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_schema2_parquet module
      • dae.annotation.annotate_utils module
      • dae.annotation.annotate_vcf module
      • dae.annotation.annotation_config module
      • dae.annotation.annotation_factory module
      • dae.annotation.annotation_pipeline module
      • dae.annotation.annotator_base module
      • dae.annotation.cnv_collection_annotator module
      • dae.annotation.debug_annotator module
      • dae.annotation.docker_annotator module
      • dae.annotation.effect_annotator module
      • dae.annotation.format_handlers module
      • dae.annotation.gene_score_annotator module
      • dae.annotation.gene_set_annotator module
      • dae.annotation.genomic_context module
      • dae.annotation.liftover_annotator module
      • dae.annotation.normalize_allele_annotator module
      • dae.annotation.parquet module
      • dae.annotation.reannotate_instance module
      • dae.annotation.record_to_annotatable module
      • dae.annotation.score_annotator module
      • dae.annotation.simple_effect_annotator module
      • 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_builder module
      • dae.enrichment_tool.enrichment_cache_builder module
      • dae.enrichment_tool.enrichment_helper module
      • dae.enrichment_tool.enrichment_serializer module
      • dae.enrichment_tool.event_counters module
      • dae.enrichment_tool.gene_weights_background module
      • dae.enrichment_tool.genotype_helper module
      • dae.enrichment_tool.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_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_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.dataset_helpers module
      • 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.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.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.filehash module
      • dae.utils.fixtures module
      • dae.utils.fs_utils module
      • dae.utils.helpers module
      • dae.utils.progress module
      • dae.utils.regions module
      • dae.utils.sql_utils module
      • dae.utils.stats_collection module
      • dae.utils.variant_utils module
      • dae.utils.verbosity_configuration module
      • 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