Index

A

abspath() (in module gain.utils.fs_utils) AbstractLiftoverAnnotator (class in gain.annotation.liftover_annotator) acgt_genome() (in module gain.testing.acgt_import) acgt_grr() (in module gain.testing.acgt_import) 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) add_arguments() (gain.task_graph.cli_tools.TaskGraphCli static method) add_common_annotation_arguments() (in module gain.annotation.annotate_utils) add_count() (gain.genomic_resources.statistics.min_max.MinMaxValue method) add_input_files_to_task_graph() (in module gain.annotation.annotate_utils) add_record_to_annotable_arguments() (in module gain.annotation.record_to_annotatable) add_score_aggregator_documentation() (gain.annotation.score_annotator.GenomicScoreAnnotatorBase method) add_task() (gain.task_graph.graph.TaskGraph method) add_tasks() (gain.task_graph.graph.TaskGraph 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) added (gain.annotation.annotation_pipeline.ReannotationPlan attribute) adjust_verbosity() (gain.utils.verbosity_configuration.VerbosityConfiguration static method) adjust_zero_based_line() (in module gain.genomic_resources.genomic_position_table.table) aggregate() (gain.genomic_resources.aggregators.Aggregator method) Aggregator (class in gain.genomic_resources.aggregators) aggregator (gain.annotation.annotation_config.Attribute attribute) (gain.annotation.annotation_config.AttributeConfig attribute) aggregator_type (gain.genomic_resources.aggregators.AggregatorDefinition attribute) AggregatorDefinition (class in gain.genomic_resources.aggregators) ALL_ATTRIBUTE_IDXS (gain.effect_annotation.cli.AnnotationAttributes attribute) 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) alla_genome() (in module gain.testing.alla_import) alla_grr() (in module gain.testing.alla_import) allele_aggregator (gain.genomic_resources.genomic_scores.AlleleScoreAggr attribute) (gain.genomic_resources.genomic_scores.AlleleScoreQuery attribute) (gain.genomic_resources.genomic_scores.ScoreDef attribute) ALLELE_FILTER_GRAMMAR (gain.annotation.score_annotator.AlleleScoreAnnotator attribute) allele_index (gain.genomic_resources.genomic_position_table.line.VCFLine attribute) (gain.genomic_resources.genomic_position_table.VCFLine attribute) AlleleEffects (class in gain.effect_annotation.effect) ALLELES (gain.genomic_resources.genomic_scores.AlleleScore.Mode attribute) 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) allow_only_whole_values_y (gain.genomic_resources.histogram.CategoricalHistogramConfig attribute) alt (gain.annotation.annotatable.VCFAllele property) (gain.genomic_resources.genomic_position_table.BigWigLine attribute) (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) (gain.genomic_resources.genomic_position_table.line.VCFLine attribute)

ALT (gain.genomic_resources.genomic_position_table.table.GenomicPositionTable attribute) alt (gain.genomic_resources.genomic_position_table.VCFLine attribute) (gain.genomic_resources.genomic_scores.ScoreLine property) alternative (gain.annotation.annotatable.VCFAllele property) 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.gene_score_annotator.GeneScoreAnnotator 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_tabular() (in module gain.annotation.annotate_tabular) 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) 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) 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) (gain.annotation.annotation_pipeline.PlanEntry 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) (gain.annotation.annotation_pipeline.ReannotationPipeline attribute) append() (gain.genomic_resources.genomic_position_table.line.LineBuffer method) (gain.genomic_resources.genomic_position_table.LineBuffer method) args (gain.task_graph.graph.TaskDesc attribute) as_dict() (gain.annotation.annotation_config.AttributeConfig method) (gain.annotation.annotation_config.ParamsUsageMonitor method) (gain.annotation.annotation_pipeline.AttributeSpec method) (gain.genomic_resources.aggregators.AggregatorDefinition method) as_directed_graph() (gain.task_graph.graph.TaskGraph method) Attribute (class in gain.annotation.annotation_config) attribute_type (gain.annotation.annotation_pipeline.AttributeSpec attribute) AttributeConfig (class in gain.annotation.annotation_config) attributes (gain.annotation.annotation_config.AnnotatorInfo attribute) (gain.annotation.annotation_pipeline.Annotator property) (gain.annotation.annotation_pipeline.AnnotatorDecorator property) (gain.annotation.annotator_base.AnnotatorBase property) (gain.genomic_resources.genomic_scores.CNV attribute) AttributeSpec (class in gain.annotation.annotation_pipeline)

B

BASE_DOC_URL (gain.annotation.annotation_pipeline.Annotator attribute) BaseAnnotationRequest (class in gain.effect_annotation.annotation_request) BaseGeneSetCollection (class in gain.gene_sets.gene_set) BaseResourceSchema (class in gain.gene_sets.gene_set) 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) (gain.annotation.gene_score_annotator.GeneScoreAnnotator method) 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) 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) BoolAggregator (class in gain.genomic_resources.aggregators) BUFFER_MAXSIZE (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) (gain.genomic_resources.genomic_position_table.table_tabix.TabixGenomicPositionTable attribute) build() (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) (gain.genomic_resources.aggregators.Aggregator static method) build_allele_score_annotator() (in module gain.annotation.score_annotator) build_annotatable_from_dict() (in module gain.annotation.record_to_annotatable) build_annotation_pipeline() (in module gain.annotation.annotation_factory) build_annotator() (in module gain.annotation.debug_annotator) build_attribute_help() (gain.annotation.score_annotator.GenomicScoreAnnotatorBase method) build_chrom_mapping() (in module gain.genomic_resources.utils) build_chrom_mapping_annotator() (in module gain.annotation.chrom_mapping_annotator) build_cli_genomic_context() (in module gain.annotation.annotate_utils) build_cnv_collection_annotator() (in module gain.annotation.cnv_collection_annotator) 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_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_fsspec_protocol() (in module gain.genomic_resources.fsspec_protocol) 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_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_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_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_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_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_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_np_score_annotator() (in module gain.annotation.score_annotator) build_output_path() (in module gain.annotation.annotate_utils) build_pipeline_annotator() (in module gain.annotation.annotation_factory) build_position_score_annotator() (in module gain.annotation.score_annotator) 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_resource_file_state() (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) build_resource_implementation() (in module gain.genomic_resources.repository_factory) 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_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_scores_agg() (gain.genomic_resources.genomic_scores.AlleleScore method) build_simple_effect_annotator() (in module gain.annotation.simple_effect_annotator) build_statistics() (gain.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeStatistics static method)

