Index A | B | C | D | E | G | H | I | L | M | N | O | P | Q | R | S | T | V A ALLOWED_ALLELE_FREQ (variant_mapper.resolvers.PopulationResolver attribute) B BaseMapper (class in variant_mapper.mapper) BaseResolver (class in variant_mapper.resolvers) best_mapping() (variant_mapper.mapper.BaseMapper method) C cache (variant_mapper.resolvers.EnsemblResolver property) cache_ref_assembly_match() (variant_mapper.norm.RefNorm method) check_new_chr_name() (variant_mapper.mapper.ScanVcfVariantMapper method) check_norm() (variant_mapper.mapper.ScanVcfVariantMapper method) check_ref() (variant_mapper.mapper.ScanVcfVariantMapper method) check_ref_alleles() (variant_mapper.mapper.BaseMapper method) close() (variant_mapper.mapper.BaseMapper method) (variant_mapper.mapper.ScanVcfVariantMapper method) (variant_mapper.mapper.TabixVcfVariantMapper method) (variant_mapper.mapper.VcfIterator method) (variant_mapper.norm.EnsemblRefNorm method) (variant_mapper.norm.RefNorm method) D decode_mapping_flags() (variant_mapper.mapper.BaseMapper class method) DEFAULT_INTERNAL_DELIMITER (variant_mapper.resolvers.BaseResolver attribute) DNA_REGEX (variant_mapper.mapper.ScanVcfVariantMapper attribute) DNA_REGEXP (variant_mapper.mapper.BaseMapper attribute) (variant_mapper.mapper.EnsemblVariantMapper attribute) E EnsemblRefNorm (class in variant_mapper.norm) EnsemblResolver (class in variant_mapper.resolvers) EnsemblVariantMapper (class in variant_mapper.mapper) extract_alt_allele() (variant_mapper.mapper.ScanVcfVariantMapper method) extract_cadd() (variant_mapper.resolvers.MappingFileResolver method) extract_datasets() (variant_mapper.resolvers.MappingFileResolver static method) extract_hierarchy_aaf_counts() (variant_mapper.resolvers.PopulationResolver static method) extract_hierarchy_aaf_freq() (variant_mapper.resolvers.PopulationResolver static method) extract_id() (variant_mapper.resolvers.MappingFileResolver static method) extract_mean_aaf_counts() (variant_mapper.resolvers.PopulationResolver static method) extract_mean_aaf_freq() (variant_mapper.resolvers.PopulationResolver static method) extract_metadata() (variant_mapper.resolvers.BaseResolver method) (variant_mapper.resolvers.EnsemblResolver method) (variant_mapper.resolvers.MappingFileResolver method) extract_no_aaf() (variant_mapper.resolvers.PopulationResolver static method) extract_nothing() (variant_mapper.mapper.ScanVcfVariantMapper method) extract_pops() (variant_mapper.resolvers.MappingFileResolver static method) extract_positive_strand() (variant_mapper.mapper.ScanVcfVariantMapper method) extract_strand() (variant_mapper.mapper.ScanVcfVariantMapper method) extract_summary_metadata_row() (variant_mapper.resolvers.BaseResolver class method) (variant_mapper.resolvers.EnsemblResolver class method) (variant_mapper.resolvers.MappingFileResolver class method) extract_var_id() (variant_mapper.mapper.ScanVcfVariantMapper method) extract_vep() (variant_mapper.resolvers.MappingFileResolver method) G get_alt_allele_freq() (variant_mapper.resolvers.EnsemblResolver method) get_buffer_sort_key() (variant_mapper.mapper.ScanVcfVariantMapper method) get_mapping_error() (variant_mapper.mapper.BaseMapper class method) (variant_mapper.resolvers.BaseResolver class method) get_mapping_join_key() (variant_mapper.mapper.ScanVcfVariantMapper method) get_mapping_var_id() (variant_mapper.mapper.BaseMapper class method) (variant_mapper.mapper.EnsemblVariantMapper class method) (variant_mapper.mapper.ScanVcfVariantMapper static method) (variant_mapper.mapper.TabixVcfVariantMapper class method) get_minimal_alleles() (variant_mapper.norm.RefNorm static method) get_no_data_mapping() (variant_mapper.mapper.BaseMapper class method) (variant_mapper.resolvers.BaseResolver class method) get_source_join_key() (variant_mapper.mapper.ScanVcfVariantMapper method) H header (variant_mapper.mapper.ScanVcfVariantMapper property) HIER_AAF (variant_mapper.resolvers.PopulationResolver attribute) I