Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W A absolute_path (gwas_norm.metadata.file.GwasFile property) add() (gwas_norm.metadata.phenotype.And method) (gwas_norm.metadata.phenotype.Or method) (gwas_norm.metadata.phenotype.Synonym method) add_analysis() (gwas_norm.metadata.study.Study method) (gwas_norm.metadata.study.StudyFile method) add_column() (gwas_norm.metadata.info.Info method) add_column_name() (in module gwas_norm.common), [1] add_definition() (gwas_norm.metadata.info.Info method) add_file() (gwas_norm.metadata.analysis.AnalysisFile method) (gwas_norm.metadata.file.FileHolderMixin method) (gwas_norm.metadata.study.StudyFile method) add_freq_pop() (gwas_norm.metadata.cohort.CaseControlPopulation method) (gwas_norm.metadata.cohort.Population method) (gwas_norm.metadata.cohort.SamplePopulation method) add_key() (gwas_norm.metadata.analysis.KeyAnalysis method) add_ld_pop() (gwas_norm.metadata.cohort.CaseControlPopulation method) (gwas_norm.metadata.cohort.Population method) (gwas_norm.metadata.cohort.SamplePopulation method) add_metafile() (gwas_norm.metadata.study.Study method) (gwas_norm.metadata.study.StudyFile method) add_pop() (gwas_norm.metadata.cohort.FreqReference method) (gwas_norm.metadata.cohort.LdReference method) add_population() (gwas_norm.metadata.cohort.CaseControlCohort method) (gwas_norm.metadata.cohort.Cohort method) (gwas_norm.metadata.cohort.SampleCohort method) add_study() (gwas_norm.metadata.gwas_data.GwasData method) add_test() (gwas_norm.metadata.analysis.AnalysisFile method) (gwas_norm.metadata.analysis.KeyAnalysis method) alias (gwas_norm.variants.constants.Column attribute) ALLELE (in module gwas_norm.variants.vcf_info) ALLELE_DELIMITER (in module gwas_norm.variants.constants) allele_idx() (in module gwas_norm.variants.mapper) ALLOWED_ALLELE_FREQ (gwas_norm.variants.resolvers.PopulationResolver attribute) ALLOWED_TYPES (in module gwas_norm.variants.constants) ALT (in module gwas_norm.variants.constants), [1] alt_allele (gwas_norm.variants.constants.MapCoord attribute) ALT_ALLELE_INFERRED (in module gwas_norm.variants.constants) analyses (gwas_norm.metadata.study.Study property) (gwas_norm.metadata.study.StudyFile property) analysis_id (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.analysis.KeyAnalysis property) ANALYSIS_ID_TAG (gwas_norm.metadata.analysis.AnalysisFile attribute) (gwas_norm.metadata.analysis.KeyAnalysis attribute) analysis_name (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.analysis.KeyAnalysis property) ANALYSIS_NAME_TAG (gwas_norm.metadata.analysis.AnalysisFile attribute) (gwas_norm.metadata.analysis.KeyAnalysis attribute) analysis_type (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.file.FileHolderMixin property) (gwas_norm.metadata.study.StudyFile property) ANALYSIS_TYPE_TAG (gwas_norm.metadata.analysis.AnalysisFile attribute) (gwas_norm.metadata.file.FileHolderMixin attribute) (gwas_norm.metadata.study.StudyFile attribute) AnalysisFile (class in gwas_norm.metadata.analysis) And (class in gwas_norm.metadata.phenotype) as_dict() (gwas_norm.config.GwasNormConfig method) ASSEMBLY_PREFIX (in module gwas_norm.config) ASSEMBLY_SYN_SECTION (in module gwas_norm.config) B BALANCED (in module gwas_norm.variants.constants) BaseMapper (class in gwas_norm.variants.mapper) basename (gwas_norm.metadata.file.GwasFile property) BaseResolver (class in gwas_norm.variants.resolvers) best_mapping() (gwas_norm.variants.mapper.BaseMapper method) bind() (gwas_norm.metadata.analysis.AnalysisFile method) (gwas_norm.metadata.analysis.KeyAnalysis method) (gwas_norm.metadata.file.GwasFile method) (gwas_norm.metadata.study.Study method) (gwas_norm.metadata.study.StudyFile method) bits (gwas_norm.variants.constants.DataSet attribute) (gwas_norm.variants.constants.MappingFlag attribute) BLANK_ALLELE (in module gwas_norm.variants.constants) bsd_chksum_file() (in module gwas_norm.common), [1] bsd_chksum_str() (in module gwas_norm.common), [1] C cache (gwas_norm.variants.resolvers.EnsemblResolver