dae Interface

• Genomic Resources
  • Classes and Functions
    • dae.genomic_resources package
      • Subpackages
        • dae.genomic_resources.gene_models package
        • dae.genomic_resources.genomic_position_table package
        • dae.genomic_resources.implementations package
        • dae.genomic_resources.statistics package
      • Submodules
      • dae.genomic_resources.aggregators module
        • Aggregator
        • ConcatAggregator
        • CountAggregator
        • DictAggregator
        • JoinAggregator
        • ListAggregator
        • MaxAggregator
        • MeanAggregator
        • MedianAggregator
        • MinAggregator
        • ModeAggregator
        • build_aggregator()
        • create_aggregator()
        • create_aggregator_definition()
        • get_aggregator_class()
        • validate_aggregator()
      • dae.genomic_resources.cached_repository module
        • CacheResource
        • CachingProtocol
        • GenomicResourceCachedRepo
        • cache_resources()
      • dae.genomic_resources.cli module
        • cli_browse()
        • cli_manage()
        • collect_dvc_entries()
      • dae.genomic_resources.draw_score_histograms module
        • main()
        • parse_cli_arguments()
      • dae.genomic_resources.fsspec_protocol module
        • FsspecReadOnlyProtocol
        • FsspecReadWriteProtocol
        • build_fsspec_protocol()
        • build_inmemory_protocol()
        • build_local_resource()
      • dae.genomic_resources.genomic_context module
        • DefaultRepositoryContextProvider
        • clear_registered_contexts()
        • context_providers_add_argparser_arguments()
        • context_providers_init()
        • context_providers_init_with_argparser()
        • get_genomic_context()
        • register_context()
        • register_context_provider()
      • dae.genomic_resources.genomic_context_base module
        • Key Constants
        • See Also
        • GenomicContext
        • GenomicContextProvider
        • PriorityGenomicContext
        • SimpleGenomicContext
      • dae.genomic_resources.genomic_context_cli module
        • CLIGenomicContextProvider
      • dae.genomic_resources.genomic_scores module
        • AlleleScore
        • AlleleScoreAggr
        • AlleleScoreQuery
        • CNV
        • CnvCollection
        • GenomicScore
        • PositionScore
        • PositionScoreAggr
        • PositionScoreQuery
        • ScoreDef
        • ScoreLine
        • build_score_from_resource()
        • build_score_from_resource_id()
      • dae.genomic_resources.group_repository module
        • GenomicResourceGroupRepo
      • dae.genomic_resources.histogram module
        • CategoricalHistogram
        • CategoricalHistogramConfig
        • HistogramError
        • HistogramStatisticMixin
        • NullHistogram
        • NullHistogramConfig
        • NumberHistogram
        • NumberHistogramConfig
        • build_default_histogram_conf()
        • build_empty_histogram()
        • build_histogram_config()
        • load_histogram()
        • plot_histogram()
        • save_histogram()
      • dae.genomic_resources.liftover_chain module
        • LiftoverChain
        • build_liftover_chain_from_resource()
        • build_liftover_chain_from_resource_id()
      • dae.genomic_resources.reference_genome module
        • ReferenceGenome
        • build_reference_genome_from_file()
        • build_reference_genome_from_resource()
        • build_reference_genome_from_resource_id()
      • dae.genomic_resources.repository module
        • GenomicResource
        • GenomicResourceProtocolRepo
        • GenomicResourceRepo
        • Manifest
        • ManifestEntry
        • ManifestUpdate
        • Mode
        • ReadOnlyRepositoryProtocol
        • ReadWriteRepositoryProtocol
        • ResourceFileState
        • is_gr_id_token()
        • is_version_constraint_satisfied()
        • parse_gr_id_version_token()
        • parse_resource_id_version()
        • version_string_to_suffix()
        • version_tuple_to_string()
        • version_tuple_to_suffix()
      • dae.genomic_resources.repository_factory module
        • build_genomic_resource_group_repository()
        • build_genomic_resource_repository()
        • build_resource_implementation()
        • get_default_grr_definition()
        • get_default_grr_definition_path()
        • load_definition_file()
      • dae.genomic_resources.resource_implementation module
        • GenomicResourceImplementation
        • InfoImplementationMixin
        • ResourceConfigValidationMixin
        • ResourceStatistics
        • get_base_resource_schema()
      • dae.genomic_resources.testing module
        • build_filesystem_test_protocol()
        • build_filesystem_test_repository()
        • build_filesystem_test_resource()
        • build_http_test_protocol()
        • build_inmemory_test_protocol()
        • build_inmemory_test_repository()
        • build_inmemory_test_resource()
        • build_s3_test_bucket()
        • build_s3_test_filesystem()
        • build_s3_test_protocol()
        • convert_to_tab_separated()
        • copy_proto_genomic_resources()
        • proto_builder()
        • resource_builder()
        • s3_test_protocol()
        • s3_test_server_endpoint()
        • setup_bigwig()
        • setup_dae_transmitted()
        • setup_denovo()
        • setup_directories()
        • setup_empty_gene_models()
        • setup_gene_models()
        • setup_genome()
        • setup_gzip()
        • setup_pedigree()
        • setup_tabix()
        • setup_vcf()
      • dae.genomic_resources.variant_utils module
        • maximally_extend_variant()
        • normalize_variant()
      • Module contents
        • get_resource_implementation_builder()
• Annotation
  • Classes and Functions
    • dae.annotation package
      • Submodules
      • dae.annotation.annotatable module
        • Annotatable
        • CNVAllele
        • Position
        • Region
        • VCFAllele
      • dae.annotation.annotate_columns module
        • cli()
      • dae.annotation.annotate_doc module
        • cli()
        • configure_argument_parser()
      • dae.annotation.annotate_utils module
        • add_common_annotation_arguments()
        • add_input_files_to_task_graph()
        • build_cli_genomic_context()
        • build_output_path()
        • cache_pipeline_resources()
        • get_grr_from_context()
        • get_pipeline_from_context()
        • handle_default_args()
        • produce_partfile_paths()
        • produce_regions()
        • stringify()
      • dae.annotation.annotate_vcf module
        • cli()
      • dae.annotation.annotation_config module
        • AnnotationConfigParser
        • AnnotationConfigurationError
        • AnnotationPreamble
        • AnnotatorInfo
        • AttributeInfo
        • ParamsUsageMonitor
        • RawFullConfig
        • RawPreamble
      • dae.annotation.annotation_factory module
        • build_annotation_pipeline()
        • check_for_repeated_attributes_in_annotator()
        • check_for_repeated_attributes_in_pipeline()
        • check_for_unused_parameters()
        • get_annotator_factory()
        • get_available_annotator_types()
        • load_pipeline_from_file()
        • load_pipeline_from_grr()