C

cache() (gain.task_graph.cache.FileTaskCache method) (gain.task_graph.cache.NoTaskCache method) (gain.task_graph.cache.TaskCache method) 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_bin_begin() (in module gain.utils.regions) calc_bin_end() (in module gain.utils.regions) calc_bin_index() (in module gain.utils.regions) 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_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) 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) call_region() (gain.annotation.simple_effect_annotator.SimpleEffectAnnotator method) camelize_string() (in module gain.utils.helpers) 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) chain_tasks() (in module gain.task_graph.graph) 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_attribute_parameters() (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_resource_locality() (in module gain.annotation.annotate_utils) check_stop_codon() (gain.effect_annotation.effect_checkers.frame_shift.FrameShiftEffectChecker method) (gain.effect_annotation.effect_checkers.utr.UTREffectChecker method) check_update_manifest() (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) ChecksumMismatchError 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.BigWigLine attribute) (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) (gain.genomic_resources.genomic_position_table.line.VCFLine 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_position_table.VCFLine attribute) (gain.genomic_resources.genomic_scores.CNV attribute) (gain.genomic_resources.genomic_scores.ScoreLine property) chrom_count (gain.genomic_resources.implementations.reference_genome_impl.GenomeStatistic property) chrom_prefix (gain.genomic_resources.reference_genome.ReferenceGenome property) ChromMappingAnnotator (class in gain.annotation.chrom_mapping_annotator) chromosome (gain.annotation.annotatable.Annotatable property) chromosomes (gain.genomic_resources.reference_genome.ReferenceGenome property) ChromosomeStatistic (class in gain.genomic_resources.implementations.reference_genome_impl) CHUNK_SIZE (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol attribute) classify_cached_resource_file() (gain.genomic_resources.cached_repository.CachingProtocol method) classify_resource_file() (gain.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) clear() (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) cli() (in module gain.annotation.annotate_columns) (in module gain.annotation.annotate_doc) (in module gain.annotation.annotate_tabular) (in module gain.annotation.annotate_vcf) (in module gain.annotation.prepare_tabular) cli_browse() (in module gain.genomic_resources.cli) cli_cache_repo() (in module gain.genomic_resources.cli_cache_repo) cli_columns() (in module gain.effect_annotation.cli) 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) CLIGenomicContextProvider (class in gain.genomic_resources.genomic_context_cli) 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)

closing (class in gain.utils.debug_closing) CNV (class in gain.genomic_resources.genomic_scores) CNV_FILTER_GRAMMAR (gain.annotation.cnv_collection_annotator.CnvCollectionAnnotator attribute) 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) coalesce() (in module gain.utils.regions) cod2aa() (gain.effect_annotation.annotation_request.BaseAnnotationRequest method) (gain.effect_annotation.annotation_request.NegativeStrandAnnotationRequest 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) 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_dvc_entries() (in module gain.genomic_resources.cli) 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_index_info() (gain.gene_scores.implementations.gene_scores_impl.GeneScoreImplementation method) (gain.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation method) (gain.genomic_resources.resource_implementation.GenomicResourceImplementation method) collect_resource_entries() (gain.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) column (gain.annotation.annotation_config.ErrorMark attribute) column_name (gain.gene_scores.gene_scores.ScoreDef attribute) (gain.gene_scores.gene_scores.ScoreDesc attribute) complement() (gain.effect_annotation.annotation_request.NegativeStrandAnnotationRequest static method) (in module gain.utils.variant_utils) COMPLEX (gain.annotation.annotatable.Annotatable.Type attribute) compression_suffix() (in module gain.utils.fs_utils) compute_md5_sum() (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) computed (gain.annotation.annotation_pipeline.ReannotationPlan attribute) COMPUTED (gain.task_graph.cache.CacheRecordType attribute) ConcatAggregator (class in gain.genomic_resources.aggregators) config (gain.genomic_resources.genomic_scores.GenomicScore attribute) (gain.genomic_resources.resource_implementation.GenomicResourceImplementation attribute) configure_argument_parser() (in module gain.annotation.annotate_doc) configure_task_logging() (in module gain.task_graph.logging) connected_component() (in module gain.utils.regions) 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) 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) convert_coordinate() (gain.genomic_resources.liftover_chain.LiftoverChain method) convert_size() (in module gain.utils.helpers) convert_to_tab_separated() (in module gain.genomic_resources.testing) copied (gain.annotation.annotation_pipeline.ReannotationPlan attribute) copy() (in module gain.utils.fs_utils) 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) CountAggregator (class in gain.genomic_resources.aggregators) counter (gain.genomic_resources.aggregators.CounterAggregator attribute) CounterAggregator (class in gain.genomic_resources.aggregators) create() (gain.task_graph.cache.TaskCache static method) create_annotation_request() (gain.effect_annotation.annotator.AnnotationRequestFactory static method) 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_executor() (gain.task_graph.cli_tools.TaskGraphCli static method) create_intronic_effect() (gain.effect_annotation.effect.EffectFactory class method) create_intronic_non_coding_effect() (gain.effect_annotation.effect.EffectFactory class method) create_negative_strand_effect() (gain.effect_annotation.effect_checkers.promoter.PromoterEffectChecker method) create_positive_strand_effect() (gain.effect_annotation.effect_checkers.promoter.PromoterEffectChecker method) create_regions_from_genes() (in module gain.genomic_resources.gene_models.gene_models) 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) create_task() (gain.task_graph.graph.TaskGraph method) create_utr_effect() (gain.effect_annotation.effect_checkers.utr.UTREffectChecker method) cshl2cnv_variant() (in module gain.utils.cnv_utils) cshl2vcf_variant() (in module gain.utils.dae_utils) CSHLAlleleRecordToAnnotatable (class in gain.annotation.record_to_annotatable)