impute_alt_allele() (variant_mapper.resolvers.BaseResolver method) (variant_mapper.resolvers.EnsemblResolver method) (variant_mapper.resolvers.MappingFileResolver method) init_mapping_file() (variant_mapper.mapper.ScanVcfVariantMapper method) init_source_file() (variant_mapper.mapper.ScanVcfVariantMapper method) is_open (variant_mapper.norm.RefNorm property) L list_populations() (variant_mapper.resolvers.EnsemblResolver method) (variant_mapper.resolvers.MappingFileResolver method) (variant_mapper.resolvers.PopulationResolver method) M map_variant() (variant_mapper.mapper.BaseMapper method) (variant_mapper.mapper.EnsemblVariantMapper method) (variant_mapper.mapper.ScanVcfVariantMapper method) (variant_mapper.mapper.TabixVcfVariantMapper method) mapping_correct() (variant_mapper.mapper.ScanVcfVariantMapper class method) MAPPING_FILE_TYPE (variant_mapper.mapper.ScanVcfVariantMapper attribute) MappingFileResolver (class in variant_mapper.resolvers) MEAN_AAF (variant_mapper.resolvers.PopulationResolver attribute) METADATA_SUMMARY_ROW_HEADER (variant_mapper.resolvers.BaseResolver attribute) (variant_mapper.resolvers.EnsemblResolver attribute) (variant_mapper.resolvers.MappingFileResolver attribute) (variant_mapper.resolvers.PopulationResolver attribute) MIN_ALT_IMPUTE_EVIDENCE (variant_mapper.resolvers.BaseResolver attribute) N normalise_alleles() (variant_mapper.norm.RefNorm method) normalise_multi_alleles() (variant_mapper.norm.RefNorm method) O open() (variant_mapper.mapper.BaseMapper method) (variant_mapper.mapper.ScanVcfVariantMapper method) (variant_mapper.mapper.TabixVcfVariantMapper method) (variant_mapper.mapper.VcfIterator method) (variant_mapper.norm.EnsemblRefNorm method) (variant_mapper.norm.RefNorm method) order_mappings() (variant_mapper.mapper.BaseMapper class method) output_sorted (variant_mapper.mapper.ScanVcfVariantMapper property) P PopulationResolver (class in variant_mapper.resolvers) Q query_allele_freq() (variant_mapper.resolvers.EnsemblResolver method) query_region() (variant_mapper.mapper.EnsemblVariantMapper method) quick_match() (variant_mapper.mapper.BaseMapper class method) R ref_assembly_match() (variant_mapper.norm.RefNorm method) RefNorm (class in variant_mapper.norm) resolve_poor_mapping() (variant_mapper.resolvers.BaseResolver method) (variant_mapper.resolvers.EnsemblResolver method) resolver (variant_mapper.mapper.BaseMapper property) S ScanVcfVariantMapper (class in variant_mapper.mapper) search_assembly() (variant_mapper.norm.EnsemblRefNorm method) (variant_mapper.norm.RefNorm method) sort_buffer() (variant_mapper.mapper.ScanVcfVariantMapper method) sort_map() (variant_mapper.mapper.BaseMapper static method) (variant_mapper.resolvers.BaseResolver static method) source (variant_mapper.mapper.ScanVcfVariantMapper property) T TabixVcfVariantMapper (class in variant_mapper.mapper) test_sort_order() (variant_mapper.mapper.ScanVcfVariantMapper method) V valid_ref() (variant_mapper.norm.RefNorm method) validate_cadd_format() (variant_mapper.resolvers.MappingFileResolver static method) validate_data_source() (variant_mapper.resolvers.BaseResolver method) (variant_mapper.resolvers.EnsemblResolver method) (variant_mapper.resolvers.MappingFileResolver method) validate_genomic_coords() (variant_mapper.mapper.BaseMapper method) validate_header_format() (variant_mapper.resolvers.MappingFileResolver static method) validate_population_kwarg() (variant_mapper.resolvers.MappingFileResolver class method) (variant_mapper.resolvers.PopulationResolver class method) validate_populations() (variant_mapper.resolvers.EnsemblResolver method) (variant_mapper.resolvers.MappingFileResolver method) validate_resolver() (variant_mapper.mapper.BaseMapper method) (variant_mapper.mapper.ScanVcfVariantMapper method) validate_vep_format() (variant_mapper.resolvers.MappingFileResolver static method) var_id_match() (variant_mapper.mapper.BaseMapper class method) VcfIterator (class in variant_mapper.mapper)