        • load_pipeline_from_yaml()
        • register_annotator_factory()
        • resolve_repeated_attributes()
      • dae.annotation.annotation_genomic_context_cli module
        • CLIAnnotationContextProvider
        • get_context_pipeline()
      • dae.annotation.annotation_pipeline module
        • AnnotationPipeline
        • Annotator
        • AnnotatorDecorator
        • InputAnnotableAnnotatorDecorator
        • ReannotationPipeline
        • ValueTransformAnnotatorDecorator
      • dae.annotation.annotator_base module
        • AnnotatorBase
        • AttributeDesc
      • dae.annotation.chromosome_annotator module
        • ChromosomeAnnotator
        • build_chromosome_annotator()
      • dae.annotation.cnv_collection_annotator module
        • CnvCollectionAnnotator
        • build_cnv_collection_annotator()
      • dae.annotation.debug_annotator module
        • HelloWorldAnnotator
        • build_annotator()
      • dae.annotation.docker_annotator module
        • DockerAnnotator
      • dae.annotation.effect_annotator module
        • EffectAnnotatorAdapter
        • build_effect_annotator()
      • dae.annotation.gene_score_annotator module
        • GeneScoreAnnotator
        • build_gene_score_annotator()
      • dae.annotation.gene_set_annotator module
        • GeneSetAnnotator
        • build_gene_set_annotator()
      • dae.annotation.liftover_annotator module
        • AbstractLiftoverAnnotator
        • BasicLiftoverAnnotator
        • BcfLiftoverAnnotator
        • LiftoverFunction
        • basic_liftover_allele()
        • basic_liftover_variant()
        • bcf_liftover_allele()
        • bcf_liftover_variant()
        • build_liftover_annotator()
      • dae.annotation.normalize_allele_annotator module
        • NormalizeAlleleAnnotator
        • build_normalize_allele_annotator()
        • normalize_allele()
      • dae.annotation.processing_pipeline module
        • Annotation
        • AnnotationPipelineAnnotatablesBatchFilter
        • AnnotationPipelineAnnotatablesFilter
        • AnnotationPipelineContextManager
        • AnnotationsWithSource
        • AnnotationsWithSourceBatchFilter
        • AnnotationsWithSourceFilter
        • DeleteAttributesFromAWSBatchFilter
        • DeleteAttributesFromAWSFilter
      • dae.annotation.record_to_annotatable module
        • CSHLAlleleRecordToAnnotatable
        • DaeAlleleRecordToAnnotatable
        • RecordToAnnotable
        • RecordToCNVAllele
        • RecordToPosition
        • RecordToRegion
        • RecordToVcfAllele
        • VcfLikeRecordToVcfAllele
        • add_record_to_annotable_arguments()
        • build_record_to_annotatable()
      • dae.annotation.score_annotator module
        • AlleleScoreAnnotator
        • GenomicScoreAnnotatorBase
        • PositionScoreAnnotator
        • build_allele_score_annotator()
        • build_np_score_annotator()
        • build_position_score_annotator()
        • get_genomic_resource()
      • dae.annotation.simple_effect_annotator module
        • SimpleEffect
        • SimpleEffectAnnotator
        • build_simple_effect_annotator()
      • dae.annotation.utils module
        • find_annotator_gene_models()
        • find_annotator_reference_genome()
      • Module contents
• Effect Annotation
  • Classes and Functions
    • dae.effect_annotation package
      • Subpackages
        • dae.effect_annotation.effect_checkers package
      • Submodules
      • dae.effect_annotation.annotation_effects module
        • get_effect_types()
        • get_effect_types_set()
      • dae.effect_annotation.annotation_request module
        • BaseAnnotationRequest
        • NegativeStrandAnnotationRequest
        • PositiveStrandAnnotationRequest
      • dae.effect_annotation.annotator module
        • AnnotationRequestFactory
        • EffectAnnotator
      • dae.effect_annotation.cli module
        • AnnotationAttributes
        • EffectAnnotatorBuilder
        • VariantColumnInputFile
        • VariantColumnOutputFile
        • cli_columns()
        • cli_vcf()
      • dae.effect_annotation.effect module
        • AlleleEffects
        • AnnotationEffect
        • EffectFactory
        • EffectGene
        • EffectTranscript
        • EffectTypesMixin
        • expand_effect_types()
        • gd2str()
        • ge2str()
        • gene_effect_get_genes()
        • gene_effect_get_genes_worst()
        • gene_effect_get_worst_effect()
      • dae.effect_annotation.gene_codes module
        • NuclearCode
      • dae.effect_annotation.variant module
        • Variant
      • Module contents
• Genomic Variants
  • Apache Parquet variants schema
    • Summary Variants/Alleles flat schema
    • Family Variants schema
    • Family Alleles schema
    • Variant Scores schema
    • Pedigree file schema
  • Family variants query interface
    • Query by regions
    • Query by genes and effect types
    • Query by inheritance
    • Query by family IDs
    • Query by person IDs
    • Query by sexes
    • Query by roles
    • Query by variant types
    • Query with real value variant attributes (scores)
    • Query with filter function
  • Genomic Variants Classes and Functions
    • dae.variants package
      • Submodules
      • dae.variants.attributes module
        • GeneticModel
        • Inheritance
        • Role
        • Sex
        • Status
        • TransmissionType
        • Zygosity
        • bitmask2inheritance()
      • dae.variants.core module
        • Allele
      • dae.variants.family_variant module
        • FamilyAllele
        • FamilyDelegate
        • FamilyVariant
        • calculate_simple_best_state()
      • dae.variants.variant module
        • SummaryAllele
        • SummaryVariant
        • SummaryVariantFactory
        • VariantDesc
        • VariantDetails
        • allele_type_from_cshl_variant()
        • allele_type_from_name()
        • cshl_format()
        • tandem_repeat()
        • vcf2cshl()
      • Module contents
• Pedigrees Tools
  • Classes and Functions
    • dae.pedigrees package
      • Submodules
      • dae.pedigrees.drawing module
        • OffsetLayoutDrawer
        • PDFLayoutDrawer
      • dae.pedigrees.families_data module
        • FamiliesData
        • merge_families()
        • tag_families_data()
      • dae.pedigrees.family module
        • Family
        • FamilyTag
        • Person
        • get_pedigree_column_names()
      • dae.pedigrees.family_role_builder module
        • FamilyRoleBuilder
        • Mating
      • dae.pedigrees.family_tag_builder module
        • FamilyTagsBuilder
        • check_affected_dad_family()
        • check_affected_mom_family()
        • check_affected_prb_family()
        • check_affected_sib_family()
        • check_control_family()
        • check_family_tags_query()
        • check_female_prb_family()
        • check_male_prb_family()
        • check_missing_dad_family()
        • check_missing_mom_family()
        • check_multiplex_family()
        • check_nuclear_family()
        • check_quad_family()
        • check_simplex_family()
        • check_tag()
        • check_trio_family()
        • check_unaffected_dad_family()
        • check_unaffected_mom_family()
        • check_unaffected_prb_family()
        • check_unaffected_sib_family()
        • set_attr()