D

dae2vcf_variant() (in module gain.utils.dae_utils) DaeAlleleRecordToAnnotatable (class in gain.annotation.record_to_annotatable) DaskExecutor (class in gain.task_graph.dask_executor) dd() (in module gain.gene_sets.gene_term) decorate() (gain.annotation.annotation_pipeline.InputAnnotableAnnotatorDecorator static method) (gain.annotation.annotation_pipeline.ValueTransformAnnotatorDecorator static method) DEFAULT_AGGREGATOR_TYPE (gain.annotation.gene_set_annotator.GeneSetAnnotator 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_parameter (gain.genomic_resources.aggregators.Aggregator attribute) (gain.genomic_resources.aggregators.JoinAggregator attribute) DefaultRepositoryContextProvider (class in gain.genomic_resources.genomic_context) definition (gain.genomic_resources.repository.GenomicResourceRepo property) 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) deleted (gain.annotation.annotation_pipeline.ReannotationPlan attribute) deps (gain.task_graph.graph.TaskDesc attribute) deque (gain.genomic_resources.genomic_position_table.line.LineBuffer attribute) (gain.genomic_resources.genomic_position_table.LineBuffer attribute) desc (gain.gene_sets.gene_set.GeneSet attribute) (gain.genomic_resources.genomic_scores.ScoreDef attribute) description (gain.annotation.annotation_config.AnnotationPreamble attribute) (gain.annotation.annotation_config.Attribute property) (gain.annotation.annotation_config.RawPreamble attribute) (gain.annotation.annotation_pipeline.AttributeSpec 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)

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) difference() (in module gain.utils.regions) directory (gain.gene_sets.gene_set.GeneSetResourceSchema 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) DockerAnnotator (class in gain.annotation.docker_annotator) documentation (gain.annotation.annotation_config.AnnotatorInfo attribute) (gain.annotation.annotation_config.Attribute property) download_cached_resource_file() (gain.genomic_resources.cached_repository.CachingProtocol method)

E

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() (gain.annotation.simple_effect_annotator.SimpleEffectAnnotator 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) EffectChecker (class in gain.effect_annotation.effect_checkers.effect_checker) EffectFactory (class in gain.effect_annotation.effect) EffectGene (class in gain.effect_annotation.effect) effects_description() (gain.effect_annotation.effect.AnnotationEffect class method) EffectTranscript (class in gain.effect_annotation.effect) EffectTypesMixin (class in gain.effect_annotation.effect) emit_annotation_plan() (in module gain.annotation.annotate_utils) empty() (gain.task_graph.graph.TaskGraph method) end (gain.utils.regions.BedRegion property) (gain.utils.regions.Region property)

end_position (gain.annotation.annotatable.Annotatable property) enforce_type (gain.gene_sets.gene_set.CategoricalHistogramSchema attribute) (gain.genomic_resources.histogram.CategoricalHistogramConfig attribute) ensure_log_dir() (in module gain.task_graph.logging) entries (gain.genomic_resources.repository.Manifest attribute) 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) error_mark (gain.annotation.annotation_config.AnnotationConfigurationError attribute) ErrorMark (class in gain.annotation.annotation_config) execute() (gain.task_graph.base_executor.TaskGraphExecutorBase method) (gain.task_graph.executor.TaskGraphExecutor method) exists() (in module gain.utils.fs_utils) Exon (class in gain.genomic_resources.gene_models) (class in gain.genomic_resources.gene_models.transcript_models) expand_effect_types() (in module gain.effect_annotation.effect) extract_tasks() (gain.task_graph.graph.TaskGraph method)

F

fchrom (gain.genomic_resources.genomic_position_table.BigWigLine attribute) (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) (gain.genomic_resources.genomic_position_table.line.VCFLine attribute) (gain.genomic_resources.genomic_position_table.VCFLine attribute) 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) fetch_allele_line() (gain.genomic_resources.genomic_scores.AlleleScore method) fetch_cnvs() (gain.genomic_resources.genomic_scores.CnvCollection method) fetch_lines() (gain.genomic_resources.genomic_scores.GenomicScore 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) 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) FileCacheVerdict (class in gain.genomic_resources.fsspec_protocol) filename (gain.gene_sets.gene_set.GeneSetResourceSchema attribute) (gain.genomic_resources.repository.ResourceFileState attribute) 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) FileTaskCache (class in gain.task_graph.cache) 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) filter_gene_effects() (gain.effect_annotation.effect.AnnotationEffect class method) filter_genes() (gain.effect_annotation.effect.AnnotationEffect class method) (gain.gene_sets.gene_term.GeneTerms method) find_annotator_gene_models() (in module gain.annotation.utils) find_annotator_reference_genome() (in module gain.annotation.utils) 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_index() (gain.genomic_resources.genomic_position_table.line.LineBuffer method) (gain.genomic_resources.genomic_position_table.LineBuffer method) find_nonlocal_resources() (in module gain.annotation.annotate_utils) 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_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) foobar_genes() (in module gain.testing.foobar_import) foobar_genome() (in module gain.testing.foobar_import) format_annotation_plan() (in module gain.annotation.annotation_pipeline) FORMAT_DEF (gain.genomic_resources.genomic_position_table.table_inmemory.InmemoryGenomicPositionTable attribute) format_plan() (gain.annotation.annotation_pipeline.ReannotationPipeline method) 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) from_dict() (gain.genomic_resources.aggregators.AggregatorDefinition class method) (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) from_effect_transcripts() (gain.effect_annotation.effect.EffectTranscript class method) from_effects() (gain.effect_annotation.effect.AlleleEffects class method) from_file_content() (gain.genomic_resources.repository.Manifest static method) from_gene_effects() (gain.effect_annotation.effect.EffectGene class method) from_manifest_entries() (gain.genomic_resources.repository.Manifest static method) from_name() (gain.genomic_resources.genomic_scores.AlleleScore.Mode 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) 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) (gain.genomic_resources.aggregators.AggregatorDefinition class method) from_tuple() (gain.effect_annotation.effect.EffectGene class method) (gain.effect_annotation.effect.EffectTranscript class method) FsspecHandler (class in gain.task_graph.logging) FsspecReadOnlyProtocol (class in gain.genomic_resources.fsspec_protocol) FsspecReadWriteProtocol (class in gain.genomic_resources.fsspec_protocol) func (gain.task_graph.graph.TaskDesc attribute)

