class in gpf.parquet.schema2.loader) mutation_type() (gain.effect_annotation.effect_checkers.protein_change.ProteinChangeEffectChecker method)

N

name (gain.annotation.annotation_config.AttributeInfo attribute) (gain.annotation.annotation_pipeline.AttributeDesc attribute) (gain.gene_sets.gene_set.GeneSet attribute) (gain.genomic_resources.repository.ManifestEntry attribute) (gain.genomic_resources.resource_implementation.InfoImplementationMixin.FileEntry attribute) (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground property) (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentResourceBackground property) (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property) (gpf.enrichment_tool.samocha_background.SamochaEnrichmentBackground property) (gpf.gene_sets.denovo_gene_sets_config.EffectsCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.SexesCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.SingleCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.TripleCriteria attribute) (gpf.genomic_scores.scores.ScoreDesc attribute) (gpf.person_sets.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.person_sets.PersonSetConfig attribute) (gpf.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.PersonSetConfig attribute) (gpf.pheno.pheno_import.ImportInstrument attribute) (gpf.studies.study.GenotypeData property) (gpf_instance.apps.WDAEConfig attribute) (groups_api.views.GroupsViewSet attribute) (studies.study_wrapper.WDAEAbstractStudy property) (user_queries.models.UserQuery attribute) (users_api.models.WdaeUser attribute) (users_api.views.UserViewSet attribute) names() (gain.genomic_resources.repository.Manifest method) nan (gpf.pheno.prepare.measure_classifier.Convertible attribute) natural_order (gain.gene_sets.gene_set.CategoricalHistogramSchema attribute) (gain.genomic_resources.histogram.CategoricalHistogramConfig attribute) NCBIGeneInfo (class in gain.gene_sets.gene_term) NEEDS_COMPUTE (gain.task_graph.cache.CacheRecordType attribute)

neg() (gpf.query_variants.attribute_queries.AttributeQueryTransformerFunction method) (gpf.query_variants.attribute_queries.AttributeQueryTransformerSQL method) (gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method) NegativeStrandAnnotationRequest (class in gain.effect_annotation.annotation_request) NO_RANK (gpf.pedigrees.pedigrees.Individual attribute) NOBODY_INTEREST_LOG_INTERVAL (gpf.query_variants.query_runners.QueryRunner attribute) NOBODY_INTEREST_THRESHOLD (gpf.query_variants.query_runners.QueryRunner attribute) non_numeric (gpf.pheno.prepare.measure_classifier.Convertible attribute) non_numeric_cutoff (gpf.pheno.common.InferenceConfig attribute) noncoding_regions() (gain.annotation.simple_effect_annotator.SimpleEffectAnnotator method) normalization_rules (gpf.configuration.gpf_config_parser.GPFConfigValidator attribute) normalize() (gpf.import_tools.import_tools.ImportConfigNormalizer method) normalize_allele() (in module gain.annotation.normalize_allele_annotator) normalize_variant() (in module gain.genomic_resources.variant_utils) NormalizeAlleleAnnotator (class in gain.annotation.normalize_allele_annotator) not_role() (gpf.variants.attributes.Role static method) not_sequenced (gpf.pedigrees.family.Person property) NoTaskCache (class in gain.task_graph.cache) NOTSET (gpf.tools.gpf_validation_runner.TestStatus attribute) ns_tokens (gain.gene_sets.gene_term.NCBIGeneInfo attribute) NUCLEAR (gpf.pedigrees.family.FamilyTag attribute) NuclearCode (class in gain.effect_annotation.gene_codes) NullHistogram (class in gain.genomic_resources.histogram) NullHistogramConfig (class in gain.genomic_resources.histogram) number_config (gpf.pheno.common.MeasureHistogramConfigs attribute) number_of_bins (gain.gene_sets.gene_set.NumericHistogramSchema attribute) (gain.genomic_resources.histogram.NumberHistogramConfig attribute) number_of_children_with_event (gpf.common_reports.denovo_report.EffectCell property) number_of_observed_events (gpf.common_reports.denovo_report.EffectCell property) NumberHistogram (class in gain.genomic_resources.histogram) NumberHistogramConfig (class in gain.genomic_resources.histogram) numeric (gpf.pheno.prepare.measure_classifier.Convertible attribute) NumericHistogramSchema (class in gain.gene_sets.gene_set)

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) oauth_app() (in module conftest) oauth_cookie_to_header() (in module utils.authentication) objects (datasets_api.models.Dataset attribute) (datasets_api.models.DatasetHierarchy attribute) (query_state_save.models.QueryState attribute) (user_queries.models.UserQuery attribute) (users_api.models.AuthenticationLog attribute) (users_api.models.GpUserState attribute) (users_api.models.ResetPasswordCode attribute) (users_api.models.SetPasswordCode attribute) (users_api.models.WdaeUser attribute) observed_rate_per_child (gpf.common_reports.denovo_report.EffectCell property) obtain_resource_file_lock() (gain.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) OffsetLayoutDrawer (class in gpf.pedigrees.drawing) omission (gpf.variants.attributes.Inheritance attribute) open() (gain.annotation.annotation_pipeline.AnnotationPipeline method) (gain.annotation.annotation_pipeline.Annotator method) (gain.annotation.annotation_pipeline.AnnotatorDecorator method) (gain.annotation.annotator_base.AnnotatorBase method) (gain.annotation.cnv_collection_annotator.CnvCollectionAnnotator method) (gain.annotation.docker_annotator.DockerAnnotator method) (gain.annotation.effect_annotator.EffectAnnotatorAdapter method) (gain.annotation.gene_set_annotator.GeneSetAnnotator method) (gain.annotation.liftover_annotator.AbstractLiftoverAnnotator method) (gain.annotation.normalize_allele_annotator.NormalizeAlleleAnnotator method) (gain.annotation.score_annotator.GenomicScoreAnnotatorBase method) (gain.annotation.simple_effect_annotator.SimpleEffectAnnotator method) (gain.gene_scores.gene_scores.GeneScore method) (gain.genomic_resources.genomic_position_table.BigWigTable method) (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table.GenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table_bigwig.BigWigTable method) (gain.genomic_resources.genomic_position_table.table_inmemory.InmemoryGenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table_tabix.TabixGenomicPositionTable method) (gain.genomic_resources.genomic_position_table.table_vcf.VCFGenomicPositionTable method) (gain.genomic_resources.genomic_position_table.VCFGenomicPositionTable method) (gain.genomic_resources.genomic_scores.AlleleScore method) (gain.genomic_resources.genomic_scores.CnvCollection method) (gain.genomic_resources.genomic_scores.GenomicScore method) (gain.genomic_resources.genomic_scores.PositionScore method) (gain.genomic_resources.liftover_chain.LiftoverChain method) (gain.genomic_resources.reference_genome.ReferenceGenome method) (gpf.variants_loaders.vcf.serializer.VcfSerializer method) open_bigwig_file() (gain.genomic_resources.cached_repository.CachingProtocol method) (gain.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (gain.genomic_resources.repository.GenomicResource method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method)

open_file() (in module gpf.pheno.pheno_import) open_raw_file() (gain.genomic_resources.cached_repository.CachingProtocol method) (gain.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (gain.genomic_resources.repository.GenomicResource method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) open_repository_sqlite3_metadata_db() (gain.genomic_resources.cached_repository.CachingProtocol method) (gain.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) open_tabix_file() (gain.genomic_resources.cached_repository.CachingProtocol method) (gain.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (gain.genomic_resources.repository.GenomicResource method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) open_vcf_file() (gain.genomic_resources.cached_repository.CachingProtocol method) (gain.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (gain.genomic_resources.repository.GenomicResource method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) operations (datasets_api.migrations.0001_initial.Migration attribute) (datasets_api.migrations.0002_dataset_groups.Migration attribute) (datasets_api.migrations.0003_alter_dataset_options.Migration attribute) (datasets_api.migrations.0004_dataset_broken.Migration attribute) (datasets_api.migrations.0005_dataset_dataset_name.Migration attribute) (datasets_api.migrations.0006_datasethierarchy.Migration attribute) (datasets_api.migrations.0007_datasethierarchy_direct.Migration attribute) (datasets_api.migrations.0008_datasethierarchy_instance_id.Migration attribute) (query_state_save.migrations.0001_initial.Migration attribute) (query_state_save.migrations.0002_auto_20190205_0736.Migration attribute) (query_state_save.migrations.0003_querystate_origin_querystate_timestamp.Migration attribute) (user_queries.migrations.0001_initial.Migration attribute) (users_api.migrations.0001_initial.Migration attribute) (users_api.migrations.0002_auto_20190424_0751.Migration attribute) (users_api.migrations.0003_authenticationlog.Migration attribute) (users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more.Migration attribute) (users_api.migrations.0005_gpuserstate.Migration attribute) OPTION (gpf.variants_loaders.raw.loader.ArgumentType attribute) or_() (gpf.query_variants.attribute_queries.AttributeQueryTransformerFunction method) (gpf.query_variants.attribute_queries.AttributeQueryTransformerSQL method) (gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method) ordinal (gpf.pheno.common.InferenceConfig attribute) (gpf.pheno.common.MeasureType attribute) origin (query_state_save.models.QueryState attribute) other (gpf.pheno.common.MeasureType attribute) (gpf.variants.attributes.Inheritance attribute) other_parent() (gpf.pedigrees.pedigrees.MatingUnit method) output_files (gain.task_graph.graph.TaskDesc attribute) overlap_enrichment_result_dict() (in module gpf.enrichment_tool.event_counters) overlap_event_counts() (in module gpf.enrichment_tool.event_counters)