        • set_tag()
        • tag_affected_dad_family()
        • tag_affected_mom_family()
        • tag_affected_prb_family()
        • tag_affected_sib_family()
        • tag_control_family()
        • tag_female_prb_family()
        • tag_male_prb_family()
        • tag_missing_dad_family()
        • tag_missing_mom_family()
        • tag_multiplex_family()
        • tag_nuclear_family()
        • tag_quad_family()
        • tag_simplex_family()
        • tag_trio_family()
        • tag_unaffected_dad_family()
        • tag_unaffected_mom_family()
        • tag_unaffected_prb_family()
        • tag_unaffected_sib_family()
        • unset_tag()
      • dae.pedigrees.layout module
        • IndividualWithCoordinates
        • Layout
        • Line
        • Point
        • layout_parser()
      • dae.pedigrees.loader module
        • FamiliesLoader
      • dae.pedigrees.pedigrees module
        • FamilyConnections
        • Individual
        • IndividualGroup
        • Interval
        • IntervalForVertex
        • MatingUnit
        • Realization
        • SandwichInstance
        • SandwichSolver
        • SibshipUnit
        • copy_graph()
      • dae.pedigrees.testing module
        • build_families_data()
        • build_family()
      • Module contents
• Variants Loaders
  • dae.variants_loaders package
    • Subpackages
      • dae.variants_loaders.cnv package
        • Submodules
        • dae.variants_loaders.cnv.flexible_cnv_loader module
        • dae.variants_loaders.cnv.loader module
        • Module contents
      • dae.variants_loaders.dae package
        • Submodules
        • dae.variants_loaders.dae.loader module
        • Module contents
      • dae.variants_loaders.parquet package
        • Submodules
        • dae.variants_loaders.parquet.loader module
        • Module contents
      • dae.variants_loaders.raw package
        • Submodules
        • dae.variants_loaders.raw.flexible_variant_loader module
        • dae.variants_loaders.raw.loader module
        • Module contents
      • dae.variants_loaders.vcf package
        • Submodules
        • dae.variants_loaders.vcf.loader module
        • dae.variants_loaders.vcf.serializer module
        • Module contents
    • Module contents
  • dae.variants_loaders.raw package
    • Submodules
    • dae.variants_loaders.raw.flexible_variant_loader module
      • adjust_chrom_prefix()
      • flexible_variant_loader()
      • location_variant_to_vcf_transformer()
      • variant_to_variant_type()
    • dae.variants_loaders.raw.loader module
      • ArgumentType
        • ArgumentType.ARGUMENT
        • ArgumentType.OPTION
      • CLIArgument
        • CLIArgument.add_to_parser()
        • CLIArgument.build_option()
        • CLIArgument.parse_cli_argument()
      • CLILoader
        • CLILoader.build_arguments_dict()
        • CLILoader.build_cli_arguments()
        • CLILoader.cli_arguments()
        • CLILoader.cli_defaults()
        • CLILoader.parse_cli_arguments()
      • FamiliesGenotypes
        • FamiliesGenotypes.family_genotype_iterator()
      • FullVariant
        • FullVariant.family_variants
        • FullVariant.summary_variant
      • VariantsGenotypesLoader
        • VariantsGenotypesLoader.full_variants_iterator()
        • VariantsGenotypesLoader.reset_regions()
      • VariantsLoader
        • VariantsLoader.annotation_schema
        • VariantsLoader.chromosomes
        • VariantsLoader.close()
        • VariantsLoader.family_variants_iterator()
        • VariantsLoader.fetch()
        • VariantsLoader.fetch_family_variants()
        • VariantsLoader.fetch_summary_variants()
        • VariantsLoader.full_variants_iterator()
        • VariantsLoader.get_attribute()
        • VariantsLoader.reset_regions()
        • VariantsLoader.set_attribute()
        • VariantsLoader.variants_filenames
      • VariantsLoaderDecorator
        • VariantsLoaderDecorator.annotation_schema
        • VariantsLoaderDecorator.build_arguments_dict()
        • VariantsLoaderDecorator.build_cli_arguments()
        • VariantsLoaderDecorator.chromosomes
        • VariantsLoaderDecorator.cli_arguments()
        • VariantsLoaderDecorator.cli_defaults()
        • VariantsLoaderDecorator.close()
        • VariantsLoaderDecorator.get_attribute()
    • Module contents
  • dae.variants_loaders.dae package
    • Submodules
    • dae.variants_loaders.dae.loader module
      • DaeTransmittedFamiliesGenotypes
        • DaeTransmittedFamiliesGenotypes.family_genotype_iterator()
        • DaeTransmittedFamiliesGenotypes.get_family_read_counts()
      • DaeTransmittedLoader
        • DaeTransmittedLoader.chromosomes
        • DaeTransmittedLoader.close()
        • DaeTransmittedLoader.parse_cli_arguments()
        • DaeTransmittedLoader.variants_filenames
      • DenovoFamiliesGenotypes
        • DenovoFamiliesGenotypes.family_genotype_iterator()
      • DenovoLoader
        • DenovoLoader.chromosomes
        • DenovoLoader.close()
        • DenovoLoader.flexible_denovo_load()
        • DenovoLoader.full_variants_iterator()
        • DenovoLoader.parse_cli_arguments()
        • DenovoLoader.produce_genotype()
        • DenovoLoader.split_location()
    • Module contents
  • dae.variants_loaders.vcf package
    • Submodules
    • dae.variants_loaders.vcf.loader module
      • SingleVcfLoader
        • SingleVcfLoader.chromosomes
        • SingleVcfLoader.close()
      • VcfFamiliesGenotypes
        • VcfFamiliesGenotypes.family_genotype_iterator()
      • VcfLoader
        • VcfLoader.chromosomes
        • VcfLoader.close()
        • VcfLoader.init_vcf_loaders()
        • VcfLoader.parse_cli_arguments()
        • VcfLoader.reset_regions()
        • VcfLoader.variants_filenames
      • vcffile_chromosomes()
    • dae.variants_loaders.vcf.serializer module
      • VcfSerializer
        • VcfSerializer.close()
        • VcfSerializer.open()
        • VcfSerializer.serialize()
        • VcfSerializer.serialize_full_variant()
    • Module contents
  • dae.variants_loaders.cnv package
    • Submodules
    • dae.variants_loaders.cnv.flexible_cnv_loader module
      • flexible_cnv_loader()
    • dae.variants_loaders.cnv.loader module
      • Copy Number Variants (CNV) loader CNVLoader
        • Location of the CNVs
        • Genotype of the CNVs
        • Variant type for CNVs
        • Additional parameters
      • CNVLoader
        • CNVLoader.chromosomes
        • CNVLoader.close()
        • CNVLoader.full_variants_iterator()
        • CNVLoader.parse_cli_arguments()
    • Module contents
• Import Tools
  • What is Import Tools
  • Import Tools config files
  • Import Tools configuration format
  • Working with the Import Tools CLI
  • Running on a SGE cluster
  • Running on a Kubernetes cluster
  • Classes and Functions
    • dae.import_tools package
      • Submodules
      • dae.import_tools.cli module
        • main()
        • run_with_project()
      • dae.import_tools.import_config module
      • dae.import_tools.import_tools module
        • Bucket
        • ImportConfigNormalizer
        • ImportProject
        • ImportStorage
        • construct_import_annotation_pipeline()
        • construct_import_annotation_pipeline_config()
        • get_import_storage_factory()
        • get_import_storage_types()