G

g2t (gain.gene_sets.gene_term.GeneTerms attribute) gain module gain.annotation module gain.annotation.annotatable module gain.annotation.annotate_columns module gain.annotation.annotate_doc module gain.annotation.annotate_tabular 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.prepare_tabular 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.cli_cache_repo module gain.genomic_resources.draw_score_histograms 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.to_gpf_gene_models_format 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.templates 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.stats_collection module gain.utils.variant_utils module gain.utils.verbosity_configuration module gd2str() (in module gain.effect_annotation.effect) ge2str() (in module gain.effect_annotation.effect) gene (gain.annotation.simple_effect_annotator.SimpleEffect 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_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_ns (gain.gene_sets.gene_term.GeneTerms attribute) gene_number (gain.genomic_resources.implementations.gene_models_impl.StatisticsData attribute) gene_sets (gain.gene_sets.gene_set.GeneSetCollection attribute) gene_sym (gain.gene_sets.gene_term.GeneInfo attribute) 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) GeneModelsImpl (class in gain.genomic_resources.implementations.gene_models_impl) GeneModelsStatistics (class in gain.genomic_resources.implementations.gene_models_impl) genes (gain.gene_sets.gene_term.NCBIGeneInfo attribute) genes() (gain.effect_annotation.effect.AnnotationEffect class method) GeneScore (class in gain.gene_scores.gene_scores) GeneScoreAnnotator (class in gain.annotation.gene_score_annotator) GeneScoreImplementation (class in gain.gene_scores.implementations.gene_scores_impl) GeneScoresDb (class in gain.gene_scores.gene_scores) 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) GeneSetResourceSchema (class in gain.gene_sets.gene_set) GeneTerms (class in gain.gene_sets.gene_term) GenomeStatistic (class in gain.genomic_resources.implementations.reference_genome_impl) GenomeStatisticsMixin (class in gain.genomic_resources.implementations.reference_genome_impl) 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) GenomicScoreImplementation (class in gain.genomic_resources.implementations.genomic_scores_impl) get() (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)

get_aggregator_class() (in module gain.genomic_resources.aggregators) get_all_chrom_lengths() (gain.genomic_resources.reference_genome.ReferenceGenome method) get_all_chromosomes() (gain.genomic_resources.genomic_scores.GenomicScore method) get_all_gene_sets() (gain.gene_sets.gene_set.BaseGeneSetCollection method) (gain.gene_sets.gene_set.GeneSetCollection 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_amino_acids() (gain.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) (gain.effect_annotation.annotation_request.PositiveStrandAnnotationRequest method) get_annotator_by_attribute_info() (gain.annotation.annotation_pipeline.AnnotationPipeline method) get_annotator_factory() (in module gain.annotation.annotation_factory) get_attribute_defaults() (gain.annotation.annotator_base.AnnotatorBase method) (gain.annotation.cnv_collection_annotator.CnvCollectionAnnotator method) (gain.annotation.effect_annotator.EffectAnnotatorAdapter method) (gain.annotation.gene_set_annotator.GeneSetAnnotator method) (gain.annotation.score_annotator.AlleleScoreAnnotator method) (gain.annotation.score_annotator.GenomicScoreAnnotatorBase method) (gain.annotation.score_annotator.PositionScoreAnnotator method) (gain.annotation.simple_effect_annotator.SimpleEffectAnnotator method) get_attribute_info() (gain.annotation.annotation_pipeline.AnnotationPipeline method) get_attribute_specs() (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.AlleleScoreAnnotator method) (gain.annotation.score_annotator.GenomicScoreAnnotatorBase method) (gain.annotation.simple_effect_annotator.SimpleEffectAnnotator 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_resource_schema() (in module gain.genomic_resources.resource_implementation) 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_gene_id() (in module gain.gene_sets.gene_term) 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_column_key() (gain.genomic_resources.genomic_position_table.table.GenomicPositionTable 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_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) 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) 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_default_annotation_attribute() (gain.genomic_resources.genomic_scores.GenomicScore method) get_default_annotation_attributes() (gain.genomic_resources.genomic_scores.GenomicScore 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_description() (gain.genomic_resources.repository.GenomicResource method) 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_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_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_final() (gain.genomic_resources.aggregators.Aggregator method) (gain.genomic_resources.aggregators.BoolAggregator method) (gain.genomic_resources.aggregators.ConcatAggregator method) (gain.genomic_resources.aggregators.CountAggregator method) (gain.genomic_resources.aggregators.CounterAggregator 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_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) 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) 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_value() (gain.gene_scores.gene_scores.GeneScore 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_global_statistic_file() (gain.genomic_resources.implementations.reference_genome_impl.GenomeStatisticsMixin static 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_public_url() (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_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) get_jinja_env() (in module gain.templates) get_labels() (gain.genomic_resources.repository.GenomicResource 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_manifest() (gain.genomic_resources.repository.GenomicResource method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) get_max() (gain.gene_scores.gene_scores.GeneScore method) get_min() (gain.gene_scores.gene_scores.GeneScore method) get_min_max_file() (gain.genomic_resources.statistics.min_max.MinMaxValueStatisticMixin static method) get_nucleotides_count_to_full_codon() (gain.effect_annotation.annotation_request.BaseAnnotationRequest static method) get_or_create_resource() (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) get_out_attributes() (gain.effect_annotation.cli.AnnotationAttributes method) get_parser() (in module gain.genomic_resources.gene_models.parsers) get_pipeline_from_context() (in module gain.annotation.annotate_utils) 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_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_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_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) 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) get_sequence() (gain.genomic_resources.reference_genome.ReferenceGenome 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) 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) get_statistics_template_data() (gain.genomic_resources.resource_implementation.InfoImplementationMixin method) get_summary() (gain.genomic_resources.repository.GenomicResource method) get_task_deps() (gain.task_graph.graph.TaskGraph method) get_task_desc() (gain.task_graph.graph.TaskGraph method) get_template() (in module gain.templates) get_template_data() (gain.genomic_resources.resource_implementation.InfoImplementationMixin method) get_total_count() (gain.genomic_resources.aggregators.Aggregator method) get_type() (gain.genomic_resources.repository.GenomicResource 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_values() (gain.effect_annotation.cli.AnnotationAttributes method) (gain.gene_scores.gene_scores.GeneScore method) get_version_str() (gain.genomic_resources.repository.GenomicResource 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) gtf_canonical_index() (in module gain.genomic_resources.gene_models.serialization)