P

page (query_state_save.models.QueryState attribute) page_size (datasets_api.views.DatasetPermissionsSingleView attribute) (datasets_api.views.DatasetPermissionsView attribute) PAGE_SIZE (gpf.gene_profile.db.GeneProfileDB attribute) (gpf.pheno.browser.PhenoBrowser attribute) page_size_query_param (utils.pagination.WdaePageNumberPagination attribute) paginate_queryset() (utils.pagination.WdaePageNumberPagination method) parameters (gain.annotation.annotation_config.AnnotatorInfo attribute) (gain.annotation.annotation_config.AttributeInfo attribute) params (gain.annotation.annotation_pipeline.AttributeDesc attribute) ParamsUsageMonitor (class in gain.annotation.annotation_config) parent (gpf.variants.attributes.Role attribute) parents (gpf.studies.study.GenotypeData property) (studies.study_wrapper.WDAEAbstractStudy property) parents_id() (gpf.pedigrees.family_role_builder.Mating static method) parents_zygosity (gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute) ParquetGenotypeStorage (class in gpf.parquet_storage.storage) ParquetImportStorage (class in gpf.parquet_storage.storage) ParquetLoader (class in gpf.parquet.schema2.loader) (class in gpf.variants_loaders.parquet.loader) ParquetLoaderException ParquetLoaderVariants (class in gpf.parquet_storage.storage) parse() (gpf.parquet.partition_descriptor.PartitionDescriptor static method) (sentry.views.PlainTextParser method) parse_and_interpolate() (gpf.configuration.gpf_config_parser.GPFConfigParser static method) parse_and_interpolate_file() (gpf.configuration.gpf_config_parser.GPFConfigParser class method) parse_ccds_gene_models_format() (in module gain.genomic_resources.gene_models.parsers) parse_cli_argument() (gpf.variants_loaders.raw.loader.CLIArgument method) parse_cli_arguments() (gpf.pedigrees.loader.FamiliesLoader class method) (gpf.variants_loaders.cnv.loader.CNVLoader class method) (gpf.variants_loaders.dae.loader.DaeTransmittedLoader class method) (gpf.variants_loaders.dae.loader.DenovoLoader class method) (gpf.variants_loaders.raw.loader.CLILoader class method) (gpf.variants_loaders.vcf.loader.VcfLoader class method) (in module gain.genomic_resources.draw_score_histograms) (in module gpf.tools.dae2vcf) (in module gpf.tools.denovo2vcf) (in module gpf.tools.vcf2tsv) parse_complete() (gain.annotation.annotation_config.AnnotationConfigParser static method) parse_default_gene_models_format() (in module gain.genomic_resources.gene_models.parsers) parse_denovo_gene_sets_config() (in module gpf.gene_sets.denovo_gene_sets_config) parse_denovo_gene_sets_study_config() (in module gpf.gene_sets.denovo_gene_sets_config) parse_dgsc_query() (in module gpf.gene_sets.denovo_gene_sets_config) parse_dict() (gpf.parquet.partition_descriptor.PartitionDescriptor static method) parse_duckdb_config() (in module gpf.duckdb_storage.duckdb_storage_config) parse_gr_id_version_token() (in module gain.genomic_resources.repository) parse_gtf_gene_models_format() (in module gain.genomic_resources.gene_models.parsers) parse_known_gene_models_format() (in module gain.genomic_resources.gene_models.parsers) parse_minimal() (gain.annotation.annotation_config.AnnotationConfigParser static method) parse_person_set_collection_config() (in module gpf.person_sets) (in module gpf.person_sets.person_sets) parse_person_set_collections_study_config() (in module gpf.person_sets) (in module gpf.person_sets.person_sets) parse_person_set_config() (in module gpf.person_sets) (in module gpf.person_sets.person_sets) parse_query_params() (in module utils.query_params) parse_raw() (gain.annotation.annotation_config.AnnotationConfigParser static method) (in module gain.genomic_resources.gene_models.parsers) parse_raw_attribute_config() (gain.annotation.annotation_config.AnnotationConfigParser static method) parse_raw_attributes() (gain.annotation.annotation_config.AnnotationConfigParser static method) parse_recurrency_criteria() (in module gpf.gene_sets.denovo_gene_sets_config) parse_ref_flat_gene_models_format() (in module gain.genomic_resources.gene_models.parsers) parse_ref_seq_gene_models_format() (in module gain.genomic_resources.gene_models.parsers) parse_resource_id_version() (in module gain.genomic_resources.repository) parse_short() (gain.annotation.annotation_config.AnnotationConfigParser static method) parse_str() (gain.annotation.annotation_config.AnnotationConfigParser static method) parse_string() (gpf.parquet.partition_descriptor.PartitionDescriptor static method) parse_ucscgenepred_models_format() (in module gain.genomic_resources.gene_models.parsers) partial_update() (groups_api.views.GroupsViewSet method) (users_api.views.UserViewSet method) Partition (class in gpf.parquet.partition_descriptor) partition_directory() (gpf.parquet.partition_descriptor.PartitionDescriptor static method) partition_filename() (gpf.parquet.partition_descriptor.PartitionDescriptor static method) PartitionDescriptor (class in gpf.parquet.partition_descriptor) PASSED (gpf.tools.gpf_validation_runner.TestStatus attribute) passed_case_count (gpf.tools.gpf_validation_runner.AbstractRunner property) (gpf.tools.gpf_validation_runner.MainRunner property) password (users_api.models.WdaeUser attribute) password_reset() (users_api.views.UserViewSet method) paternal_aunt (gpf.variants.attributes.Role attribute) paternal_cousin (gpf.variants.attributes.Role attribute) paternal_grandfather (gpf.variants.attributes.Role attribute) paternal_grandmother (gpf.variants.attributes.Role attribute) paternal_half_sibling (gpf.variants.attributes.Role attribute) paternal_uncle (gpf.variants.attributes.Role attribute) path (gpf.pheno.common.DataDictionaryConfig attribute) (gpf.pheno.common.GPFInstanceConfig attribute) (gpf.pheno.common.InstrumentConfig attribute) (gpf.pheno.common.InstrumentDictionaryConfig attribute) (users_api.models.BaseVerificationCode attribute) (users_api.models.ResetPasswordCode attribute) (users_api.models.SetPasswordCode attribute) path_to_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor static method) PDFLayoutDrawer (class in gpf.pedigrees.drawing) ped_df (gpf.pedigrees.families_data.FamiliesData property) pedigree (gpf.pheno.common.PhenoImportConfig attribute) (gpf.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute) (gpf.schema2_storage.schema2_layout.Schema2DatasetLayout attribute) (gpf.testing.import_helpers.StudyInputLayout attribute) pedigree_import() (in module gpf.testing.import_helpers) pedigree_parquet_schema() (in module gpf.parquet.parquet_writer) pedigree_samples() (gpf.pedigrees.families_data.FamiliesData method) peek_first() (gain.genomic_resources.genomic_position_table.line.LineBuffer method) (gain.genomic_resources.genomic_position_table.LineBuffer method) peek_last() (gain.genomic_resources.genomic_position_table.line.LineBuffer method) (gain.genomic_resources.genomic_position_table.LineBuffer method) PeopleCounter (class in gpf.common_reports.people_counter) PeopleCounters (class in gpf.common_reports.people_counter) PeopleReport (class in gpf.common_reports.people_counter) percent_of_children_with_events (gpf.common_reports.denovo_report.EffectCell property) peripheral_regions() (gain.annotation.simple_effect_annotator.SimpleEffectAnnotator method) permission_classes (groups_api.views.GroupsViewSet attribute) (query_base.query_base.DatasetAccessRightsView attribute) (users_api.views.UserViewSet attribute) permitted_datasets() (datasets_api.permissions.IsDatasetAllowed static method) Person (class in gpf.pedigrees.family) person_column (gpf.pheno.common.InstrumentConfig attribute) (gpf.pheno.common.PhenoImportConfig attribute) (gpf.pheno.pheno_import.ImportInstrument attribute) person_ids (gpf.studies.study.PSCQueryAdjustments attribute) person_ids() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) person_set_collections (gpf.pheno.common.StudyConfig attribute) (gpf.pheno.pheno_data.PhenotypeData property) (gpf.pheno.pheno_data.PhenotypeGroup property) (gpf.pheno.pheno_data.PhenotypeStudy property) (gpf.studies.study.GenotypeData property) (studies.study_wrapper.WDAEAbstractStudy property) person_sets_api module person_sets_api.urls module person_sets_api.views module PersonFilter (class in gpf.person_filters) (class in gpf.person_filters.person_filters) PersonFilterRange (class in gpf.person_filters) (class in gpf.person_filters.person_filters) PersonFilterSet (class in gpf.person_filters) (class in gpf.person_filters.person_filters) persons (gpf.enrichment_tool.genotype_helper.AlleleEvent attribute) persons_with_parent() (gpf.pedigrees.families_data.FamiliesData method) persons_with_parents() (gpf.pedigrees.families_data.FamiliesData method) persons_without_parents() (gpf.pedigrees.families_data.FamiliesData method) PersonSet (class in gpf.person_sets) (class in gpf.person_sets.person_sets) PersonSetCollection (class in gpf.person_sets) (class in gpf.person_sets.person_sets) PersonSetCollectionConfig (class in gpf.person_sets) (class in gpf.person_sets.person_sets) PersonSetConfig (class in gpf.person_sets) (class in gpf.person_sets.person_sets) pheno_browser_api module pheno_browser_api.pheno_browser_helper module pheno_browser_api.urls module pheno_browser_api.views module pheno_cli_parser() (in module gpf.pheno.build_pheno_browser) (in module gpf.pheno.import_tools) (in module gpf.pheno.pheno_import) (in module gpf.pheno.update_pheno_descriptions) pheno_id (gpf.pheno.pheno_data.PhenotypeData property) pheno_tool_api module pheno_tool_api.adapter module pheno_tool_api.urls module pheno_tool_api.views module PhenoBrowser (class in gpf.pheno.browser) PhenoBrowserHelper (class in pheno_browser_api.pheno_browser_helper) PhenoDataRoleListView (class in measures_api.views) PhenoDb (class in gpf.pheno.db) PhenoFilter (class in gpf.person_filters) (class in gpf.person_filters.person_filters)