        • register_import_storage_factory()
        • save_study_config()
      • Module contents
• Genotype Data Parquet Writers
  • dae.parquet package
    • Subpackages
      • dae.parquet.schema2 package
        • Submodules
        • dae.parquet.schema2.annotate_schema2_parquet module
        • dae.parquet.schema2.loader module
        • dae.parquet.schema2.merge_parquet module
        • dae.parquet.schema2.parquet_io module
        • dae.parquet.schema2.processing_pipeline module
        • dae.parquet.schema2.serializers module
        • dae.parquet.schema2.variants_parquet_writer module
        • Module contents
    • Submodules
    • dae.parquet.helpers module
      • merge_parquets()
      • url_to_pyarrow_fs()
    • dae.parquet.parquet_writer module
      • add_missing_parquet_fields()
      • append_meta_to_parquet()
      • collect_pedigree_parquet_schema()
      • fill_family_bins()
      • merge_variants_parquets()
      • pedigree_parquet_schema()
      • save_ped_df_to_parquet()
      • serialize_summary_schema()
    • dae.parquet.partition_descriptor module
      • Partition
        • Partition.coding_bin
        • Partition.family_bin
        • Partition.frequency_bin
        • Partition.from_pylist()
        • Partition.is_empty()
        • Partition.region_bin
        • Partition.to_pylist()
      • PartitionDescriptor
        • PartitionDescriptor.build_family_partitions()
        • PartitionDescriptor.build_summary_partitions()
        • PartitionDescriptor.family_partition()
        • PartitionDescriptor.family_partition_schema()
        • PartitionDescriptor.get_variant_partitions()
        • PartitionDescriptor.has_coding_bins()
        • PartitionDescriptor.has_family_bins()
        • PartitionDescriptor.has_family_partitions()
        • PartitionDescriptor.has_frequency_bins()
        • PartitionDescriptor.has_partitions()
        • PartitionDescriptor.has_region_bins()
        • PartitionDescriptor.has_summary_partitions()
        • PartitionDescriptor.make_all_region_bins()
        • PartitionDescriptor.make_coding_bin()
        • PartitionDescriptor.make_family_bin()
        • PartitionDescriptor.make_frequency_bin()
        • PartitionDescriptor.make_region_bin()
        • PartitionDescriptor.make_region_bins_regions()
        • PartitionDescriptor.parse()
        • PartitionDescriptor.parse_dict()
        • PartitionDescriptor.parse_string()
        • PartitionDescriptor.partition_directory()
        • PartitionDescriptor.partition_filename()
        • PartitionDescriptor.path_to_partitions()
        • PartitionDescriptor.region_bins_count()
        • PartitionDescriptor.region_to_region_bins()
        • PartitionDescriptor.schema1_partition()
        • PartitionDescriptor.serialize()
        • PartitionDescriptor.summary_partition()
        • PartitionDescriptor.summary_partition_schema()
        • PartitionDescriptor.to_dict()
    • Module contents
  • dae.parquet.schema2 package
    • Submodules
    • dae.parquet.schema2.annotate_schema2_parquet module
      • backup_schema2_study()
      • cli()
      • merge_partitions()
      • process_parquet()
      • produce_regions()
      • produce_schema2_annotation_tasks()
      • produce_schema2_merging_tasks()
      • symlink_pedigree_and_family_variants()
      • write_new_meta()
    • dae.parquet.schema2.loader module
      • MultiReader
        • MultiReader.close()
        • MultiReader.current_idx
      • ParquetLoader
        • ParquetLoader.FAMILY_COLUMNS
        • ParquetLoader.SUMMARY_COLUMNS
        • ParquetLoader.fetch_family_variants()
        • ParquetLoader.fetch_summary_variants()
        • ParquetLoader.fetch_variants()
        • ParquetLoader.get_family_pq_filepaths()
        • ParquetLoader.get_summary_pq_filepaths()
        • ParquetLoader.load_from_dir()
      • ParquetLoaderException
      • Reader
        • Reader.close()
        • Reader.current_idx
    • dae.parquet.schema2.merge_parquet module
      • merge_parquet_directory()
      • merge_parquets()
      • merge_variants_parquets()
    • dae.parquet.schema2.parquet_io module
      • ContinuousParquetFileWriter
        • ContinuousParquetFileWriter.BATCH_ROWS
        • ContinuousParquetFileWriter.DEFAULT_COMPRESSION
        • ContinuousParquetFileWriter.append_allele()
        • ContinuousParquetFileWriter.build_batch()
        • ContinuousParquetFileWriter.build_table()
        • ContinuousParquetFileWriter.close()
        • ContinuousParquetFileWriter.data_reset()
        • ContinuousParquetFileWriter.size()
      • VariantsParquetWriterDeprecated()
    • dae.parquet.schema2.processing_pipeline module
      • AnnotationPipelineVariantsBatchFilter
        • AnnotationPipelineVariantsBatchFilter.filter()
      • AnnotationPipelineVariantsFilter
        • AnnotationPipelineVariantsFilter.filter()
      • AnnotationPipelineVariantsFilterMixin
      • DeleteAttributesFromVariantFilter
        • DeleteAttributesFromVariantFilter.filter()
      • DeleteAttributesFromVariantsBatchFilter
        • DeleteAttributesFromVariantsBatchFilter.filter()
      • Schema2SummaryVariantsBatchSource
        • Schema2SummaryVariantsBatchSource.fetch()
      • Schema2SummaryVariantsSource
        • Schema2SummaryVariantsSource.fetch()
      • VariantsLoaderBatchSource
        • VariantsLoaderBatchSource.fetch()
      • VariantsLoaderSource
        • VariantsLoaderSource.fetch()
    • dae.parquet.schema2.serializers module
      • AlleleParquetSerializer
        • AlleleParquetSerializer.blob_column()
        • AlleleParquetSerializer.build_allele_record_dict()
        • AlleleParquetSerializer.schema()
      • FamilyAlleleParquetSerializer
        • FamilyAlleleParquetSerializer.blob_column()
        • FamilyAlleleParquetSerializer.build_allele_record_dict()
        • FamilyAlleleParquetSerializer.build_schema()
        • FamilyAlleleParquetSerializer.schema()
      • JsonVariantsDataSerializer
        • JsonVariantsDataSerializer.deserialize_family_record()
        • JsonVariantsDataSerializer.deserialize_summary_record()
        • JsonVariantsDataSerializer.serialize_family()
        • JsonVariantsDataSerializer.serialize_summary()
      • SummaryAlleleParquetSerializer
        • SummaryAlleleParquetSerializer.blob_column()
        • SummaryAlleleParquetSerializer.build_allele_record_dict()
        • SummaryAlleleParquetSerializer.build_blob_schema()
        • SummaryAlleleParquetSerializer.build_schema()
        • SummaryAlleleParquetSerializer.schema()
      • VariantsDataSerializer
        • VariantsDataSerializer.build_serializer()
        • VariantsDataSerializer.deserialize_family_record()
        • VariantsDataSerializer.deserialize_summary_record()
        • VariantsDataSerializer.serialize_family()
        • VariantsDataSerializer.serialize_summary()
      • build_family_schema()
      • build_summary_schema()
    • dae.parquet.schema2.variants_parquet_writer module
      • ContinuousParquetFileWriter
        • ContinuousParquetFileWriter.DEFAULT_COMPRESSION
        • ContinuousParquetFileWriter.append_allele()
        • ContinuousParquetFileWriter.close()
        • ContinuousParquetFileWriter.size()
      • Schema2SummaryVariantBatchConsumer
        • Schema2SummaryVariantBatchConsumer.filter()
      • Schema2SummaryVariantConsumer