H

handle_default_args() (in module gain.annotation.annotate_utils) has_chromosome() (gain.genomic_resources.gene_models.gene_models.GeneModels method) (gain.genomic_resources.gene_models.GeneModels method) has_task() (gain.task_graph.graph.TaskGraph method) 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_view_range() (gain.genomic_resources.histogram.NumberHistogramConfig method) has_wildcard() (gain.annotation.annotation_config.AnnotationConfigParser static method)

HasClose (class in gain.utils.debug_closing) header (gain.effect_annotation.cli.VariantColumnInputFile attribute) (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) HelloWorldAnnotator (class in gain.annotation.debug_annotator) help (gain.gene_scores.gene_scores.ScoreDesc attribute) hist (gain.gene_scores.gene_scores.ScoreDesc attribute) hist_conf (gain.gene_scores.gene_scores.ScoreDef attribute) (gain.genomic_resources.genomic_scores.ScoreDef attribute) HistogramError histograms (gain.gene_sets.gene_set.GeneSetResourceSchema attribute) HistogramStatisticMixin (class in gain.genomic_resources.histogram)

I

in_start_codons() (gain.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) (gain.effect_annotation.annotation_request.PositiveStrandAnnotationRequest method) inc() (gain.utils.stats_collection.StatsCollection method) infer_gene_model_parser() (in module gain.genomic_resources.gene_models.parsers) info (gain.genomic_resources.genomic_position_table.line.VCFLine attribute) (gain.genomic_resources.genomic_position_table.VCFLine attribute) info_meta (gain.genomic_resources.genomic_position_table.line.VCFLine attribute) (gain.genomic_resources.genomic_position_table.VCFLine attribute) InfoImplementationMixin (class in gain.genomic_resources.resource_implementation) InfoImplementationMixin.FileEntry (class in gain.genomic_resources.resource_implementation) infos_new (gain.annotation.annotation_pipeline.ReannotationPipeline attribute) infos_rerun (gain.annotation.annotation_pipeline.ReannotationPipeline attribute) 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) inject() (gain.annotation.annotation_config.ParamsUsageMonitor method) InmemoryGenomicPositionTable (class in gain.genomic_resources.genomic_position_table.table_inmemory) input_files (gain.task_graph.graph.TaskDesc attribute) (gain.task_graph.graph.TaskGraph 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) intermediate_output_files (gain.task_graph.graph.TaskDesc attribute) internal (gain.annotation.annotation_config.Attribute attribute) (gain.annotation.annotation_config.AttributeConfig attribute) (gain.annotation.annotation_pipeline.PlanEntry attribute) internal_default (gain.annotation.annotation_pipeline.AttributeSpec attribute) intersection() (gain.utils.regions.Region method) (in module gain.utils.regions) intersects() (gain.utils.regions.Region method)

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) 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_default (gain.annotation.annotation_pipeline.AttributeSpec attribute) is_gr_id_token() (in module gain.genomic_resources.repository) 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) 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_pseudoautosomal() (gain.genomic_resources.reference_genome.ReferenceGenome method) is_s3url() (in module gain.utils.fs_utils) is_start_codon_affected() (gain.effect_annotation.annotation_request.BaseAnnotationRequest method) (gain.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) is_stop_codon_affected() (gain.effect_annotation.annotation_request.BaseAnnotationRequest method) (gain.effect_annotation.annotation_request.NegativeStrandAnnotationRequest method) is_version_constraint_satisfied() (in module gain.genomic_resources.repository) isin() (gain.utils.regions.Region method) isnan() (in module gain.utils.helpers)

J

join() (in module gain.utils.fs_utils) 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) JoinAggregator (class in gain.genomic_resources.aggregators) jump_threshold (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute)

K

kwargs (gain.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol attribute) (gain.task_graph.graph.TaskDesc attribute)

L

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_DUPLICATION (gain.annotation.annotatable.Annotatable.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) 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) 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) Line (class in gain.genomic_resources.genomic_position_table) (class in gain.genomic_resources.genomic_position_table.line) line_iterator (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute) 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) ListAggregator (class in gain.genomic_resources.aggregators)

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) load_contents() (gain.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) load_definition_file() (in module gain.genomic_resources.repository_factory) 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_manifest() (gain.genomic_resources.cached_repository.CachingProtocol method) (gain.genomic_resources.fsspec_protocol.FsspecReadOnlyProtocol method) (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method) load_ncbi_gene_info() (in module gain.gene_sets.gene_term) load_pipeline_from_file() (in module gain.annotation.annotation_factory) load_pipeline_from_file_or_resource() (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_transcript_models() (in module gain.genomic_resources.gene_models.parsers) load_yaml() (gain.genomic_resources.repository.ReadOnlyRepositoryProtocol method)