PhenoFilterRange (class in gpf.person_filters) (class in gpf.person_filters.person_filters) PhenoFilterSet (class in gpf.person_filters) (class in gpf.person_filters.person_filters) PhenoImagesView (class in pheno_browser_api.views) PhenoImportConfig (class in gpf.pheno.common) PhenoInstrumentsView (class in pheno_browser_api.views) PhenoMeasureDescriptionView (class in pheno_browser_api.views) PhenoMeasureHistogramView (class in measures_api.views) PhenoMeasureHistogramViewBeta (class in measures_api.views) PhenoMeasureListView (class in measures_api.views) PhenoMeasurePartitionsView (class in measures_api.views) PhenoMeasureRegressionsView (class in measures_api.views) PhenoMeasuresCount (class in pheno_browser_api.views) PhenoMeasuresDownload (class in pheno_browser_api.views) PhenoMeasuresInfoView (class in pheno_browser_api.views) PhenoMeasuresView (class in measures_api.views) (class in pheno_browser_api.views) PhenoRegistry (class in gpf.pheno.registry) PhenoResult (class in gpf.pheno_tool.tool) PhenoTool (class in gpf.pheno_tool.tool) PhenoToolAdapter (class in gpf.pheno_tool.pheno_tool_adapter) (class in pheno_tool_api.adapter) PhenoToolAdapterBase (class in gpf.pheno_tool.pheno_tool_adapter) (class in pheno_tool_api.adapter) PhenoToolDownload (class in pheno_tool_api.views) PhenoToolHelper (class in gpf.pheno_tool.tool) PhenoToolInstruments (class in pheno_tool_api.views) PhenoToolMeasure (class in pheno_tool_api.views) PhenoToolMeasures (class in pheno_tool_api.views) PhenoToolPeopleValues (class in pheno_tool_api.views) PhenoToolView (class in pheno_tool_api.views) phenotype (gpf.studies.study.GenotypeData property) PHENOTYPE_ATTRS (studies.response_transformer.ResponseTransformer attribute) phenotype_data (studies.study_wrapper.WDAEAbstractStudy property) phenotype_storages (gpf.gpf_instance.gpf_instance.GPFInstance property) (gpf.gpf_instance.GPFInstance property) PhenotypeData (class in gpf.pheno.pheno_data) PhenotypeGroup (class in gpf.pheno.pheno_data) PhenotypeStorage (class in gpf.pheno.storage) PhenotypeStorageRegistry (class in gpf.pheno.storage) PhenotypeStudy (class in gpf.pheno.pheno_data) PipelineProcessor (class in gain.utils.processing_pipeline) PlainTextParser (class in sentry.views) plot() (gain.genomic_resources.histogram.CategoricalHistogram method) (gain.genomic_resources.histogram.NullHistogram method) (gain.genomic_resources.histogram.NumberHistogram method) plot_function (gain.gene_sets.gene_set.CategoricalHistogramSchema attribute) (gain.gene_sets.gene_set.NumericHistogramSchema attribute) (gain.genomic_resources.histogram.CategoricalHistogramConfig attribute) (gain.genomic_resources.histogram.NumberHistogramConfig attribute) plot_histogram() (in module gain.genomic_resources.histogram) Point (class in gpf.pedigrees.layout) poisson_test() (in module gpf.enrichment_tool.samocha_background) pop_first() (gain.genomic_resources.genomic_position_table.line.LineBuffer method) (gain.genomic_resources.genomic_position_table.LineBuffer method) pos (gain.annotation.annotatable.Annotatable property) pos_aggregator (gain.genomic_resources.genomic_scores.ScoreDef attribute) pos_begin (gain.genomic_resources.genomic_position_table.Line attribute) (gain.genomic_resources.genomic_position_table.line.Line attribute) (gain.genomic_resources.genomic_position_table.line.LineBase attribute) POS_BEGIN (gain.genomic_resources.genomic_position_table.table.GenomicPositionTable attribute) (gain.genomic_resources.genomic_position_table.table_vcf.VCFGenomicPositionTable attribute) (gain.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) pos_begin (gain.genomic_resources.genomic_scores.CNV attribute) (gain.genomic_resources.genomic_scores.ScoreLine property) pos_begin_key (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (gain.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) pos_end (gain.annotation.annotatable.Annotatable property) (gain.genomic_resources.genomic_position_table.Line attribute) (gain.genomic_resources.genomic_position_table.line.Line attribute) (gain.genomic_resources.genomic_position_table.line.LineBase attribute) POS_END (gain.genomic_resources.genomic_position_table.table.GenomicPositionTable attribute) (gain.genomic_resources.genomic_position_table.table_vcf.VCFGenomicPositionTable attribute) (gain.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) pos_end (gain.genomic_resources.genomic_scores.CNV attribute) (gain.genomic_resources.genomic_scores.ScoreLine property) pos_end_key (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (gain.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) Position (class in gain.annotation.annotatable) position (gain.annotation.annotatable.Annotatable property) POSITION (gain.annotation.annotatable.Annotatable.Type attribute) position (gpf.variants.core.Allele property) (gpf.variants.core.Allele.Type attribute) (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) (gpf.variants.variant.SummaryVariant property) position_aggregator (gain.genomic_resources.genomic_scores.AlleleScoreAggr attribute) (gain.genomic_resources.genomic_scores.AlleleScoreQuery attribute) (gain.genomic_resources.genomic_scores.PositionScoreAggr attribute) (gain.genomic_resources.genomic_scores.PositionScoreQuery attribute) PositionScore (class in gain.genomic_resources.genomic_scores) PositionScoreAggr (class in gain.genomic_resources.genomic_scores) PositionScoreAnnotator (class in gain.annotation.score_annotator) PositionScoreQuery (class in gain.genomic_resources.genomic_scores) PositiveStrandAnnotationRequest (class in gain.effect_annotation.annotation_request) possible_denovo (gpf.variants.attributes.Inheritance attribute) possible_omission (gpf.variants.attributes.Inheritance attribute) post() (common_reports_api.views.FamiliesDataDownloadView method) (common_reports_api.views.FamilyCounterDownloadView method) (common_reports_api.views.FamilyCounterListView method) (datasets_api.views.DatasetDescriptionView method) (enrichment_api.views.EnrichmentTestView method) (gene_scores.views.GeneScoresPartitionsView method) (gene_sets.views.GeneSetDownloadView method) (gene_sets.views.GeneSetsView method) (gene_view.views.DownloadSummaryVariantsView method) (gene_view.views.QuerySummaryVariantsView method) (genomes_api.views.GeneSymbolsValidate method) (genotype_browser.views.GenotypeBrowserQueryDownloadView method) (genotype_browser.views.GenotypeBrowserQueryView method) (gpf_instance.views.MarkdownFileView method) (measures_api.views.PhenoDataRoleListView method) (measures_api.views.PhenoMeasureHistogramView method) (measures_api.views.PhenoMeasureHistogramViewBeta method) (measures_api.views.PhenoMeasurePartitionsView method) (pheno_tool_api.views.PhenoToolDownload method) (pheno_tool_api.views.PhenoToolPeopleValues method) (pheno_tool_api.views.PhenoToolView method) (query_state_save.views.QueryStateDeleteView method) (query_state_save.views.QueryStateLoadView method) (query_state_save.views.QueryStateSaveView method) (user_queries.views.UserQuerySaveView method) (users_api.views.BasePasswordView method) (users_api.views.FederationCredentials method) (users_api.views.ForgotPassword method) (users_api.views.RESTLoginView method) (users_api.views.UserGpStateView method) (users_api.views.WdaeLoginView method) prb (gpf.variants.attributes.Role attribute) preamble (gain.annotation.annotation_config.RawFullConfig attribute) prepare_allowed_datasets_query() (datasets_api.permissions.IsDatasetAllowed static method) PreparePhenoBrowserBase (class in gpf.pheno.prepare_data) print() (gain.annotation.annotation_pipeline.AnnotationPipeline method) PriorityGenomicContext (class in gain.genomic_resources.genomic_context_base) probe_columns() (in module gain.genomic_resources.gene_models.parsers) probe_header() (in module gain.genomic_resources.gene_models.parsers) process() (gain.utils.processing_pipeline.PipelineProcessor method) process_completed_tasks() (gain.task_graph.graph.TaskGraph method) process_config() (gpf.configuration.gpf_config_parser.GPFConfigParser static method) process_config_raw() (gpf.configuration.gpf_config_parser.GPFConfigParser static method) process_graph() (gain.task_graph.cli_tools.TaskGraphCli static method) process_parquet() (in module gpf.parquet.schema2.annotate_schema2_parquet) process_region() (gain.utils.processing_pipeline.PipelineProcessor method) (in module gpf.gene_profile.generate_gene_profile) ProcessPoolTaskExecutor (class in gain.task_graph.process_pool_executor) produce_download() (pheno_tool_api.adapter.PhenoToolAdapter method) (pheno_tool_api.adapter.PhenoToolAdapterBase method) produce_genotype() (gpf.variants_loaders.dae.loader.DenovoLoader static method) produce_partfile_paths() (in module gain.annotation.annotate_utils) produce_regions() (in module gain.annotation.annotate_utils) (in module gpf.parquet.schema2.annotate_schema2_parquet) produce_schema2_annotation_tasks() (in module gpf.parquet.schema2.annotate_schema2_parquet) produce_schema2_merging_tasks() (in module gpf.parquet.schema2.annotate_schema2_parquet) produce_tree() (datasets_api.views.DatasetHierarchyView method) ProfileView (class in gene_profiles_api.views) PromoterEffectChecker (class in gain.effect_annotation.effect_checkers.promoter) protein_coding_gene_number (gain.genomic_resources.implementations.gene_models_impl.StatisticsData attribute) protein_coding_transcript_number (gain.genomic_resources.implementations.gene_models_impl.StatisticsData attribute) ProteinChangeEffectChecker (class in gain.effect_annotation.effect_checkers.protein_change) proto_builder() (in module gain.genomic_resources.testing) prune() (gain.genomic_resources.genomic_position_table.line.LineBuffer method) (gain.genomic_resources.genomic_position_table.LineBuffer method) (gain.task_graph.graph.TaskGraph method) psc_id (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (gpf.person_sets.person_sets.PSCQuery attribute) (gpf.person_sets.PSCQuery attribute) PSCQuery (class in gpf.person_sets) (class in gpf.person_sets.person_sets) PSCQueryAdjustments (class in gpf.studies.study) pseudo_autosomal (gpf.variants.attributes.GeneticModel attribute) pub_med (gpf.studies.study.GenotypeData property) put() (users_api.views.FederationCredentials method) put_value_in_result_queue() (gpf.query_variants.query_runners.QueryRunner method) pvalues (gpf.pheno.utils.lin_regress.LinearRegression property) pysam_file (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (gain.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute)

Q

QUAD (gpf.pedigrees.family.FamilyTag attribute) query (user_queries.models.UserQuery attribute) query_base module query_base.query_base module query_fpids() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) query_gp_statistics() (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) query_gps() (gpf.gene_profile.db.GeneProfileDB method) query_id (user_queries.models.UserQuery attribute) query_person_ids() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) query_resources() (gain.annotation.annotation_config.AnnotationConfigParser static method) query_state_save module query_state_save.migrations module query_state_save.migrations.0001_initial module query_state_save.migrations.0002_auto_20190205_0736 module query_state_save.migrations.0003_querystate_origin_querystate_timestamp module query_state_save.models module query_state_save.serializers module query_state_save.urls module query_state_save.views module

query_summary_variants() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) (gpf.parquet_storage.storage.ParquetLoaderVariants method) (gpf.studies.study.GenotypeData method) query_variants() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) (gpf.parquet_storage.storage.ParquetLoaderVariants method) (gpf.studies.study.GenotypeData method) query_variants_download_wdae() (studies.study_wrapper.WDAEAbstractStudy method) (studies.study_wrapper.WDAEStudy method) query_variants_preview_wdae() (studies.study_wrapper.WDAEAbstractStudy method) (studies.study_wrapper.WDAEStudy method) query_variants_raw() (studies.study_wrapper.WDAEStudy method) query_variants_wdae() (studies.study_wrapper.WDAEAbstractStudy method) (studies.study_wrapper.WDAEStudy method) QueryBaseView (class in query_base.query_base) QueryBuilderBase (class in gpf.query_variants.sql.schema2.sql_query_builder) QueryCompoundAdditionTransformer (class in gpf.query_variants.attribute_queries) QueryHeuristics (class in gpf.query_variants.sql.schema2.sql_query_builder) QueryResult (class in gpf.query_variants.query_runners) QueryRunner (class in gpf.query_variants.query_runners) queryset (users_api.views.UserViewSet attribute) QueryState (class in query_state_save.models) QueryState.DoesNotExist QueryState.MultipleObjectsReturned QueryStateDeleteView (class in query_state_save.views) QueryStateLoadView (class in query_state_save.views) QueryStateSaveView (class in query_state_save.views) QueryStateSerializer (class in query_state_save.serializers) QueryStateSerializer.Meta (class in query_state_save.serializers) QuerySummaryVariantsView (class in gene_view.views) QueryTransformer (class in studies.query_transformer) QueryTransformerProtocol (class in studies.study_wrapper) QueryVariants (class in gpf.query_variants.base_query_variants) QueryVariantsBase (class in gpf.query_variants.base_query_variants) QUOTE (gpf.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute)