        • Schema2SummaryVariantConsumer.filter()
      • Schema2VariantBatchConsumer
        • Schema2VariantBatchConsumer.filter()
      • Schema2VariantConsumer
        • Schema2VariantConsumer.filter()
      • VariantsParquetWriter
        • VariantsParquetWriter.close()
        • VariantsParquetWriter.write()
        • VariantsParquetWriter.write_summary_variant()
    • Module contents
• Query Genomic Variants
  • dae.query_variants package
    • Subpackages
      • dae.query_variants.sql package
        • Subpackages
        • Module contents
    • Submodules
    • dae.query_variants.attribute_queries module
      • AttributeQueryNotSupported
      • AttributeQueryTransformer
      • AttributeQueryTransformerFunction
        • AttributeQueryTransformerFunction.and_()
        • AttributeQueryTransformerFunction.compound()
        • AttributeQueryTransformerFunction.grouping()
        • AttributeQueryTransformerFunction.literal()
        • AttributeQueryTransformerFunction.neg()
        • AttributeQueryTransformerFunction.or_()
      • AttributeQueryTransformerSQL
        • AttributeQueryTransformerSQL.and_()
        • AttributeQueryTransformerSQL.compound()
        • AttributeQueryTransformerSQL.grouping()
        • AttributeQueryTransformerSQL.literal()
        • AttributeQueryTransformerSQL.neg()
        • AttributeQueryTransformerSQL.or_()
      • AttributeQueryTransformerSQLLegacy
        • AttributeQueryTransformerSQLLegacy.compound()
        • AttributeQueryTransformerSQLLegacy.literal()
      • CompoundStripTransformer
        • CompoundStripTransformer.compound()
      • Matcher
      • QueryCompoundAdditionTransformer
        • QueryCompoundAdditionTransformer.all()
        • QueryCompoundAdditionTransformer.and_()
        • QueryCompoundAdditionTransformer.any()
        • QueryCompoundAdditionTransformer.compound()
        • QueryCompoundAdditionTransformer.grouping()
        • QueryCompoundAdditionTransformer.literal()
        • QueryCompoundAdditionTransformer.neg()
        • QueryCompoundAdditionTransformer.or_()
      • SyntaxSugarTransformer
        • SyntaxSugarTransformer.all()
        • SyntaxSugarTransformer.any()
      • create_and_node()
      • create_or_node()
      • transform_attribute_query_to_function()
      • transform_attribute_query_to_sql_expression()
      • transform_attribute_query_to_sql_expression_schema1()
      • update_attribute_query_with_compounds()
    • dae.query_variants.base_query_variants module
      • QueryVariants
        • QueryVariants.build_family_variants_query_runner()
        • QueryVariants.build_summary_variants_query_runner()
        • QueryVariants.families
        • QueryVariants.has_affected_status_queries()
        • QueryVariants.tags_to_family_ids()
        • QueryVariants.transform_roles_to_single_role_string()
      • QueryVariantsBase
        • QueryVariantsBase.RUNNER_CLASS
        • QueryVariantsBase.deserialize_family_variant()
        • QueryVariantsBase.deserialize_summary_variant()
        • QueryVariantsBase.has_affected_status_queries()
    • dae.query_variants.query_runners module
      • QueryResult
        • QueryResult.CHECK_VERBOSITY
        • QueryResult.close()
        • QueryResult.get()
        • QueryResult.is_done()
        • QueryResult.start()
      • QueryRunner
        • QueryRunner.adapt()
        • QueryRunner.close()
        • QueryRunner.is_closed()
        • QueryRunner.is_done()
        • QueryRunner.is_started()
        • QueryRunner.put_value_in_result_queue()
        • QueryRunner.result_queue
        • QueryRunner.run()
        • QueryRunner.set_result_queue()
        • QueryRunner.set_study_id()
        • QueryRunner.start()
    • Module contents
  • dae.query_variants.sql package
    • Subpackages
      • dae.query_variants.sql.schema2 package
        • Submodules
        • dae.query_variants.sql.schema2.base_query_builder module
        • dae.query_variants.sql.schema2.base_variants module
        • dae.query_variants.sql.schema2.family_builder module
        • dae.query_variants.sql.schema2.sql_query_builder module
        • dae.query_variants.sql.schema2.summary_builder module
        • Module contents
    • Module contents
  • dae.query_variants.sql.schema2 package
    • Submodules
    • dae.query_variants.sql.schema2.base_query_builder module
      • BaseQueryBuilder
        • BaseQueryBuilder.GENE_REGIONS_HEURISTIC_CUTOFF
        • BaseQueryBuilder.GENE_REGIONS_HEURISTIC_EXTEND
        • BaseQueryBuilder.MAX_CHILD_NUMBER
        • BaseQueryBuilder.QUOTE
        • BaseQueryBuilder.WHERE
        • BaseQueryBuilder.build_query()
      • Dialect
        • Dialect.add_unnest_in_join()
        • Dialect.array_item_suffix()
        • Dialect.build_array_join()
        • Dialect.build_table_name()
        • Dialect.escape_char()
        • Dialect.escape_quote_char()
        • Dialect.float_type()
        • Dialect.int_type()
        • Dialect.string_type()
        • Dialect.use_bit_and_function()
    • dae.query_variants.sql.schema2.base_variants module
      • SqlSchema2Variants
        • SqlSchema2Variants.RUNNER_CLASS
        • SqlSchema2Variants.build_family_variants_query_runner()
        • SqlSchema2Variants.build_summary_variants_query_runner()
    • dae.query_variants.sql.schema2.family_builder module
      • FamilyQueryBuilder
    • dae.query_variants.sql.schema2.sql_query_builder module
      • Db2Layout
        • Db2Layout.db
        • Db2Layout.family
        • Db2Layout.meta
        • Db2Layout.pedigree
        • Db2Layout.study
        • Db2Layout.summary
      • QueryBuilderBase
        • QueryBuilderBase.FAMILY_BIN_HEURISTIC_CUTOFF
        • QueryBuilderBase.GENE_REGIONS_HEURISTIC_CUTOFF
        • QueryBuilderBase.GENE_REGIONS_HEURISTIC_EXTEND
        • QueryBuilderBase.REGION_BINS_HEURISTIC_CUTOFF
        • QueryBuilderBase.all_region_bins()
        • QueryBuilderBase.build_gene_regions()
        • QueryBuilderBase.build_schema()
        • QueryBuilderBase.build_variant_types_query()
        • QueryBuilderBase.calc_batched_heuristics()
        • QueryBuilderBase.calc_coding_bins()
        • QueryBuilderBase.calc_family_bins()
        • QueryBuilderBase.calc_frequency_bins()
        • QueryBuilderBase.calc_heuristics()
        • QueryBuilderBase.calc_region_bins()
        • QueryBuilderBase.check_inheritance_denovo_only()
        • QueryBuilderBase.check_inheritance_query_value()
        • QueryBuilderBase.check_roles_denovo_only()
        • QueryBuilderBase.check_roles_query_value()
        • QueryBuilderBase.check_variant_types_value()
        • QueryBuilderBase.split_heuristics()
      • QueryHeuristics
        • QueryHeuristics.coding_bins
        • QueryHeuristics.family_bins
        • QueryHeuristics.frequency_bins
        • QueryHeuristics.is_empty()
        • QueryHeuristics.region_bins
      • SqlQueryBuilder
        • SqlQueryBuilder.apply_family_heuristics()
        • SqlQueryBuilder.apply_summary_heuristics()
        • SqlQueryBuilder.build()
        • SqlQueryBuilder.build_family_variants_query()
        • SqlQueryBuilder.build_summary_variants_query()
        • SqlQueryBuilder.categorical_attr()
        • SqlQueryBuilder.coding_bins()
        • SqlQueryBuilder.effect_types()
        • SqlQueryBuilder.family_base()