M

main() (in module gain.genomic_resources.draw_score_histograms) (in module gain.genomic_resources.gene_models.to_gpf_gene_models_format) (in module gain.task_graph.demo_graphs_cli) make_task() (gain.task_graph.graph.TaskGraph static 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) match_labels_query() (gain.annotation.annotation_config.AnnotationConfigParser static method) max (gain.gene_sets.gene_set.ViewRangeSchema attribute) MAX_RUNNING_TASKS (gain.task_graph.dask_executor.DaskExecutor attribute) max_value (gain.genomic_resources.histogram.NumberHistogram attribute) MaxAggregator (class in gain.genomic_resources.aggregators) maximally_extend_variant() (in module gain.genomic_resources.variant_utils) maybe_remove_work_dir() (in module gain.annotation.annotate_utils) maybe_wrap_reannotation() (in module gain.annotation.annotate_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) MedianAggregator (class in gain.genomic_resources.aggregators) 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) message (gain.annotation.annotation_config.AnnotationConfigurationError attribute) meta (gain.gene_sets.gene_set.BaseResourceSchema attribute) metadata (gain.annotation.annotation_config.AnnotationPreamble attribute) (gain.annotation.annotation_config.RawPreamble attribute) MetaSchema (class in gain.gene_sets.gene_set) min (gain.gene_sets.gene_set.ViewRangeSchema attribute) min_value (gain.genomic_resources.histogram.NumberHistogram 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) 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_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) modified() (in module gain.utils.fs_utils) module gain gain.annotation gain.annotation.annotatable gain.annotation.annotate_columns gain.annotation.annotate_doc gain.annotation.annotate_tabular 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.prepare_tabular 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.cli_cache_repo gain.genomic_resources.draw_score_histograms 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.to_gpf_gene_models_format 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.templates 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.stats_collection gain.utils.variant_utils gain.utils.verbosity_configuration

mutation_type() (gain.effect_annotation.effect_checkers.protein_change.ProteinChangeEffectChecker method)

N

name (gain.annotation.annotation_config.Attribute attribute) (gain.annotation.annotation_config.AttributeConfig attribute) (gain.annotation.annotation_pipeline.PlanEntry attribute) (gain.gene_sets.gene_set.GeneSet attribute) (gain.genomic_resources.repository.ManifestEntry attribute) (gain.genomic_resources.resource_implementation.InfoImplementationMixin.FileEntry attribute) names() (gain.genomic_resources.repository.Manifest method) 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) needs_download (gain.genomic_resources.fsspec_protocol.FileCacheVerdict attribute) NegativeStrandAnnotationRequest (class in gain.effect_annotation.annotation_request)

noncoding_regions() (gain.annotation.simple_effect_annotator.SimpleEffectAnnotator 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) NoTaskCache (class in gain.task_graph.cache) ns_tokens (gain.gene_sets.gene_term.NCBIGeneInfo attribute) NuclearCode (class in gain.effect_annotation.gene_codes) NullHistogram (class in gain.genomic_resources.histogram) NullHistogramConfig (class in gain.genomic_resources.histogram) number_of_bins (gain.gene_sets.gene_set.NumericHistogramSchema attribute) (gain.genomic_resources.histogram.NumberHistogramConfig attribute) NumberHistogram (class in gain.genomic_resources.histogram) NumberHistogramConfig (class in gain.genomic_resources.histogram) NumericHistogramSchema (class in gain.gene_sets.gene_set)

O

obtain_resource_file_lock() (gain.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) 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)

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_fasta_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_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) out_of_range_bins (gain.genomic_resources.histogram.NumberHistogram attribute) out_of_range_values (gain.genomic_resources.histogram.NumberHistogram attribute) output_files (gain.task_graph.graph.TaskDesc attribute)

P

parameters (gain.annotation.annotation_config.AnnotatorInfo attribute) (gain.annotation.annotation_config.Attribute attribute) (gain.annotation.annotation_config.AttributeConfig attribute) (gain.genomic_resources.aggregators.AggregatorDefinition attribute) parametrized (gain.genomic_resources.aggregators.Aggregator attribute) (gain.genomic_resources.aggregators.JoinAggregator attribute) ParamsUsageMonitor (class in gain.annotation.annotation_config) parse_ccds_gene_models_format() (in module gain.genomic_resources.gene_models.parsers) parse_cli_arguments() (in module gain.genomic_resources.draw_score_histograms) parse_complete() (gain.annotation.annotation_config.AnnotationConfigParser static method) parse_default_gene_models_format() (in module gain.genomic_resources.gene_models.parsers) 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_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_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_ucscgenepred_models_format() (in module gain.genomic_resources.gene_models.parsers) 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) peripheral_regions() (gain.annotation.simple_effect_annotator.SimpleEffectAnnotator method) PipelineProcessor (class in gain.utils.processing_pipeline) PlanEntry (class in gain.annotation.annotation_pipeline) 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) 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.BigWigLine attribute) (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) (gain.genomic_resources.genomic_position_table.line.VCFLine 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_position_table.VCFLine attribute) (gain.genomic_resources.genomic_scores.CNV attribute) (gain.genomic_resources.genomic_scores.ScoreLine property) pos_end (gain.annotation.annotatable.Annotatable property) (gain.genomic_resources.genomic_position_table.BigWigLine attribute) (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) (gain.genomic_resources.genomic_position_table.line.VCFLine 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_position_table.VCFLine attribute) (gain.genomic_resources.genomic_scores.CNV attribute) (gain.genomic_resources.genomic_scores.ScoreLine property) Position (class in gain.annotation.annotatable) position (gain.annotation.annotatable.Annotatable property) POSITION (gain.annotation.annotatable.Annotatable.Type attribute) 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) preamble (gain.annotation.annotation_config.RawFullConfig attribute) print() (gain.annotation.annotation_pipeline.AnnotationPipeline method) print_annotation_plan() (in module gain.annotation.annotation_pipeline) print_plan() (gain.annotation.annotation_pipeline.ReannotationPipeline 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_graph() (gain.task_graph.cli_tools.TaskGraphCli static method) process_region() (gain.utils.processing_pipeline.PipelineProcessor method) ProcessPoolTaskExecutor (class in gain.task_graph.process_pool_executor) produce_partfile_paths() (in module gain.annotation.annotate_utils) produce_regions() (in module gain.annotation.annotate_utils) 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) pysam_file (gain.genomic_resources.genomic_position_table.TabixGenomicPositionTable attribute)