R

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

register_storage_config() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) (gpf.pheno.storage.PhenotypeStorageRegistry method) register_storages_configs() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) (gpf.pheno.storage.PhenotypeStorageRegistry method) regression_display_names (gpf.pheno.browser.PhenoBrowser property) regression_display_names_with_ids (gpf.pheno.browser.PhenoBrowser property) regression_ids (gpf.pheno.browser.PhenoBrowser property) RegressionMeasure (class in gpf.pheno.common) regressions (gpf.pheno.common.StudyConfig attribute) reload() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) (gpf.gpf_instance.gpf_instance.GPFInstance method) (gpf.gpf_instance.GPFInstance method) (gpf.studies.variants_db.VariantsDb method) reload_statistics() (gain.genomic_resources.resource_implementation.GenomicResourceImplementation method) remove_annoying_characters() (in module gpf.pheno.utils.commons) remove_elements() (gpf.common_reports.denovo_report.EffectRow method) remove_empty_person_sets() (gpf.person_sets.person_sets.PersonSetCollection static method) (gpf.person_sets.PersonSetCollection static method) remove_group_perm_from_dataset() (in module datasets_api.permissions) remove_none_values() (in module studies.study_wrapper) remove_study_config() (gpf.tools.dataset_helpers.DatasetHelpers method) remove_wdae_dataset_and_groups() (users_api.management.commands.dataset_mixin.DatasetBaseMixin method) rename_gene_terms() (in module gain.gene_sets.gene_term) rename_genes() (gain.gene_sets.gene_term.GeneTerms method) rename_study_config() (gpf.tools.dataset_helpers.DatasetHelpers method) rename_wdae_dataset_and_groups() (users_api.management.commands.dataset_mixin.DatasetBaseMixin method) replace_tables() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) repo_id (gain.genomic_resources.repository.GenomicResourceRepo property) report_variant() (gpf.tools.liftover_tools.VCFLiftoverTool static method) report_vcf_variant() (gpf.tools.liftover_tools.VCFLiftoverTool static method) request_logging() (in module utils.logger) request_logging_function_view() (in module utils.logger) REQUIRED_FIELDS (users_api.models.WdaeUser attribute) reset (gpf_web.default_settings.CustomFormatter attribute) reset_password() (users_api.models.WdaeUser method) reset_regions() (gpf.variants_loaders.raw.loader.VariantsGenotypesLoader method) (gpf.variants_loaders.raw.loader.VariantsLoader method) (gpf.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 gain.annotation.annotation_factory) resolve_tags() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) resource (gain.genomic_resources.resource_implementation.InfoImplementationMixin attribute) resource_builder() (in module gain.genomic_resources.testing) resource_format (gain.gene_sets.gene_set.GeneSetResourceSchema attribute) resource_id (gain.gene_scores.gene_scores.ScoreDef attribute) (gain.gene_scores.gene_scores.ScoreDesc attribute) (gain.gene_sets.gene_set.GeneSetResourceSchema attribute) (gain.genomic_resources.gene_models.gene_models.GeneModels property) (gain.genomic_resources.gene_models.GeneModels property) (gain.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation property) (gain.genomic_resources.reference_genome.ReferenceGenome property) (gain.genomic_resources.resource_implementation.GenomicResourceImplementation property) (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground property) (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property) (gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation property) (gpf.genomic_scores.scores.ScoreDesc attribute) resource_ids (gain.annotation.annotation_pipeline.Annotator property) ResourceConfigValidationMixin (class in gain.genomic_resources.resource_implementation) ResourceFileState (class in gain.genomic_resources.repository) resources (gain.annotation.annotation_config.AnnotatorInfo attribute) (gain.annotation.annotation_pipeline.Annotator property) ResourceStatistics (class in gain.genomic_resources.resource_implementation) RESPONSE_LIMIT (genomes_api.views.GeneSymbolsSearch attribute) ResponseTransformer (class in studies.response_transformer) ResponseTransformerProtocol (class in studies.study_wrapper) RESTLoginView (class in users_api.views) result (gain.task_graph.cache.CacheRecord property) result_or_error (gain.task_graph.cache.CacheRecord attribute) result_queue (gpf.query_variants.query_runners.QueryRunner property) retrieve() (users_api.views.UserViewSet method) rev_chrom_map (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (gain.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) reverse_complement() (in module gain.utils.variant_utils) rm_file() (in module gain.utils.fs_utils) Role (class in gpf.variants.attributes) role (gpf.pedigrees.family.Person property) role_labels() (in module gpf.pheno.graphs) roles (gpf.studies.study.PSCQueryAdjustments attribute) roles() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) row (gain.annotation.annotation_config.ErrorMark attribute) row() (gain.genomic_resources.genomic_position_table.BigWigLine method) (gain.genomic_resources.genomic_position_table.Line method) (gain.genomic_resources.genomic_position_table.line.BigWigLine method) (gain.genomic_resources.genomic_position_table.line.Line method) (gain.genomic_resources.genomic_position_table.line.LineBase method) (gain.genomic_resources.genomic_position_table.line.VCFLine method) (gain.genomic_resources.genomic_position_table.VCFLine method) rules (gpf.configuration.gpf_config_parser.GPFConfigValidator attribute) run() (gain.annotation.docker_annotator.DockerAnnotator method) (gpf.duckdb_storage.duckdb2_variants.DuckDb2Runner method) (gpf.duckdb_storage.duckdb_variants.DuckDbRunner method) (gpf.inmemory_storage.raw_variants.RawVariantsQueryRunner method) (gpf.pheno.prepare_data.PreparePhenoBrowserBase method) (gpf.query_variants.query_runners.QueryRunner method) (gpf.tools.gpf_validation_runner.GenotypeBrowserRunner method) (gpf.tools.liftover_tools.LiftoverTool method) (gpf.tools.reannotate_instance.ReannotateInstanceTool method) run_annotate() (gain.annotation.simple_effect_annotator.SimpleEffectAnnotator method) run_validation() (users_api.serializers.UserSerializer method) run_with_project() (in module gpf.import_tools.cli) RUNNER_CLASS (gpf.duckdb_storage.duckdb_variants.DuckDbVariants attribute) (gpf.query_variants.base_query_variants.QueryVariantsBase attribute) (gpf.query_variants.sql.schema2.base_variants.SqlSchema2Variants attribute)