        • SqlQueryBuilder.family_bins()
        • SqlQueryBuilder.family_ids()
        • SqlQueryBuilder.family_query()
        • SqlQueryBuilder.family_variants()
        • SqlQueryBuilder.frequency()
        • SqlQueryBuilder.frequency_bins()
        • SqlQueryBuilder.genes()
        • SqlQueryBuilder.inheritance()
        • SqlQueryBuilder.person_ids()
        • SqlQueryBuilder.real_attr()
        • SqlQueryBuilder.region_bins()
        • SqlQueryBuilder.regions()
        • SqlQueryBuilder.replace_tables()
        • SqlQueryBuilder.resolve_tags()
        • SqlQueryBuilder.roles()
        • SqlQueryBuilder.sexes()
        • SqlQueryBuilder.statuses()
        • SqlQueryBuilder.summary_base()
        • SqlQueryBuilder.summary_query()
        • SqlQueryBuilder.summary_variants()
        • SqlQueryBuilder.ultra_rare()
      • TagsQuery
        • TagsQuery.deselected_family_tags
        • TagsQuery.model_computed_fields
        • TagsQuery.model_config
        • TagsQuery.model_fields
        • TagsQuery.selected_family_tags
        • TagsQuery.tags_or_mode
      • ZygosityQuery
        • ZygosityQuery.children_zygosity
        • ZygosityQuery.model_computed_fields
        • ZygosityQuery.model_config
        • ZygosityQuery.model_fields
        • ZygosityQuery.parents_zygosity
        • ZygosityQuery.sex_zygosity
        • ZygosityQuery.status_zygosity
    • dae.query_variants.sql.schema2.summary_builder module
      • SummaryQueryBuilder
    • Module contents
• Genotype Storage
  • dae.genotype_storage package
    • Submodules
    • dae.genotype_storage.genotype_storage module
      • GenotypeStorage
        • GenotypeStorage.build_backend()
        • GenotypeStorage.create_runner()
        • GenotypeStorage.create_summary_runner()
        • GenotypeStorage.get_storage_types()
        • GenotypeStorage.is_read_only()
        • GenotypeStorage.loaded_variants
        • GenotypeStorage.read_only
        • GenotypeStorage.shutdown()
        • GenotypeStorage.start()
        • GenotypeStorage.study_configs
        • GenotypeStorage.validate_and_normalize_config()
    • dae.genotype_storage.genotype_storage_genomic_context_cli module
      • Key Constants
      • See Also
      • CLIGenotypeStorageContextProvider
        • CLIGenotypeStorageContextProvider.add_argparser_arguments()
        • CLIGenotypeStorageContextProvider.init()
      • get_context_genotype_storages()
    • dae.genotype_storage.genotype_storage_registry module
      • GenotypeStorageRegistry
        • GenotypeStorageRegistry.find_storage()
        • GenotypeStorageRegistry.get_all_genotype_storage_ids()
        • GenotypeStorageRegistry.get_all_genotype_storages()
        • GenotypeStorageRegistry.get_default_genotype_storage()
        • GenotypeStorageRegistry.get_genotype_storage()
        • GenotypeStorageRegistry.query_summary_variants()
        • GenotypeStorageRegistry.query_variants()
        • GenotypeStorageRegistry.register_default_storage()
        • GenotypeStorageRegistry.register_genotype_storage()
        • GenotypeStorageRegistry.register_storage_config()
        • GenotypeStorageRegistry.register_storages_configs()
        • GenotypeStorageRegistry.shutdown()
      • get_genotype_storage_factory()
      • get_genotype_storage_types()
      • register_genotype_storage_factory()
    • Module contents
• In-Memory Genotype Storage
  • dae.inmemory_storage package
    • Submodules
    • dae.inmemory_storage.annotation_serialization module
      • build_annotation_filename()
      • variants_loader_annotate_and_save()
      • variants_loader_load_annotation()
    • dae.inmemory_storage.inmemory_genotype_storage module
      • InmemoryGenotypeStorage
        • InmemoryGenotypeStorage.VALIDATION_SCHEMA
        • InmemoryGenotypeStorage.get_data_dir()
        • InmemoryGenotypeStorage.get_storage_types()
        • InmemoryGenotypeStorage.shutdown()
        • InmemoryGenotypeStorage.start()
        • InmemoryGenotypeStorage.validate_and_normalize_config()
    • dae.inmemory_storage.inmemory_import_storage module
      • InmemoryImportStorage
        • InmemoryImportStorage.generate_import_task_graph()
    • dae.inmemory_storage.raw_variants module
      • RawFamilyVariants
        • RawFamilyVariants.build_family_variants_query_runner()
        • RawFamilyVariants.build_summary_variants_query_runner()
        • RawFamilyVariants.family_variant_filter_function()
        • RawFamilyVariants.family_variants_iterator()
        • RawFamilyVariants.filter_allele()
        • RawFamilyVariants.filter_family_variant()
        • RawFamilyVariants.filter_gene_effects()
        • RawFamilyVariants.filter_real_attr()
        • RawFamilyVariants.filter_regions()
        • RawFamilyVariants.filter_summary_allele()
        • RawFamilyVariants.filter_summary_variant()
        • RawFamilyVariants.full_variants_iterator()
        • RawFamilyVariants.summary_variant_filter_function()
        • RawFamilyVariants.summary_variants_iterator()
      • RawMemoryVariants
        • RawMemoryVariants.full_variants
        • RawMemoryVariants.full_variants_iterator()
        • RawMemoryVariants.has_affected_status_queries()
      • RawVariantsQueryRunner
        • RawVariantsQueryRunner.run()
    • Module contents
• Configuration
  • Classes and Functions
    • dae.configuration package
      • Subpackages
        • dae.configuration.schemas package
      • Submodules
      • dae.configuration.gpf_config_parser module
        • DefaultBox
        • FrozenBox
        • GPFConfigParser
        • GPFConfigValidator
      • dae.configuration.study_config_builder module
        • ConfigDumper
        • StudyConfigBuilder
        • TOMLDict
        • TOMLList
      • dae.configuration.utils module
        • validate_existing_path()
        • validate_path()
      • Module contents
• Genotype Data
  • Classes and Functions
    • dae.studies package
      • Submodules
      • dae.studies.study module
        • CommonStudyMixin
        • GenotypeData
        • GenotypeDataGroup
        • GenotypeDataStudy
        • PSCQueryAdjustments
      • dae.studies.variants_db module
        • VariantsDb
      • Module contents
• Phenotype Data
  • Pheno DB access
  • Example usage of PhenoDB
  • Classes and Functions
    • dae.pheno package
      • Subpackages
        • dae.pheno.prepare package
        • dae.pheno.utils package
      • Submodules
      • dae.pheno.browser module
        • PhenoBrowser
      • dae.pheno.build_pheno_browser module
        • build_pheno_browser()
        • main()
        • pheno_cli_parser()
      • dae.pheno.common module
        • DataDictionaryConfig
        • DestinationConfig
        • GPFInstanceConfig
        • ImportManifest
        • InferenceConfig
        • InstrumentConfig
        • InstrumentDescriptionsConfig
        • InstrumentDictionaryConfig
        • MeasureDescriptionsConfig
        • MeasureHistogramConfigs
        • MeasureType
        • PhenoImportConfig
        • RankRange
        • RegressionMeasure
        • StudyConfig
      • dae.pheno.db module
        • PhenoDb
        • generate_instrument_table_name()
        • safe_db_name()
      • dae.pheno.graphs module
        • GraphColumn
        • column_counts()
        • draw_categorical_violin_distribution()
        • draw_linregres()