Q

query_resources() (gain.annotation.annotation_config.AnnotationConfigParser static method)

R

raw_values (gain.genomic_resources.histogram.CategoricalHistogram property) RawFullConfig (class in gain.annotation.annotation_config) RawPreamble (class in gain.annotation.annotation_config) read_ewa_set_file() (in module gain.gene_sets.gene_term) read_gmt_file() (in module gain.gene_sets.gene_term) read_mapping_file() (in module gain.gene_sets.gene_term) READONLY (gain.genomic_resources.repository.Mode attribute) ReadOnlyRepositoryProtocol (class in gain.genomic_resources.repository) READWRITE (gain.genomic_resources.repository.Mode attribute) ReadWriteRepositoryProtocol (class in gain.genomic_resources.repository) ready_tasks() (gain.task_graph.graph.TaskGraph method) ReannotationPipeline (class in gain.annotation.annotation_pipeline) ReannotationPlan (class in gain.annotation.annotation_pipeline) reason (gain.annotation.annotation_pipeline.PlanEntry attribute) (gain.genomic_resources.histogram.NullHistogramConfig 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) recursive_dict_update() (in module gain.utils.dict_utils) recursive_dict_update_inplace() (in module gain.utils.dict_utils) ref (gain.annotation.annotatable.VCFAllele property) (gain.genomic_resources.genomic_position_table.BigWigLine attribute) (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) (gain.genomic_resources.genomic_position_table.line.VCFLine attribute) REF (gain.genomic_resources.genomic_position_table.table.GenomicPositionTable attribute) ref (gain.genomic_resources.genomic_position_table.VCFLine attribute) (gain.genomic_resources.genomic_scores.ScoreLine property) reference (gain.annotation.annotatable.VCFAllele property) reference_genome_files() (in module gain.genomic_resources.reference_genome) 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) 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) regions2bedfile() (in module gain.utils.regions) 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) reload_statistics() (gain.genomic_resources.resource_implementation.GenomicResourceImplementation method) rename_gene_terms() (in module gain.gene_sets.gene_term) rename_genes() (gain.gene_sets.gene_term.GeneTerms method) repo_id (gain.genomic_resources.repository.GenomicResourceRepo property) rerun_triggers (gain.annotation.annotation_pipeline.ReannotationPipeline attribute) resolve_repeated_attributes() (in module gain.annotation.annotation_factory) 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) 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) result (gain.task_graph.cache.CacheRecord property) result_or_error (gain.task_graph.cache.CacheRecord attribute) reverse_complement() (in module gain.utils.variant_utils) rm_file() (in module gain.utils.fs_utils) 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) run() (gain.annotation.docker_annotator.DockerAnnotator method) run_annotate() (gain.annotation.simple_effect_annotator.SimpleEffectAnnotator method)

S

s3_test_protocol() (in module gain.genomic_resources.testing) s3_test_server_endpoint() (in module gain.genomic_resources.testing) safe_task_id() (in module gain.task_graph.logging) save() (gain.gene_sets.gene_term.GeneTerms method) (gain.utils.stats_collection.StatsCollection 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_histogram() (in module gain.genomic_resources.histogram) save_index() (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) save_manifest() (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) save_resource_file_state() (gain.genomic_resources.fsspec_protocol.FsspecReadWriteProtocol method) (gain.genomic_resources.repository.ReadWriteRepositoryProtocol method) 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_id (gain.gene_scores.gene_scores.ScoreDef attribute) (gain.gene_scores.gene_scores.ScoreDesc attribute) (gain.genomic_resources.genomic_scores.ScoreDef attribute) ScoreDef (class in gain.gene_scores.gene_scores) (class in gain.genomic_resources.genomic_scores) ScoreDesc (class in gain.gene_scores.gene_scores) ScoreLine (class in gain.genomic_resources.genomic_scores) 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) SequentialExecutor (class in gain.task_graph.sequential_executor) serialize() (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) 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_position() (gain.effect_annotation.variant.Variant method) set_ref_alt() (gain.effect_annotation.variant.Variant method) set_ref_alt_from_variant() (gain.effect_annotation.variant.Variant 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) 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_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_genome_bgz() (in module gain.genomic_resources.testing) setup_gzip() (in module gain.genomic_resources.testing) setup_pedigree() (in module gain.genomic_resources.testing) setup_t4c8_grr() (in module gain.testing.t4c8_import) setup_tabix() (in module gain.genomic_resources.testing)

setup_vcf() (in module gain.genomic_resources.testing) SEVERITY (gain.effect_annotation.effect.AnnotationEffect attribute) sign() (in module gain.utils.fs_utils) simple_score_queries (gain.annotation.score_annotator.GenomicScoreAnnotatorBase attribute) 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) simplify_effects() (gain.effect_annotation.effect.AnnotationEffect class method) size (gain.genomic_resources.fsspec_protocol.FileCacheVerdict attribute) (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) SMALL_DELETION (gain.annotation.annotatable.Annotatable.Type attribute) SMALL_INSERTION (gain.annotation.annotatable.Annotatable.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) sort_effects() (gain.effect_annotation.effect.AnnotationEffect class method) Source (class in gain.utils.processing_pipeline) source (gain.annotation.annotation_config.Attribute attribute) (gain.annotation.annotation_config.AttributeConfig attribute) (gain.annotation.annotation_pipeline.AttributeSpec attribute) (gain.annotation.processing_pipeline.AnnotationsWithSource attribute) spec (gain.annotation.annotation_config.Attribute attribute) SpliceSiteEffectChecker (class in gain.effect_annotation.effect_checkers.splice_site) split_into_regions() (gain.genomic_resources.reference_genome.ReferenceGenome method) (in module gain.utils.regions) split_iterable() (in module gain.utils.dae_utils) 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) 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) StatsCollection (class in gain.utils.stats_collection) 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) str2bool() (in module gain.utils.helpers) stringify() (in module gain.annotation.annotate_utils) strip_compression_suffix() (in module gain.utils.fs_utils) study_id_from_path() (in module gain.utils.helpers) styles_template_name (gain.gene_scores.implementations.gene_scores_impl.GeneScoreImplementation attribute) (gain.gene_sets.implementations.gene_sets_impl.GeneSetCollectionImpl attribute) (gain.genomic_resources.implementations.gene_models_impl.GeneModelsImpl attribute) (gain.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation attribute) (gain.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeImplementation attribute) (gain.genomic_resources.resource_implementation.InfoImplementationMixin attribute) SUBSTITUTION (gain.annotation.annotatable.Annotatable.Type attribute) SUBSTITUTIONS (gain.genomic_resources.genomic_scores.AlleleScore.Mode attribute) substitutions_mode() (gain.genomic_resources.genomic_scores.AlleleScore method) summary (gain.annotation.annotation_config.AnnotationPreamble attribute) (gain.annotation.annotation_config.RawPreamble attribute) supports_aggregation (gain.annotation.annotation_pipeline.AttributeSpec attribute) syms (gain.gene_sets.gene_set.GeneSet attribute) sync_tasks() (in module gain.task_graph.graph) synonyms (gain.gene_sets.gene_term.GeneInfo attribute)