S

s3_test_protocol() (in module gain.genomic_resources.testing) s3_test_server_endpoint() (in module gain.genomic_resources.testing) safe_db_name() (in module gpf.pheno.db) safe_task_id() (in module gain.task_graph.logging) SamochaEnrichmentBackground (class in gpf.enrichment_tool.samocha_background) sample_dataset() (in module conftest) sample_index (gpf.pedigrees.family.Person property) samples_index (gpf.pedigrees.family.Family property) SandwichInstance (class in gpf.pedigrees.pedigrees) SandwichSolver (class in gpf.pedigrees.pedigrees) save() (gain.gene_sets.gene_term.GeneTerms method) (gain.utils.stats_collection.StatsCollection method) (gpf.common_reports.common_report.CommonReport method) (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method) (gpf.pheno.browser.PhenoBrowser method) save_as_default_gene_models() (in module gain.genomic_resources.gene_models.serialization) save_as_tabix_table() (in module gain.genomic_resources.genomic_position_table.utils) save_descriptions() (gpf.pheno.browser.PhenoBrowser method) (gpf.pheno.db.PhenoDb method) (in module gpf.pheno.update_pheno_descriptions) save_families() (gpf.pedigrees.loader.FamiliesLoader static method) save_fig() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method) save_histogram() (in module gain.genomic_resources.histogram) save_index() (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) save_manifest() (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) save_ped_df_to_parquet() (in module gpf.parquet.parquet_writer) save_pedigree() (gpf.pedigrees.loader.FamiliesLoader static method) save_regression() (gpf.pheno.browser.PhenoBrowser method) save_regression_values() (gpf.pheno.browser.PhenoBrowser method) save_resource_file_state() (gain.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) save_study_config() (in module gpf.import_tools.import_tools) scale() (gpf.pedigrees.layout.Layout method) schema() (gpf.parquet.schema2.serializers.AlleleParquetSerializer method) (gpf.parquet.schema2.serializers.FamilyAlleleParquetSerializer method) (gpf.parquet.schema2.serializers.SummaryAlleleParquetSerializer method) schema1_partition() (gpf.parquet.partition_descriptor.PartitionDescriptor method) schema2_project_dataset_layout() (in module gpf.schema2_storage.schema2_import_storage) Schema2DatasetLayout (class in gpf.schema2_storage.schema2_layout) Schema2ImportStorage (class in gpf.schema2_storage.schema2_import_storage) Schema2SummaryVariantBatchConsumer (class in gpf.parquet.schema2.variants_parquet_writer) Schema2SummaryVariantConsumer (class in gpf.parquet.schema2.variants_parquet_writer) Schema2SummaryVariantsBatchSource (class in gpf.parquet.schema2.processing_pipeline) Schema2SummaryVariantsSource (class in gpf.parquet.schema2.processing_pipeline) Schema2VariantBatchConsumer (class in gpf.parquet.schema2.variants_parquet_writer) Schema2VariantConsumer (class in gpf.parquet.schema2.variants_parquet_writer) score (gain.genomic_resources.genomic_scores.AlleleScoreAggr attribute) (gain.genomic_resources.genomic_scores.AlleleScoreQuery attribute) (gain.genomic_resources.genomic_scores.PositionScoreAggr attribute) (gain.genomic_resources.genomic_scores.PositionScoreQuery attribute) SCORE_HISTOGRAM (gain.annotation.score_annotator.GenomicScoreAnnotatorBase attribute) score_id (gain.gene_scores.gene_scores.ScoreDef attribute) (gain.gene_scores.gene_scores.ScoreDesc attribute) (gain.genomic_resources.genomic_scores.ScoreDef attribute) (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property) ScoreDef (class in gain.gene_scores.gene_scores) (class in gain.genomic_resources.genomic_scores) ScoreDesc (class in gain.gene_scores.gene_scores) (class in gpf.genomic_scores.scores) ScoreLine (class in gain.genomic_resources.genomic_scores) search_fields (groups_api.views.GroupsViewSet attribute) (users_api.views.UserViewSet attribute) search_measures() (gpf.pheno.browser.PhenoBrowser method) (gpf.pheno.pheno_data.PhenotypeData method) (pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method) (pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method) search_resources() (gain.genomic_resources.cached_repository.GenomicResourceCachedRepo method) (gain.genomic_resources.group_repository.GenomicResourceGroupRepo method) (gain.genomic_resources.repository.GenomicResourceProtocolRepo method) (gain.genomic_resources.repository.GenomicResourceRepo method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) select_events_in_person_set() (gpf.enrichment_tool.event_counters.CounterBase method) selected_family_tags (gpf.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute) selected_person_set_collections (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) selected_person_sets (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (gpf.person_sets.person_sets.PSCQuery attribute) (gpf.person_sets.PSCQuery attribute) send_already_existing_email() (in module users_api.models) send_reset_email() (in module users_api.models) send_reset_inactive_acc_email() (in module users_api.models) send_verif_email() (in module users_api.models) sentry module sentry() (in module sentry.views) sentry.urls module sentry.views module SequentialExecutor (class in gain.task_graph.sequential_executor) serialize() (enrichment_api.enrichment_serializer.EnrichmentSerializer method) (gain.genomic_resources.histogram.CategoricalHistogram method) (gain.genomic_resources.histogram.NullHistogram method) (gain.genomic_resources.histogram.NumberHistogram method) (gain.genomic_resources.implementations.gene_models_impl.GeneModelsStatistics method) (gain.genomic_resources.implementations.reference_genome_impl.ChromosomeStatistic method) (gain.genomic_resources.implementations.reference_genome_impl.GenomeStatistic method) (gain.genomic_resources.statistics.base_statistic.Statistic method) (gain.genomic_resources.statistics.min_max.MinMaxValue method) (gpf.parquet.partition_descriptor.PartitionDescriptor method) (gpf.variants_loaders.vcf.serializer.VcfSerializer method) serialize_all() (enrichment_api.enrichment_serializer.EnrichmentSerializer method) serialize_common_filter() (enrichment_api.enrichment_serializer.EnrichmentSerializer method) serialize_enrichment_result() (enrichment_api.enrichment_serializer.EnrichmentSerializer method) serialize_family() (gpf.parquet.schema2.serializers.JsonVariantsDataSerializer method) (gpf.parquet.schema2.serializers.VariantsDataSerializer method) serialize_female() (enrichment_api.enrichment_serializer.EnrichmentSerializer method) serialize_full_variant() (gpf.variants_loaders.vcf.serializer.VcfSerializer method) serialize_male() (enrichment_api.enrichment_serializer.EnrichmentSerializer method) serialize_overlap_filter() (enrichment_api.enrichment_serializer.EnrichmentSerializer method) serialize_people_groups() (enrichment_api.enrichment_serializer.EnrichmentSerializer method) serialize_rec() (enrichment_api.enrichment_serializer.EnrichmentSerializer method) serialize_rec_filter() (enrichment_api.enrichment_serializer.EnrichmentSerializer method) serialize_summary() (gpf.parquet.schema2.serializers.JsonVariantsDataSerializer method) (gpf.parquet.schema2.serializers.VariantsDataSerializer method) serialize_summary_schema() (in module gpf.parquet.parquet_writer) serializer_class (groups_api.views.GroupsViewSet attribute) (users_api.views.UserViewSet attribute) session_t4c8_wgpf_instance() (in module conftest) SessionAuthenticationWithoutCSRF (class in utils.authentication) SessionAuthenticationWithUnauthenticatedCSRF (class in utils.authentication) set() (gain.utils.verbosity_configuration.VerbosityConfiguration static method) set_argument() (gain.effect_annotation.cli.AnnotationAttributes static method) (gain.effect_annotation.cli.VariantColumnInputFile static method) (gain.effect_annotation.cli.VariantColumnOutputFile static method) set_arguments() (gain.effect_annotation.cli.EffectAnnotatorBuilder static method) (gain.utils.verbosity_configuration.VerbosityConfiguration static method) set_attr() (gpf.pedigrees.family.Person method) (in module gpf.pedigrees.family_tag_builder) set_attribute() (gpf.variants_loaders.raw.loader.VariantsLoader method) set_broken() (datasets_api.models.Dataset class method) set_context() (users_api.validators.SomeSuperuserLeftValidator method) set_figure_size() (in module gpf.pheno.graphs) set_fit_request() (gpf.pheno.utils.lin_regress.LinearRegression method) set_matched_alleles() (gpf.variants.variant.SummaryVariant method) set_negative_stats() (gpf.pheno_tool.tool.PhenoResult method) set_password() (users_api.models.WdaeUser method) set_position() (gain.effect_annotation.variant.Variant method) set_positive_stats() (gpf.pheno_tool.tool.PhenoResult method) set_ref_alt() (gain.effect_annotation.variant.Variant method) set_ref_alt_from_variant() (gain.effect_annotation.variant.Variant method) set_result_queue() (gpf.query_variants.query_runners.QueryRunner method) set_score_request() (gpf.pheno.utils.lin_regress.LinearRegression method) set_study_id() (gpf.query_variants.query_runners.QueryRunner method) set_tag() (gpf.pedigrees.family.Family method) (gpf.pedigrees.family.Person method) (in module gpf.pedigrees.family_tag_builder) set_unusable_password() (users_api.models.WdaeUser method) set_up_kubernetes_cluster() (in module gain.dask.named_cluster) set_up_local_cluster() (in module gain.dask.named_cluster) set_up_manual_client() (in module gain.dask.named_cluster) set_up_sge_cluster() (in module gain.dask.named_cluster) set_up_slurm_cluster() (in module gain.dask.named_cluster) SetPassword (class in users_api.views) SetPasswordCode (class in users_api.models) setpasswordcode (users_api.models.WdaeUser attribute) SetPasswordCode.DoesNotExist SetPasswordCode.MultipleObjectsReturned setup() (gpf_instance.extension.GPFExtensionBase method) setup_bigwig() (in module gain.genomic_resources.testing) setup_client() (in module gain.dask.named_cluster) setup_client_from_config() (in module gain.dask.named_cluster) setup_dae_transmitted() (in module gain.genomic_resources.testing) setup_dataset() (in module gpf.testing.import_helpers) setup_dataset_config() (in module gpf.testing.import_helpers) setup_denovo() (in module gain.genomic_resources.testing) setup_directories() (in module gain.genomic_resources.testing) setup_empty_gene_models() (in module gain.genomic_resources.testing) setup_gene_models() (in module gain.genomic_resources.testing) setup_genome() (in module gain.genomic_resources.testing) setup_gpf_instance() (in module gpf.testing.setup_helpers) setup_gzip() (in module gain.genomic_resources.testing) setup_import_project() (in module gpf.testing.import_helpers) setup_import_project_config() (in module gpf.testing.import_helpers) setup_pedigree() (in module gain.genomic_resources.testing) setup_t4c8_grr() (in module gain.testing.t4c8_import) (in module utils.testing) setup_t4c8_instance() (in module gpf.utils.testing) (in module utils.testing) setup_tabix() (in module gain.genomic_resources.testing) setup_vcf() (in module gain.genomic_resources.testing) setup_wgpf_instance() (in module utils.testing) SEVERITY (gain.effect_annotation.effect.AnnotationEffect attribute) Sex (class in gpf.variants.attributes) sex (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute) (gpf.pedigrees.family.Person property) sex_zygosity (gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute) sexes (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute) (gpf.gene_sets.denovo_gene_sets_config.SexesCriteria attribute) (gpf.studies.study.PSCQueryAdjustments attribute) sexes() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)