        • draw_measure_violinplot()
        • draw_ordinal_violin_distribution()
        • gender_palette()
        • gender_palette_light()
        • get_columns_to_draw()
        • male_female_legend()
        • role_labels()
        • set_figure_size()
      • dae.pheno.import_tools module
        • main()
        • pheno_cli_parser()
      • dae.pheno.pheno_data module
        • Instrument
        • Measure
        • PhenotypeData
        • PhenotypeGroup
        • PhenotypeStudy
        • get_pheno_browser_images_dir()
        • get_pheno_db_dir()
      • dae.pheno.pheno_import module
        • ImportInstrument
        • MeasureReport
        • add_pheno_common_inference()
        • collect_instruments()
        • create_import_tasks()
        • create_tables()
        • determine_destination()
        • generate_phenotype_data_config()
        • get_gpf_instance()
        • get_output_parquet_files_dir()
        • handle_measure_inference_tasks()
        • import_pheno_data()
        • infer_measures()
        • load_histogram_configs()
        • load_inference_configs()
        • load_instrument_description_file()
        • load_instrument_descriptions()
        • load_measure_description_file()
        • load_measure_descriptions()
        • main()
        • merge_histogram_configs()
        • merge_inference_configs()
        • open_file()
        • pheno_cli_parser()
        • read_and_classify_measure()
        • read_instrument_measure_names()
        • read_pedigree()
        • transform_cli_args()
        • write_descriptions()
        • write_reports_to_parquet()
        • write_results()
        • write_to_parquet()
      • dae.pheno.prepare_data module
        • PreparePhenoBrowserBase
      • dae.pheno.registry module
        • PhenoRegistry
      • dae.pheno.storage module
        • PhenotypeStorage
        • PhenotypeStorageRegistry
      • dae.pheno.update_pheno_descriptions module
        • main()
        • pheno_cli_parser()
        • save_descriptions()
      • Module contents
• Phenotype tool
  • Example usage of PhenoTool class
  • Example usage of PhenoTool class with pheno filters
  • Example with vineland_ii
  • Classes and Functions
    • dae.pheno_tool package
      • Submodules
      • dae.pheno_tool.pheno_tool_adapter module
        • PhenoToolAdapter
        • PhenoToolAdapterBase
      • dae.pheno_tool.tool module
        • PhenoResult
        • PhenoTool
        • PhenoToolHelper
      • Module contents
• Enrichment Tool
  • Example usage of EnrichmentTool class
  • Classes and Functions
    • dae.pheno_tool package
      • Submodules
      • dae.pheno_tool.pheno_tool_adapter module
        • PhenoToolAdapter
        • PhenoToolAdapterBase
      • dae.pheno_tool.tool module
        • PhenoResult
        • PhenoTool
        • PhenoToolHelper
      • Module contents
• dae
  • dae package
    • Subpackages
      • dae.annotation package
        • Submodules
        • dae.annotation.annotatable module
        • dae.annotation.annotate_columns module
        • dae.annotation.annotate_doc module
        • dae.annotation.annotate_utils module
        • dae.annotation.annotate_vcf module
        • dae.annotation.annotation_config module
        • dae.annotation.annotation_factory module
        • dae.annotation.annotation_genomic_context_cli module
        • dae.annotation.annotation_pipeline module
        • dae.annotation.annotator_base module
        • dae.annotation.chromosome_annotator module
        • dae.annotation.cnv_collection_annotator module
        • dae.annotation.debug_annotator module
        • dae.annotation.docker_annotator module
        • dae.annotation.effect_annotator module
        • dae.annotation.gene_score_annotator module
        • dae.annotation.gene_set_annotator module
        • dae.annotation.liftover_annotator module
        • dae.annotation.normalize_allele_annotator module
        • dae.annotation.processing_pipeline module
        • dae.annotation.record_to_annotatable module
        • dae.annotation.score_annotator module
        • dae.annotation.simple_effect_annotator module
        • dae.annotation.utils module
        • Module contents
      • dae.common_reports package
        • Submodules
        • dae.common_reports.common_report module
        • dae.common_reports.denovo_report module
        • dae.common_reports.family_counter module
        • dae.common_reports.family_report module
        • dae.common_reports.people_counter module
        • Module contents
      • dae.configuration package
        • Subpackages
        • Submodules
        • dae.configuration.gpf_config_parser module
        • dae.configuration.study_config_builder module
        • dae.configuration.utils module
        • Module contents
      • dae.dask package
        • Submodules
        • dae.dask.config module
        • dae.dask.named_cluster module
        • Module contents
      • dae.duckdb_storage package
        • Submodules
        • dae.duckdb_storage.duckdb2_variants module
        • dae.duckdb_storage.duckdb_connection_factory module
        • dae.duckdb_storage.duckdb_genotype_storage module
        • dae.duckdb_storage.duckdb_import_storage module
        • dae.duckdb_storage.duckdb_legacy_genotype_storage module
        • dae.duckdb_storage.duckdb_storage_config module
        • dae.duckdb_storage.duckdb_storage_helpers module
        • dae.duckdb_storage.duckdb_variants module
        • Module contents
      • dae.effect_annotation package
        • Subpackages
        • Submodules
        • dae.effect_annotation.annotation_effects module
        • dae.effect_annotation.annotation_request module
        • dae.effect_annotation.annotator module
        • dae.effect_annotation.cli module
        • dae.effect_annotation.effect module
        • dae.effect_annotation.gene_codes module
        • dae.effect_annotation.variant module
        • Module contents
      • dae.enrichment_tool package
        • Subpackages
        • Submodules
        • dae.enrichment_tool.base_enrichment_background module
        • dae.enrichment_tool.build_coding_length_enrichment_background module
        • dae.enrichment_tool.build_ur_synonymous_enrichment_background module
        • dae.enrichment_tool.enrichment_cache_builder module
        • dae.enrichment_tool.enrichment_utils module
        • dae.enrichment_tool.event_counters module
        • dae.enrichment_tool.gene_weights_background module
        • dae.enrichment_tool.genotype_helper module
        • dae.enrichment_tool.samocha_background module
        • Module contents
      • dae.gene_profile package
        • Submodules
        • dae.gene_profile.convert_gene_profile_to_duckdb module
        • dae.gene_profile.db module
        • dae.gene_profile.exporter module
        • dae.gene_profile.generate_gene_profile module
        • dae.gene_profile.statistic module
        • Module contents
      • dae.gene_scores package
        • Subpackages
        • Submodules
        • dae.gene_scores.gene_scores module
        • Module contents
      • dae.gene_sets package
        • Subpackages
        • Submodules
        • dae.gene_sets.denovo_gene_set_collection module
        • dae.gene_sets.denovo_gene_set_helpers module
        • dae.gene_sets.denovo_gene_sets_config module