T

t2g (gain.gene_sets.gene_term.GeneTerms attribute) t4c8_genes() (in module gain.testing.t4c8_import) t4c8_genome() (in module gain.testing.t4c8_import) t4c8_grr() (in module gain.testing.t4c8_import) t_desc (gain.gene_sets.gene_term.GeneTerms attribute) 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) 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_name (gain.gene_scores.implementations.gene_scores_impl.GeneScoreImplementation attribute) (gain.gene_sets.implementations.gene_sets_impl.GeneSetCollectionImpl attribute) (gain.genomic_resources.implementations.annotation_pipeline_impl.AnnotationPipelineImplementation attribute) (gain.genomic_resources.implementations.gene_models_impl.GeneModelsImpl attribute) (gain.genomic_resources.implementations.genomic_scores_impl.GenomicScoreImplementation attribute) (gain.genomic_resources.implementations.liftover_chain_impl.LiftoverChainImplementation attribute) (gain.genomic_resources.implementations.reference_genome_impl.ReferenceGenomeImplementation attribute) (gain.genomic_resources.resource_implementation.InfoImplementationMixin attribute) test_frames() (gain.genomic_resources.gene_models.transcript_models.TranscriptModel method) (gain.genomic_resources.gene_models.TranscriptModel method) timeout() (in module gain.task_graph.demo_graphs_cli) timestamp (gain.genomic_resources.repository.ResourceFileState attribute) to_bed_region() (gain.utils.regions.Region 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) to_manifest_entries() (gain.genomic_resources.repository.Manifest method) to_response_json() (in module gain.utils.helpers) to_tsv() (gain.gene_scores.gene_scores.GeneScore method) tokenize() (gain.annotation.annotatable.Annotatable static method) topological_order() (gain.task_graph.graph.TaskGraph method) 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_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) 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) type (gain.annotation.annotation_config.AnnotatorInfo 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) types (gain.effect_annotation.effect.AlleleEffects property)

U

union() (in module gain.utils.regions) unique_regions() (in module gain.utils.regions) UNIQUE_VALUES_LIMIT (gain.genomic_resources.histogram.CategoricalHistogram attribute) unmap_chromosome() (gain.genomic_resources.genomic_position_table.table.GenomicPositionTable method) update() (gain.genomic_resources.repository.Manifest method) update_frames() (gain.genomic_resources.gene_models.transcript_models.TranscriptModel method) (gain.genomic_resources.gene_models.TranscriptModel method) update_manifest() (gain.genomic_resources.repository.ReadWriteRepositoryProtocol 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) 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)

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)

V

validate_aggregator() (in module gain.genomic_resources.aggregators) validate_and_normalize_schema() (gain.genomic_resources.resource_implementation.ResourceConfigValidationMixin class method) value_counts (gain.genomic_resources.aggregators.ModeAggregator 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.Attribute property) (gain.annotation.annotation_pipeline.AttributeSpec attribute) (gain.gene_scores.gene_scores.ScoreDef attribute) (gain.gene_scores.gene_scores.ScoreDesc attribute) (gain.genomic_resources.genomic_scores.ScoreDef attribute) values (gain.genomic_resources.aggregators.BoolAggregator attribute) (gain.genomic_resources.aggregators.JoinAggregator attribute) (gain.genomic_resources.aggregators.ListAggregator attribute) (gain.genomic_resources.aggregators.MedianAggregator 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_attribute_index (gain.effect_annotation.cli.VariantColumnInputFile attribute)

variant_columns (gain.effect_annotation.cli.VariantColumnInputFile attribute) VariantColumnInputFile (class in gain.effect_annotation.cli) VariantColumnOutputFile (class in gain.effect_annotation.cli) VCFAllele (class in gain.annotation.annotatable) VCFGenomicPositionTable (class in gain.genomic_resources.genomic_position_table) (class in gain.genomic_resources.genomic_position_table.table_vcf) 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) verbosity() (gain.utils.verbosity_configuration.VerbosityConfiguration static method) VerbosityConfiguration (class in gain.utils.verbosity_configuration) version (gain.genomic_resources.repository.GenomicResource attribute) 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.NumberHistogram attribute) (gain.genomic_resources.histogram.NumberHistogramConfig attribute) ViewRangeSchema (class in gain.gene_sets.gene_set)

W

web_format_str (gain.gene_sets.gene_set.GeneSetResourceSchema attribute) web_label (gain.gene_sets.gene_set.GeneSetResourceSchema attribute) WILDCARD_LIMIT (gain.annotation.annotation_config.AnnotationConfigParser attribute)

worst (gain.effect_annotation.effect.AlleleEffects property) worst_effect() (gain.effect_annotation.effect.AnnotationEffect class method) write_columns() (gain.effect_annotation.cli.VariantColumnOutputFile method)

X

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_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)

Z

zero_based_adjust() (in module gain.genomic_resources.genomic_position_table.table)