SexesCriteria (class in gpf.gene_sets.denovo_gene_sets_config) short() (gpf.variants.attributes.Sex method) (gpf.variants.attributes.Status method) shutdown() (gpf.duckdb_storage.duckdb_genotype_storage.AbstractDuckDbStorage method) (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) (gpf.genotype_storage.genotype_storage.GenotypeStorage method) (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method) (gpf.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage method) (gpf.parquet_storage.storage.ParquetGenotypeStorage method) (gpf.pheno.registry.PhenoRegistry method) (gpf.pheno.storage.PhenotypeStorage method) (gpf.pheno.storage.PhenotypeStorageRegistry method) sib (gpf.variants.attributes.Role attribute) SibshipUnit (class in gpf.pedigrees.pedigrees) sign() (in module gain.utils.fs_utils) SimpleEffect (class in gain.annotation.simple_effect_annotator) SimpleEffectAnnotator (class in gain.annotation.simple_effect_annotator) SimpleGenomicContext (class in gain.genomic_resources.genomic_context_base) SIMPLEX (gpf.pedigrees.family.FamilyTag attribute) simplify_effects() (gain.effect_annotation.effect.AnnotationEffect class method) SingleCriteria (class in gpf.gene_sets.denovo_gene_sets_config) SingleVcfLoader (class in gpf.variants_loaders.vcf.loader) size (gain.genomic_resources.genomic_scores.CNV property) (gain.genomic_resources.repository.ManifestEntry attribute) (gain.genomic_resources.repository.ResourceFileState attribute) (gain.genomic_resources.resource_implementation.InfoImplementationMixin.FileEntry attribute) SIZE (gpf.pedigrees.layout.IndividualWithCoordinates attribute) size() (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter method) (gpf.parquet.schema2.variants_parquet_writer.ContinuousParquetFileWriter method) skip (gpf.pheno.common.InferenceConfig attribute) skip_pedigree_measures (gpf.pheno.common.PhenoImportConfig attribute) skipped (gpf.pheno.common.MeasureType attribute) SMALL_DELETION (gain.annotation.annotatable.Annotatable.Type attribute) small_deletion (gpf.variants.core.Allele.Type attribute) SMALL_DPI (gpf.pheno.prepare_data.PreparePhenoBrowserBase attribute) SMALL_INSERTION (gain.annotation.annotatable.Annotatable.Type attribute) small_insertion (gpf.variants.core.Allele.Type attribute) small_values_desc (gain.gene_scores.gene_scores.ScoreDef attribute) (gain.gene_scores.gene_scores.ScoreDesc attribute) (gain.genomic_resources.genomic_scores.ScoreDef attribute) (gpf.genomic_scores.scores.ScoreDesc attribute) solve() (gpf.pedigrees.pedigrees.SandwichSolver static method) SomeSuperuserLeftValidator (class in users_api.validators) sort_effects() (gain.effect_annotation.effect.AnnotationEffect class method) Source (class in gain.utils.processing_pipeline) source (gain.annotation.annotation_config.AttributeInfo attribute) (gain.annotation.annotation_pipeline.AttributeDesc attribute) (gain.annotation.processing_pipeline.AnnotationsWithSource attribute) (gpf.genomic_scores.scores.ScoreDesc attribute) (gpf.person_sets.person_sets.SourceConfig attribute) (gpf.person_sets.SourceConfig attribute) SourceConfig (class in gpf.person_sets) (class in gpf.person_sets.person_sets) sources (gpf.person_sets.person_sets.PersonSetCollectionConfig attribute) (gpf.person_sets.PersonSetCollectionConfig attribute) SPECIAL_ATTRS (studies.response_transformer.ResponseTransformer attribute) SpliceSiteEffectChecker (class in gain.effect_annotation.effect_checkers.splice_site) split_events() (gpf.enrichment_tool.event_counters.CounterBase method) split_heuristics() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method) split_into_regions() (gain.genomic_resources.reference_genome.ReferenceGenome method) (in module gain.utils.regions) split_iterable() (in module gain.utils.dae_utils) split_location() (gpf.variants_loaders.dae.loader.DenovoLoader static method) spouse (gpf.variants.attributes.Role attribute) SqlQueryBuilder (class in gpf.query_variants.sql.schema2.sql_query_builder) SqlSchema2Variants (class in gpf.query_variants.sql.schema2.base_variants) staff_update() (in module users_api.models) start (gain.genomic_resources.gene_models.Exon property) (gain.genomic_resources.gene_models.transcript_models.Exon property) (gain.utils.regions.BedRegion property) (gain.utils.regions.Region property) (gpf.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.SingleCriteria attribute) (gpf.gene_sets.denovo_gene_sets_config.TripleCriteria attribute) start() (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbParquetStorage method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3ParquetStorage method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3Storage method) (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbStorage method) (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method) (gpf.genotype_storage.genotype_storage.GenotypeStorage method) (gpf.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage method) (gpf.parquet_storage.storage.ParquetGenotypeStorage method) (gpf.query_variants.query_runners.QueryResult method) (gpf.query_variants.query_runners.QueryRunner method) startCodons (gain.effect_annotation.gene_codes.NuclearCode attribute) StartLossEffectChecker (class in gain.effect_annotation.effect_checkers.start_loss) Statistic (class in gain.genomic_resources.statistics.base_statistic) statistic_id (gain.genomic_resources.statistics.base_statistic.Statistic attribute) StatisticsData (class in gain.genomic_resources.implementations.gene_models_impl) stats (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (gain.genomic_resources.genomic_position_table.VCFGenomicPositionTable attribute) StatsCollection (class in gain.utils.stats_collection) Status (class in gpf.variants.attributes) status (gpf.pedigrees.family.Person property) status_zygosity (gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute) statuses() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) step_dad (gpf.variants.attributes.Role attribute) step_mom (gpf.variants.attributes.Role attribute) stop (gain.genomic_resources.gene_models.Exon property) (gain.genomic_resources.gene_models.transcript_models.Exon property) (gain.utils.regions.BedRegion property) (gain.utils.regions.Region property) stopCodons (gain.effect_annotation.gene_codes.NuclearCode attribute) StopLossEffectChecker (class in gain.effect_annotation.effect_checkers.stop_loss) storage_dir (gpf.pheno.common.DestinationConfig attribute) storage_id (gpf.pheno.common.DestinationConfig attribute) storage_type (gpf.duckdb_storage.duckdb_storage_config.DuckDbConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbParquetConf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute) store_junit_results() (gpf.tools.gpf_validation_runner.MainRunner static method) store_results() (gpf.tools.gpf_validation_runner.GenotypeBrowserRunner method) (gpf.tools.gpf_validation_runner.MainRunner method) str2bool() (in module gain.utils.helpers) str2fgt() (in module gpf.utils.variant_utils) str2gt() (in module gpf.utils.variant_utils) str2lists() (in module gpf.utils.variant_utils) str2mat() (in module gpf.utils.variant_utils) str2mat_adjust_colsep() (in module gpf.utils.variant_utils) STREAMING_CHUNK_SIZE (studies.response_transformer.ResponseTransformer attribute) streaming_search() (users_api.views.UserViewSet method) string_type() (gpf.query_variants.sql.schema2.base_query_builder.Dialect static method) stringify() (in module gain.annotation.annotate_utils) studies module studies.conftest module studies.query_transformer module studies.response_transformer module studies.study_wrapper module study (gpf.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute) (gpf.schema2_storage.schema2_layout.Schema2DatasetLayout attribute) study_config (gpf.pheno.common.PhenoImportConfig attribute) study_configs (gpf.genotype_storage.genotype_storage.GenotypeStorage property) study_id (gpf.import_tools.import_tools.ImportProject property) (gpf.studies.study.GenotypeData property) (gpf.testing.import_helpers.StudyInputLayout attribute) (studies.study_wrapper.WDAEAbstractStudy property) study_id_from_path() (in module gain.utils.helpers) study_phenotype (gpf.studies.study.GenotypeDataStudy property) study_type (gpf.studies.study.GenotypeData property) study_update() (in module gpf.testing.import_helpers) StudyConfig (class in gpf.pheno.common) StudyConfigBuilder (class in gpf.configuration.study_config_builder) StudyConfigsAdjustmentCommand (class in gpf.gpf_instance.adjustments.gpf_instance_adjustments) StudyInputLayout (class in gpf.testing.import_helpers) SUBSTITUTION (gain.annotation.annotatable.Annotatable.Type attribute) substitution (gpf.variants.core.Allele.Type attribute) SUBSTITUTIONS (gain.genomic_resources.genomic_scores.AlleleScore.Mode attribute) substitutions_mode() (gain.genomic_resources.genomic_scores.AlleleScore method) suffix (groups_api.views.GroupsViewSet attribute) (users_api.views.UserViewSet attribute) summary (gain.annotation.annotation_config.AnnotationPreamble attribute) (gain.annotation.annotation_config.RawPreamble attribute) (gpf.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute) (gpf.schema2_storage.schema2_layout.Schema2DatasetLayout attribute) summary() (gpf.tools.gpf_validation_runner.MainRunner method) summary_allele (gpf.variants.family_variant.FamilyAllele attribute) summary_allele_from_record() (gpf.variants.variant.SummaryVariantFactory static method) summary_attributes (gpf.variants.family_variant.FamilyAllele property) summary_base() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) SUMMARY_COLUMNS (gpf.parquet.schema2.loader.ParquetLoader attribute) summary_index (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) (gpf.variants.variant.SummaryAllele property) (gpf.variants.variant.SummaryVariant property) summary_partition() (gpf.parquet.partition_descriptor.PartitionDescriptor method) summary_partition_schema() (gpf.parquet.partition_descriptor.PartitionDescriptor method) summary_query() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) summary_variant (gpf.variants_loaders.raw.loader.FullVariant attribute) summary_variant_filter_function() (gpf.inmemory_storage.raw_variants.RawFamilyVariants class method) summary_variant_from_records() (gpf.variants.variant.SummaryVariantFactory static method) summary_variant_from_vcf() (gpf.variants.variant.SummaryVariantFactory static method) summary_variants() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method) summary_variants_iterator() (gpf.inmemory_storage.raw_variants.RawFamilyVariants method) SummaryAllele (class in gpf.variants.variant) SummaryAlleleParquetSerializer (class in gpf.parquet.schema2.serializers) SummaryQueryBuilder (class in gpf.query_variants.sql.schema2.summary_builder) SummaryVariant (class in gpf.variants.variant) SummaryVariantFactory (class in gpf.variants.variant) SUPERUSER_GROUP (users_api.models.WdaeUser attribute) svuid (gpf.variants.variant.SummaryVariant property) symlink_pedigree_and_family_variants() (in module gpf.parquet.schema2.annotate_schema2_parquet) syms (gain.gene_sets.gene_set.GeneSet attribute) sync_tasks() (in module gain.task_graph.graph) synonyms (gain.gene_sets.gene_term.GeneInfo attribute) SyntaxSugarTransformer (class in gpf.query_variants.attribute_queries)

T

t4c8_dataset() (in module conftest) t4c8_genes() (in module gain.testing.t4c8_import) t4c8_genome() (in module gain.testing.t4c8_import) t4c8_gpf() (in module gpf.testing.t4c8_import) t4c8_grr() (in module gain.testing.t4c8_import) t4c8_instance() (in module conftest) t4c8_query_transformer() (in module conftest) t4c8_response_transformer() (in module conftest) t4c8_study_1() (in module conftest) t4c8_study_1_wrapper() (in module conftest) t4c8_study_2() (in module conftest) t4c8_study_2_wrapper() (in module conftest) t4c8_wgpf() (in module conftest) t4c8_wgpf_instance() (in module conftest) tabix_index_filename() (in module gain.utils.fs_utils) TabixGenomicPositionTable (class in gain.genomic_resources.genomic_position_table) (class in gain.genomic_resources.genomic_position_table.table_tabix) TableRowsView (class in gene_profiles_api.table_views) tag_affected_dad_family() (in module gpf.pedigrees.family_tag_builder) tag_affected_mom_family() (in module gpf.pedigrees.family_tag_builder) tag_affected_prb_family() (in module gpf.pedigrees.family_tag_builder) tag_affected_sib_family() (in module gpf.pedigrees.family_tag_builder) tag_control_family() (in module gpf.pedigrees.family_tag_builder) tag_families_data() (in module gpf.pedigrees.families_data) tag_family() (gpf.pedigrees.family_tag_builder.FamilyTagsBuilder method) tag_family_type() (gpf.pedigrees.family_tag_builder.FamilyTagsBuilder method) tag_female_prb_family() (in module gpf.pedigrees.family_tag_builder) tag_labels (gpf.pedigrees.family.Family property) tag_male_prb_family() (in module gpf.pedigrees.family_tag_builder) tag_missing_dad_family() (in module gpf.pedigrees.family_tag_builder) tag_missing_mom_family() (in module gpf.pedigrees.family_tag_builder) tag_multiplex_family() (in module gpf.pedigrees.family_tag_builder) tag_nuclear_family() (in module gpf.pedigrees.family_tag_builder) tag_quad_family() (in module gpf.pedigrees.family_tag_builder) tag_simplex_family() (in module gpf.pedigrees.family_tag_builder) tag_trio_family() (in module gpf.pedigrees.family_tag_builder) tag_unaffected_dad_family() (in module gpf.pedigrees.family_tag_builder) tag_unaffected_mom_family() (in module gpf.pedigrees.family_tag_builder) tag_unaffected_prb_family() (in module gpf.pedigrees.family_tag_builder) tag_unaffected_sib_family() (in module gpf.pedigrees.family_tag_builder) tags (gpf.pedigrees.family.Family property) (gpf.pedigrees.family.Person property) TAGS (gpf.pedigrees.family_tag_builder.FamilyTagsBuilder attribute) tags_or_mode (gpf.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute) tags_to_family_ids() (gpf.query_variants.base_query_variants.QueryVariants method) TagsQuery (class in gpf.query_variants.sql.schema2.sql_query_builder) TagsView (class in family_api.views) tandem_repeat (gpf.variants.core.Allele.Type attribute) tandem_repeat() (in module gpf.variants.variant) tandem_repeat_del (gpf.variants.core.Allele.Type attribute) tandem_repeat_ins (gpf.variants.core.Allele.Type attribute) Task (class in gain.task_graph.graph) task (gain.task_graph.graph.TaskDesc attribute) task_graph_all_done() (in module gain.task_graph.cli_tools) task_graph_run() (in module gain.task_graph.cli_tools) task_graph_run_with_results() (in module gain.task_graph.cli_tools) task_graph_status() (in module gain.task_graph.cli_tools) task_id (gain.task_graph.graph.Task attribute) task_part() (in module gain.task_graph.demo_graphs_cli) task_part_b() (in module gain.task_graph.demo_graphs_cli) task_part_c() (in module gain.task_graph.demo_graphs_cli) task_summary() (in module gain.task_graph.demo_graphs_cli) task_summary_b() (in module gain.task_graph.demo_graphs_cli) task_summary_c() (in module gain.task_graph.demo_graphs_cli) TaskCache (class in gain.task_graph.cache) TaskDesc (class in gain.task_graph.graph) TaskGraph (class in gain.task_graph.graph) TaskGraphCli (class in gain.task_graph.cli_tools) TaskGraphExecutor (class in gain.task_graph.executor) TaskGraphExecutorBase (class in gain.task_graph.base_executor) tasks (gain.task_graph.graph.TaskGraph property) template (users_api.views.BasePasswordView attribute) (users_api.views.ResetPassword attribute) (users_api.views.SetPassword attribute) test_frames() (gain.genomic_resources.gene_models.transcript_models.TranscriptModel method) (gain.genomic_resources.gene_models.TranscriptModel method) TestResult (class in gpf.tools.gpf_validation_runner) TestStatus (class in gpf.tools.gpf_validation_runner) TestSuite (class in gpf.tools.gpf_validation_runner) text (gpf.pheno.common.MeasureType attribute) time (users_api.models.AuthenticationLog attribute) time_fmt (gpf_web.default_settings.CustomFormatter attribute) timeout() (in module gain.task_graph.demo_graphs_cli) timestamp (gain.genomic_resources.repository.ResourceFileState attribute) (query_state_save.models.QueryState attribute) to_bed_region() (gain.utils.regions.Region method) to_cshl_full() (gpf.variants.variant.VariantDesc method) to_cshl_short() (gpf.variants.variant.VariantDesc method) to_dict() (gain.annotation.annotatable.Annotatable method) (gain.annotation.annotatable.CNVAllele method) (gain.annotation.annotatable.Position method) (gain.annotation.annotatable.Region method) (gain.annotation.annotatable.VCFAllele method) (gain.annotation.annotation_config.AnnotatorInfo method) (gain.genomic_resources.histogram.CategoricalHistogram method) (gain.genomic_resources.histogram.CategoricalHistogramConfig method) (gain.genomic_resources.histogram.NullHistogram method) (gain.genomic_resources.histogram.NullHistogramConfig method) (gain.genomic_resources.histogram.NumberHistogram method) (gain.genomic_resources.histogram.NumberHistogramConfig method) (gpf.common_reports.common_report.CommonReport method) (gpf.common_reports.denovo_report.DenovoReport method) (gpf.common_reports.denovo_report.DenovoReportTable method) (gpf.common_reports.denovo_report.EffectCell method) (gpf.common_reports.denovo_report.EffectRow method) (gpf.common_reports.family_counter.FamiliesGroupCounters method) (gpf.common_reports.family_counter.FamilyCounter method) (gpf.common_reports.family_report.FamiliesReport method) (gpf.common_reports.people_counter.PeopleCounter method) (gpf.common_reports.people_counter.PeopleCounters method) (gpf.common_reports.people_counter.PeopleReport method) (gpf.parquet.partition_descriptor.PartitionDescriptor method)