        • dae.gene_sets.denovo_gene_sets_db module
        • dae.gene_sets.gene_sets_db module
        • dae.gene_sets.gene_term module
        • Module contents
      • dae.genomic_resources package
        • Subpackages
        • Submodules
        • dae.genomic_resources.aggregators module
        • dae.genomic_resources.cached_repository module
        • dae.genomic_resources.cli module
        • dae.genomic_resources.draw_score_histograms module
        • dae.genomic_resources.fsspec_protocol module
        • dae.genomic_resources.genomic_context module
        • dae.genomic_resources.genomic_context_base module
        • dae.genomic_resources.genomic_context_cli module
        • dae.genomic_resources.genomic_scores module
        • dae.genomic_resources.group_repository module
        • dae.genomic_resources.histogram module
        • dae.genomic_resources.liftover_chain module
        • dae.genomic_resources.reference_genome module
        • dae.genomic_resources.repository module
        • dae.genomic_resources.repository_factory module
        • dae.genomic_resources.resource_implementation module
        • dae.genomic_resources.testing module
        • dae.genomic_resources.variant_utils module
        • Module contents
      • dae.genomic_scores package
        • Submodules
        • dae.genomic_scores.scores module
        • Module contents
      • dae.genotype_storage package
        • Submodules
        • dae.genotype_storage.genotype_storage module
        • dae.genotype_storage.genotype_storage_genomic_context_cli module
        • dae.genotype_storage.genotype_storage_registry module
        • Module contents
      • dae.gpf_instance package
        • Subpackages
        • Submodules
        • dae.gpf_instance.gpf_instance module
        • Module contents
      • dae.gpf_instance_plugin package
        • Submodules
        • dae.gpf_instance_plugin.gpf_instance_context_plugin module
        • Module contents
      • dae.import_tools package
        • Submodules
        • dae.import_tools.cli module
        • dae.import_tools.import_config module
        • dae.import_tools.import_tools module
        • Module contents
      • dae.inmemory_storage package
        • Submodules
        • dae.inmemory_storage.annotation_serialization module
        • dae.inmemory_storage.inmemory_genotype_storage module
        • dae.inmemory_storage.inmemory_import_storage module
        • dae.inmemory_storage.raw_variants module
        • Module contents
      • dae.parquet package
        • Subpackages
        • Submodules
        • dae.parquet.helpers module
        • dae.parquet.parquet_writer module
        • dae.parquet.partition_descriptor module
        • Module contents
      • dae.parquet_storage package
        • Submodules
        • dae.parquet_storage.storage module
        • Module contents
      • dae.pedigrees package
        • Submodules
        • dae.pedigrees.drawing module
        • dae.pedigrees.families_data module
        • dae.pedigrees.family module
        • dae.pedigrees.family_role_builder module
        • dae.pedigrees.family_tag_builder module
        • dae.pedigrees.layout module
        • dae.pedigrees.loader module
        • dae.pedigrees.pedigrees module
        • dae.pedigrees.testing module
        • Module contents
      • dae.person_filters package
        • Submodules
        • dae.person_filters.person_filters module
        • Module contents
      • dae.person_sets package
        • Submodules
        • dae.person_sets.person_sets module
        • Module contents
      • dae.pheno package
        • Subpackages
        • Submodules
        • dae.pheno.browser module
        • dae.pheno.build_pheno_browser module
        • dae.pheno.common module
        • dae.pheno.db module
        • dae.pheno.graphs module
        • dae.pheno.import_tools module
        • dae.pheno.pheno_data module
        • dae.pheno.pheno_import module
        • dae.pheno.prepare_data module
        • dae.pheno.registry module
        • dae.pheno.storage module
        • dae.pheno.update_pheno_descriptions module
        • Module contents
      • dae.pheno_tool package
        • Submodules
        • dae.pheno_tool.pheno_tool_adapter module
        • dae.pheno_tool.tool module
        • Module contents
      • dae.query_variants package
        • Subpackages
        • Submodules
        • dae.query_variants.attribute_queries module
        • dae.query_variants.base_query_variants module
        • dae.query_variants.query_runners module
        • Module contents
      • dae.schema2_storage package
        • Submodules
        • dae.schema2_storage.schema2_import_storage module
        • dae.schema2_storage.schema2_layout module
        • Module contents
      • dae.studies package
        • Submodules
        • dae.studies.study module
        • dae.studies.variants_db module
        • Module contents
      • dae.task_graph package
        • Submodules
        • dae.task_graph.cache module
        • dae.task_graph.cli_tools module
        • dae.task_graph.demo_graphs_cli module
        • dae.task_graph.executor module
        • dae.task_graph.graph module
        • dae.task_graph.logging module
        • Module contents
      • dae.testing package
        • Submodules
        • dae.testing.acgt_import module
        • dae.testing.alla_import module
        • dae.testing.foobar_import module
        • dae.testing.import_helpers module
        • dae.testing.setup_helpers module
        • dae.testing.t4c8_import module
        • Module contents
      • dae.tools package
        • Submodules
        • dae.tools.cnv_liftover module
        • dae.tools.dae2vcf module
        • dae.tools.dae_liftover module
        • dae.tools.dataset_helpers module
        • dae.tools.denovo2vcf module
        • dae.tools.denovo_liftover module
        • dae.tools.draw_pedigree module
        • dae.tools.generate_common_report module
        • dae.tools.generate_denovo_gene_sets module
        • dae.tools.gpf_convert_study_config module
        • dae.tools.gpf_validation_runner module
        • dae.tools.grr_cache_repo module
        • dae.tools.ped2ped module
        • dae.tools.reannotate_instance module
        • dae.tools.simple_study_import module
        • dae.tools.to_gpf_gene_models_format module
        • dae.tools.vcf2tsv module
        • dae.tools.vcf_liftover module
        • Module contents
      • dae.utils package
        • Submodules
        • dae.utils.cnv_utils module
        • dae.utils.dae_utils module
        • dae.utils.debug_closing module
        • dae.utils.dict_utils module
        • dae.utils.fs_utils module
        • dae.utils.helpers module
        • dae.utils.processing_pipeline module
        • dae.utils.regions module
        • dae.utils.sql_utils module
        • dae.utils.stats_collection module
        • dae.utils.variant_utils module
        • dae.utils.verbosity_configuration module
        • Module contents
      • dae.variants package
        • Submodules
        • dae.variants.attributes module
        • dae.variants.core module
        • dae.variants.family_variant module
        • dae.variants.variant module
        • Module contents
      • dae.variants_loaders package
        • Subpackages
        • Module contents
    • Module contents