to_duckdb_transpile() (in module gain.utils.sql_utils) to_internal_value() (users_api.serializers.CreatableSlugRelatedField method) (users_api.serializers.DatasetSerializer method) to_json() (gpf.gene_profile.statistic.GPStatistic method) (gpf.genomic_scores.scores.ScoreDesc method) (gpf.pedigrees.family.Family method) (gpf.pedigrees.family.Person method) (gpf.person_sets.person_sets.PersonSet method) (gpf.person_sets.PersonSet method) (gpf.pheno.pheno_data.Measure method) to_manifest_entries() (gain.genomic_resources.repository.Manifest method) to_name() (gpf.variants.attributes.Role static method) (gpf.variants.attributes.Sex static method) (gpf.variants.attributes.Status static method) to_pylist() (gpf.parquet.partition_descriptor.Partition method) to_record() (gpf.variants.family_variant.FamilyVariant method) (gpf.variants.variant.SummaryAllele method) (gpf.variants.variant.SummaryVariant method) to_representation() (groups_api.serializers.GroupRetrieveSerializer method) (users_api.serializers.DatasetSerializer method) (users_api.serializers.UserSerializer method) to_response_json() (in module gain.utils.helpers) to_tsv() (gain.gene_scores.gene_scores.GeneScore method) (gpf.pedigrees.loader.FamiliesLoader static method) to_value() (gpf.variants.attributes.Role static method) (gpf.variants.attributes.Sex static method) (gpf.variants.attributes.Status static method) to_xml_element() (gpf.tools.gpf_validation_runner.TestResult method) (gpf.tools.gpf_validation_runner.TestSuite method) tokenize() (gain.annotation.annotatable.Annotatable static method) tokens() (in module conftest) TOMLDict (class in gpf.configuration.study_config_builder) TOMLList (class in gpf.configuration.study_config_builder) tool_id (gpf_instance.extension.GPFTool property) topological_order() (gain.task_graph.graph.TaskGraph method) total (gpf.person_sets.ChildrenStats property) (gpf.person_sets.person_sets.ChildrenStats property) total_len() (gain.genomic_resources.gene_models.transcript_models.TranscriptModel method) (gain.genomic_resources.gene_models.TranscriptModel method) total_length() (in module gain.utils.regions) transcript_effects() (gain.effect_annotation.effect.AnnotationEffect class method) transcript_id (gain.annotation.simple_effect_annotator.SimpleEffect attribute) transcript_number (gain.genomic_resources.implementations.gene_models_impl.StatisticsData attribute) transcript_to_dict() (genomes_api.views.GeneModels method) transcript_to_gtf() (in module gain.genomic_resources.gene_models.serialization) TranscriptModel (class in gain.genomic_resources.gene_models) (class in gain.genomic_resources.gene_models.transcript_models) transform_attribute_query_to_function() (in module gpf.query_variants.attribute_queries) transform_attribute_query_to_sql_expression() (in module gpf.query_variants.attribute_queries) transform_attribute_query_to_sql_expression_schema1() (in module gpf.query_variants.attribute_queries) transform_cli_args() (in module gpf.pheno.pheno_import) transform_gene_view_summary_variant() (studies.response_transformer.ResponseTransformer method) (studies.study_wrapper.ResponseTransformerProtocol method) transform_gene_view_summary_variant_download() (studies.response_transformer.ResponseTransformer method) (studies.study_wrapper.ResponseTransformerProtocol method) transform_kwargs() (studies.query_transformer.QueryTransformer method) (studies.study_wrapper.QueryTransformerProtocol method) transform_ps_query_to_attribute_queries() (gpf.person_sets.person_sets.PersonSetCollection method) (gpf.person_sets.PersonSetCollection method) transform_roles_to_single_role_string() (gpf.query_variants.base_query_variants.QueryVariants static method) translate() (gpf.pedigrees.layout.Layout method) transmission_type (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.variant.SummaryAllele property) (gpf.variants.variant.SummaryVariant property) TransmissionType (class in gpf.variants.attributes) transmitted (gpf.variants.attributes.TransmissionType attribute) trim_equal_ref_alt_parts() (gain.effect_annotation.variant.Variant method) trim_parsimonious() (in module gain.utils.variant_utils) trim_str_left() (in module gain.utils.variant_utils) trim_str_left_right() (in module gain.utils.variant_utils) trim_str_right() (in module gain.utils.variant_utils) trim_str_right_left() (in module gain.utils.variant_utils) TRIO (gpf.pedigrees.family.FamilyTag attribute) trios (gpf.pedigrees.family.Family property) TripleCriteria (class in gpf.gene_sets.denovo_gene_sets_config) try_solve() (gpf.pedigrees.pedigrees.SandwichSolver static method) tvalues (gpf.pheno.utils.lin_regress.LinearRegression property) type (gain.annotation.annotation_config.AnnotatorInfo attribute) (gain.annotation.annotation_pipeline.AttributeDesc attribute) (gain.gene_sets.gene_set.BaseResourceSchema attribute) (gain.gene_sets.gene_set.CategoricalHistogramSchema attribute) (gain.gene_sets.gene_set.NumericHistogramSchema attribute) (gain.genomic_resources.histogram.CategoricalHistogram attribute) (gain.genomic_resources.histogram.NullHistogram attribute) (gain.genomic_resources.histogram.NumberHistogram attribute) (gain.task_graph.cache.CacheRecord attribute) (gpf.import_tools.import_tools.Bucket attribute) TYPE_DISPLAY_NAME (gpf.variants.core.Allele attribute) types (gain.effect_annotation.effect.AlleleEffects property)

U

U (gpf.variants.attributes.Sex attribute) ultra_rare() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method) UMLIMITED_DOWNLOAD_GROUP (users_api.models.WdaeUser attribute) unaffected (gpf.variants.attributes.Status attribute) UNAFFECTED_DAD (gpf.pedigrees.family.FamilyTag attribute) UNAFFECTED_MOM (gpf.pedigrees.family.FamilyTag attribute) UNAFFECTED_PRB (gpf.pedigrees.family.FamilyTag attribute) UNAFFECTED_SIB (gpf.pedigrees.family.FamilyTag attribute) undefined (gpf.variants.attributes.Zygosity attribute) union() (in module gain.utils.regions) unique_regions() (in module gain.utils.regions) UNIQUE_VALUES_LIMIT (gain.genomic_resources.histogram.CategoricalHistogram attribute) unix_timestamp (gpf.pheno.common.ImportManifest attribute) unknown (gpf.variants.attributes.Inheritance attribute) (gpf.variants.attributes.Role attribute) (gpf.variants.attributes.TransmissionType attribute) unmap_chromosome() (gain.genomic_resources.genomic_position_table.table.GenomicPositionTable method) unregister_genotype_data() (gpf.studies.variants_db.VariantsDb method) unset_tag() (gpf.pedigrees.family.Family method) (gpf.pedigrees.family.Person method) (in module gpf.pedigrees.family_tag_builder) unspecified (gpf.enrichment_tool.event_counters.EnrichmentResult attribute) (gpf.enrichment_tool.event_counters.EventCountersResult attribute) (gpf.enrichment_tool.event_counters.EventsResult attribute) (gpf.enrichment_tool.event_counters.VariantEventsResult attribute) (gpf.person_sets.ChildrenBySex attribute) (gpf.person_sets.ChildrenStats attribute) (gpf.person_sets.person_sets.ChildrenBySex attribute) (gpf.person_sets.person_sets.ChildrenStats attribute) (gpf.variants.attributes.Sex attribute) (gpf.variants.attributes.Status attribute) update() (gain.genomic_resources.repository.Manifest method) (groups_api.views.GroupsViewSet method) (users_api.serializers.DatasetSerializer method) (users_api.serializers.UserSerializer method) (users_api.views.UserViewSet method) update_attribute_query_with_compounds() (in module gpf.query_variants.attribute_queries) update_attributes() (gpf.variants.family_variant.FamilyAllele method) (gpf.variants.variant.SummaryAllele method) (gpf.variants.variant.SummaryVariant method) update_cache() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method) update_frames() (gain.genomic_resources.gene_models.transcript_models.TranscriptModel method) (gain.genomic_resources.gene_models.TranscriptModel method) update_gps_with_values() (gpf.gene_profile.db.GeneProfileDBWriter method) update_manifest() (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) update_name() (datasets_api.models.Dataset class method) update_resource() (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) update_resource_file() (gain.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) update_study_config() (in module gpf.testing.import_helpers) url_to_pyarrow_fs() (in module gpf.parquet.helpers) use_bit_and_function() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method) (gpf.query_variants.sql.schema2.base_query_builder.Dialect static method) use_ssl (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute) (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute) used_context_attributes (gain.annotation.annotation_pipeline.Annotator property) (gain.annotation.annotation_pipeline.InputAnnotableAnnotatorDecorator property) (gain.annotation.gene_score_annotator.GeneScoreAnnotator property) (gain.annotation.gene_set_annotator.GeneSetAnnotator property) user (user_queries.models.UserQuery attribute) (users_api.models.BaseVerificationCode attribute) (users_api.models.GpUserState attribute) (users_api.models.ResetPasswordCode attribute) (users_api.models.SetPasswordCode attribute) user() (in module conftest) user_client() (in module conftest) user_has_permission() (in module datasets_api.permissions) user_id (user_queries.models.UserQuery attribute) (users_api.models.BaseVerificationCode attribute) (users_api.models.GpUserState attribute) (users_api.models.ResetPasswordCode attribute) (users_api.models.SetPasswordCode attribute) user_permissions (users_api.models.WdaeUser attribute) user_queries module user_queries.migrations module user_queries.migrations.0001_initial module user_queries.models module user_queries.urls module user_queries.views module user_without_password() (in module conftest) UserGpStateView (class in users_api.views) USERNAME_FIELD (users_api.models.WdaeUser attribute) UserQuery (class in user_queries.models) UserQuery.DoesNotExist UserQuery.MultipleObjectsReturned userquery_set (query_state_save.models.QueryState attribute) (users_api.models.WdaeUser attribute) UserQueryCollectView (class in user_queries.views) UserQuerySaveView (class in user_queries.views) users_api module users_api.forms module users_api.management module

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

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 gain.genomic_resources.aggregators) validate_and_normalize_config() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage class method) (gpf.genotype_storage.genotype_storage.GenotypeStorage class method) (gpf.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage class method) (gpf.parquet_storage.storage.ParquetGenotypeStorage class method) validate_and_normalize_schema() (gain.genomic_resources.resource_implementation.ResourceConfigValidationMixin class method) validate_config() (gpf.configuration.gpf_config_parser.GPFConfigParser static method) validate_existing_path() (in module gpf.configuration.utils) validate_path() (in module gpf.configuration.utils) validation_rules (gpf.configuration.gpf_config_parser.GPFConfigValidator attribute) VALIDATION_SCHEMA (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage attribute) (gpf.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage attribute) (gpf.parquet_storage.storage.ParquetGenotypeStorage attribute) value_max_len (gpf.pheno.common.InferenceConfig attribute) value_order (gain.gene_sets.gene_set.CategoricalHistogramSchema attribute) (gain.gene_sets.gene_set.NumericHistogramSchema attribute) (gain.genomic_resources.histogram.CategoricalHistogramConfig attribute) value_type (gain.annotation.annotation_config.AttributeInfo attribute) (gain.gene_scores.gene_scores.ScoreDef attribute) (gain.gene_scores.gene_scores.ScoreDesc attribute) (gain.genomic_resources.genomic_scores.ScoreDef attribute) (gpf.pheno.common.InferenceConfig attribute) (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) values (gpf.person_sets.person_sets.PersonSetConfig attribute) (gpf.person_sets.PersonSetConfig attribute) values() (gpf.pedigrees.families_data.FamiliesData method) values_domain (gpf.pheno.prepare.measure_classifier.InferenceReport attribute) values_domain() (gain.genomic_resources.histogram.CategoricalHistogram method) (gain.genomic_resources.histogram.NullHistogram method) (gain.genomic_resources.histogram.NumberHistogram method) ValueTransformAnnotatorDecorator (class in gain.annotation.annotation_pipeline) Variant (class in gain.effect_annotation.variant) variant_columns (gain.effect_annotation.cli.VariantColumnInputFile attribute) variant_in_member_fpids (gpf.variants.family_variant.FamilyAllele property) variant_in_members (gpf.variants.family_variant.FamilyAllele property) (gpf.variants.family_variant.FamilyVariant property) variant_in_roles (gpf.variants.family_variant.FamilyAllele property) variant_in_sexes (gpf.variants.family_variant.FamilyAllele property) variant_in_statuses (gpf.variants.family_variant.FamilyAllele property) variant_to_variant_type() (in module gpf.variants_loaders.raw.flexible_variant_loader) variant_transformer() (studies.response_transformer.ResponseTransformer method) (studies.study_wrapper.ResponseTransformerProtocol method) variant_type (gpf.variants.variant.SummaryAllele property) variant_types (gpf.variants.variant.SummaryVariant property) VariantColumnInputFile (class in gain.effect_annotation.cli) VariantColumnOutputFile (class in gain.effect_annotation.cli)

VariantDesc (class in gpf.variants.variant) VariantDetails (class in gpf.variants.variant) VariantEvent (class in gpf.enrichment_tool.genotype_helper) VariantEventsResult (class in gpf.enrichment_tool.event_counters) VariantReportsFullView (class in common_reports_api.views) VariantReportsView (class in common_reports_api.views) variants_filenames (gpf.variants_loaders.dae.loader.DaeTransmittedLoader property) (gpf.variants_loaders.raw.loader.VariantsLoader property) (gpf.variants_loaders.vcf.loader.VcfLoader property) variants_loader_annotate_and_save() (in module gpf.inmemory_storage.annotation_serialization) variants_loader_load_annotation() (in module gpf.inmemory_storage.annotation_serialization) VariantsDataSerializer (class in gpf.parquet.schema2.serializers) VariantsDb (class in gpf.studies.variants_db) VariantsGenotypesLoader (class in gpf.variants_loaders.raw.loader) VariantsLoader (class in gpf.variants_loaders.raw.loader) VariantsLoaderBatchSource (class in gpf.parquet.schema2.processing_pipeline) VariantsLoaderDecorator (class in gpf.variants_loaders.raw.loader) VariantsLoaderSource (class in gpf.parquet.schema2.processing_pipeline) VariantsParquetWriter (class in gpf.parquet.schema2.variants_parquet_writer) VariantsParquetWriterDeprecated() (in module gpf.parquet.schema2.parquet_io) vcf (gpf.testing.import_helpers.StudyInputLayout attribute) vcf2cshl() (in module gpf.variants.variant) vcf_import() (in module gpf.testing.import_helpers) vcf_liftover_main() (in module gpf.tools.liftover_tools) vcf_study() (in module gpf.testing.import_helpers) VCFAllele (class in gain.annotation.annotatable) VcfFamiliesGenotypes (class in gpf.variants_loaders.vcf.loader) vcffile_chromosomes() (in module gpf.variants_loaders.vcf.loader) VCFGenomicPositionTable (class in gain.genomic_resources.genomic_position_table) (class in gain.genomic_resources.genomic_position_table.table_vcf) VCFLiftoverTool (class in gpf.tools.liftover_tools) VcfLikeRecordToVcfAllele (class in gain.annotation.record_to_annotatable) VCFLine (class in gain.genomic_resources.genomic_position_table) (class in gain.genomic_resources.genomic_position_table.line) VcfLoader (class in gpf.variants_loaders.vcf.loader) VcfSerializer (class in gpf.variants_loaders.vcf.serializer) verbosity() (gain.utils.verbosity_configuration.VerbosityConfiguration static method) VerbosityConfiguration (class in gain.utils.verbosity_configuration) verification_code_model (users_api.views.BasePasswordView attribute) (users_api.views.ResetPassword attribute) (users_api.views.SetPassword attribute) version() (in module gpf_instance.views) version_string_to_suffix() (in module gain.genomic_resources.repository) version_tuple_to_string() (in module gain.genomic_resources.repository) version_tuple_to_suffix() (in module gain.genomic_resources.repository) view_max() (gain.genomic_resources.histogram.NumberHistogram method) view_min() (gain.genomic_resources.histogram.NumberHistogram method) view_range (gain.gene_sets.gene_set.NumericHistogramSchema attribute) (gain.genomic_resources.histogram.NumberHistogramConfig attribute) ViewRangeSchema (class in gain.gene_sets.gene_set) VisibleDatasetsView (class in datasets_api.views)

W

WDAEAbstractStudy (class in studies.study_wrapper) WDAEConfig (class in gpf_instance.apps) WdaeLoginForm (class in users_api.forms) WdaeLoginView (class in users_api.views) WdaePageNumberPagination (class in utils.pagination) WdaePasswordForgottenForm (class in users_api.forms) WdaeRegisterPasswordForm (class in users_api.forms) WdaeResetPasswordForm (class in users_api.forms) WDAEStudy (class in studies.study_wrapper) WDAEStudyGroup (class in studies.study_wrapper) WdaeUser (class in users_api.models) WdaeUser.DoesNotExist WdaeUser.MultipleObjectsReturned WdaeUserManager (class in users_api.models) web_format_str (gain.gene_sets.gene_set.GeneSetResourceSchema attribute) web_label (gain.gene_sets.gene_set.GeneSetResourceSchema attribute)

WHERE (gpf.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute) WILDCARD_LIMIT (gain.annotation.annotation_config.AnnotationConfigParser attribute) work_dir (gpf.import_tools.import_tools.ImportProject property) (gpf.pheno.common.PhenoImportConfig attribute) worst (gain.effect_annotation.effect.AlleleEffects property) worst_effect (gpf.variants.variant.SummaryAllele property) worst_effect() (gain.effect_annotation.effect.AnnotationEffect class method) write() (gpf.parquet.schema2.variants_parquet_writer.VariantsParquetWriter method) write_columns() (gain.effect_annotation.cli.VariantColumnOutputFile method) write_descriptions() (in module gpf.pheno.pheno_import) write_new_meta() (in module gpf.parquet.schema2.annotate_schema2_parquet) write_reports_to_parquet() (in module gpf.pheno.pheno_import) write_results() (in module gpf.pheno.pheno_import) write_summary_variant() (gpf.parquet.schema2.variants_parquet_writer.VariantsParquetWriter method) write_to_db() (gpf.pheno.common.ImportManifest static method) write_to_parquet() (in module gpf.pheno.pheno_import)

X

x (gpf.pedigrees.layout.Point attribute) X (gpf.variants.attributes.GeneticModel attribute) X_broken (gpf.variants.attributes.GeneticModel attribute) x_center (gpf.pedigrees.layout.IndividualWithCoordinates property)

x_log_scale (gain.gene_sets.gene_set.NumericHistogramSchema attribute) (gain.genomic_resources.histogram.NumberHistogramConfig attribute) x_min_log (gain.gene_sets.gene_set.NumericHistogramSchema attribute) (gain.genomic_resources.histogram.NumberHistogramConfig attribute)

Y

y (gpf.pedigrees.layout.Point attribute) y_center (gpf.pedigrees.layout.IndividualWithCoordinates property) y_log_scale (gain.gene_sets.gene_set.CategoricalHistogramSchema attribute) (gain.gene_sets.gene_set.NumericHistogramSchema attribute) (gain.genomic_resources.histogram.CategoricalHistogramConfig attribute) (gain.genomic_resources.histogram.NumberHistogramConfig attribute)

year (gpf.studies.study.GenotypeData property) yellow (gpf_web.default_settings.CustomFormatter attribute)

Z

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

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