property) cache_ref_assembly_match() (gwas_norm.variants.norm.RefNorm method) CADD_INFO_FIELD (in module gwas_norm.variants.vcf_info) cadd_info_parser() (in module gwas_norm.variants.vcf_info) CADD_KEY_LOOKUP (in module gwas_norm.variants.vcf_info) CADD_MAIN_DELIMITER (in module gwas_norm.variants.vcf_info) cadd_name (gwas_norm.variants.vcf_info.CaddKeys attribute) CADD_PHRED (in module gwas_norm.variants.vcf_info) CADD_RAW (in module gwas_norm.variants.vcf_info) CaddKeys (class in gwas_norm.variants.vcf_info) CaseControlCohort (class in gwas_norm.metadata.cohort) CaseControlMixin (class in gwas_norm.metadata.cohort) CaseControlPopulation (class in gwas_norm.metadata.cohort) Caveat (class in gwas_norm.metadata.phenotype) caveat (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.analysis.KeyAnalysis property) CHAIN_FILE_PREFIX (in module gwas_norm.config) check_abs_path() (in module gwas_norm.common), [1] check_analysis_type() (in module gwas_norm.common), [1] check_effect_type() (in module gwas_norm.common), [1] check_file() (gwas_norm.metadata.file.GwasFile method) check_new_chr_name() (gwas_norm.variants.mapper.ScanVcfVariantMapper method) check_norm() (gwas_norm.variants.mapper.ScanVcfVariantMapper method) check_old_analysis_ids() (gwas_norm.metadata.study.Study method) (gwas_norm.metadata.study.StudyFile method) check_parent() (in module gwas_norm.common), [1] chksum (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.analysis.KeyAnalysis property) (gwas_norm.metadata.study.Study property) (gwas_norm.metadata.study.StudyFile property) CHR (in module gwas_norm.variants.constants), [1] chr_name (gwas_norm.variants.constants.MapCoord attribute) CHR_NAME_TAG (gwas_norm.metadata.test.Test attribute) CHR_POS_SPEC_TAG (gwas_norm.metadata.file.GwasFile attribute) chrpos_spec (gwas_norm.metadata.file.GwasFile property) ChrPosSpec (class in gwas_norm.common), [1] CLINORIGIN_BI (in module gwas_norm.variants.vcf_info) CLINORIGIN_DEN (in module gwas_norm.variants.vcf_info) CLINORIGIN_GERM (in module gwas_norm.variants.vcf_info) CLINORIGIN_INC (in module gwas_norm.variants.vcf_info) CLINORIGIN_INH (in module gwas_norm.variants.vcf_info) CLINORIGIN_LOOKUP (in module gwas_norm.variants.vcf_info) CLINORIGIN_MAT (in module gwas_norm.variants.vcf_info) CLINORIGIN_NT (in module gwas_norm.variants.vcf_info) CLINORIGIN_OTH (in module gwas_norm.variants.vcf_info) CLINORIGIN_PAT (in module gwas_norm.variants.vcf_info) CLINORIGIN_SOM (in module gwas_norm.variants.vcf_info) CLINORIGIN_UNI (in module gwas_norm.variants.vcf_info) CLINORIGIN_UNKN (in module gwas_norm.variants.vcf_info) CLINSIG_AFF (in module gwas_norm.variants.vcf_info) CLINSIG_ASSC (in module gwas_norm.variants.vcf_info) CLINSIG_BEN (in module gwas_norm.variants.vcf_info) CLINSIG_CONF (in module gwas_norm.variants.vcf_info) CLINSIG_DRUG (in module gwas_norm.variants.vcf_info) CLINSIG_ERR (in module gwas_norm.variants.vcf_info) CLINSIG_LBEN (in module gwas_norm.variants.vcf_info) CLINSIG_LOOKUP (in module gwas_norm.variants.vcf_info) CLINSIG_LPATH (in module gwas_norm.variants.vcf_info) CLINSIG_NP (in module gwas_norm.variants.vcf_info) CLINSIG_OTH (in module gwas_norm.variants.vcf_info) CLINSIG_PATH (in module gwas_norm.variants.vcf_info) CLINSIG_PROT (in module gwas_norm.variants.vcf_info) CLINSIG_RISK (in module gwas_norm.variants.vcf_info) CLINSIG_SEN (in module gwas_norm.variants.vcf_info) CLINSIG_USIG (in module gwas_norm.variants.vcf_info) CLINVAR_ID_DELIMITER (in module gwas_norm.variants.vcf_info) CLINVAR_MAIN_DELIMITER (in module gwas_norm.variants.vcf_info) CLINVAR_MAPPED_FIELDS (in module gwas_norm.variants.vcf_info) clinvar_most_significant() (in module gwas_norm.variants.vcf_info) clinvar_name (gwas_norm.variants.vcf_info.ClinVarKeys attribute) CLINVAR_ORIGIN (in module gwas_norm.variants.vcf_info) CLINVAR_SIGNIF (in module gwas_norm.variants.vcf_info) CLINVAR_SUB_DELIMITER (in module gwas_norm.variants.vcf_info) ClinVarKeys (class in gwas_norm.variants.vcf_info) ClinVarOri (class in gwas_norm.variants.vcf_info) ClinVarSig (class in gwas_norm.variants.vcf_info) CLNACC (in module gwas_norm.variants.vcf_info) CLNDISDB (in module gwas_norm.variants.vcf_info) CLNDN (in module gwas_norm.variants.vcf_info) CLNHGVS (in module gwas_norm.variants.vcf_info) CLNORIGIN (in module gwas_norm.variants.vcf_info) CLNREVSTAT (in module gwas_norm.variants.vcf_info) CLNSIG (in module gwas_norm.variants.vcf_info) CLNVI (in module gwas_norm.variants.vcf_info) close() (gwas_norm.variants.mapper.BaseMapper method) (gwas_norm.variants.mapper.ScanVcfVariantMapper method) (gwas_norm.variants.mapper.TabixVcfVariantMapper method) (gwas_norm.variants.mapper.VcfIterator method) (gwas_norm.variants.norm.EnsemblRefNorm method) (gwas_norm.variants.norm.RefNorm method) CODING_SEQUENCE (in module gwas_norm.variants.vcf_info) Cohort (class in gwas_norm.metadata.cohort) cohort (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.file.FileHolderMixin property) (gwas_norm.metadata.study.StudyFile property) Column (class in gwas_norm.metadata.column) (class in gwas_norm.variants.constants) column_map (gwas_norm.metadata.file.GwasFile property) columns (gwas_norm.metadata.info.Info property) COLUMNS_TAG (gwas_norm.metadata.file.GwasFile attribute) COMMENT_CHAR_TAG (gwas_norm.metadata.file.GwasFile attribute) COMP_TRANSLATE (in module gwas_norm.variants.constants) compress_file() (in module gwas_norm.common), [1] compression (gwas_norm.metadata.file.GwasFile property) COMPRESSION_TAG (gwas_norm.metadata.file.GwasFile attribute) CONFIG_DEFAULT_NAME (in module gwas_norm.config) CONFIG_ENV (in module gwas_norm.config) CONSEQUENCE (in module gwas_norm.variants.vcf_info) CONSEQUENCE_LOOKUP (in module gwas_norm.variants.vcf_info) CONSEQUENCES (in module gwas_norm.variants.vcf_info) CONSORTIUM_TAG (gwas_norm.metadata.study.Study attribute) (gwas_norm.metadata.study.StudyFile attribute) contents (gwas_norm.metadata.phenotype.And property) (gwas_norm.metadata.phenotype.Or property) convert() (in module gwas_norm.common), [1] convert_bgi_to_text() (in module gwas_norm.utils.genome_chunks) convert_xml() (in module gwas_norm.metadata.convert) COORD_OFFSET (in module gwas_norm.variants.constants) count() (gwas_norm.metadata.test.Test.TestResult method) count_lines() (in module gwas_norm.common), [1] create_analysis_type_xml() (gwas_norm.metadata.analysis.AnalysisFile method) (gwas_norm.metadata.file.FileHolderMixin method) (gwas_norm.metadata.study.StudyFile method) create_analysis_xml() (gwas_norm.metadata.study.Study method) (gwas_norm.metadata.study.StudyFile method) create_case_xml() (gwas_norm.metadata.cohort.CaseControlCohort method) (gwas_norm.metadata.cohort.CaseControlMixin method) (gwas_norm.metadata.cohort.CaseControlPopulation method) create_chrpos_spec_str() (in module gwas_norm.common), [1] create_chunk_file() (in module gwas_norm.utils.genome_chunks) create_cohort_xml() (gwas_norm.metadata.analysis.AnalysisFile method) (gwas_norm.metadata.file.FileHolderMixin method) (gwas_norm.metadata.study.StudyFile method) create_effect_type_xml() (gwas_norm.metadata.analysis.AnalysisFile method) (gwas_norm.metadata.file.FileHolderMixin method) (gwas_norm.metadata.study.StudyFile method) create_files_xml() (gwas_norm.metadata.analysis.AnalysisFile method) (gwas_norm.metadata.file.FileHolderMixin method) (gwas_norm.metadata.study.StudyFile method) create_nsamples_xml() (gwas_norm.metadata.cohort.SampleCohort method) (gwas_norm.metadata.cohort.SamplePopulation method) (gwas_norm.metadata.cohort.SampleSizeMixin method) create_uni_id() (in module gwas_norm.common), [1] create_units_xml() (gwas_norm.metadata.analysis.AnalysisFile method) (gwas_norm.metadata.file.FileHolderMixin method) (gwas_norm.metadata.study.StudyFile method) create_xml() (gwas_norm.metadata.analysis.AnalysisFile method) (gwas_norm.metadata.file.FileHolderMixin method) (gwas_norm.metadata.study.StudyFile method) CSV_DELIMITER_TAG (gwas_norm.metadata.file.GwasFile attribute) CSV_DOUBLE_QUOTE_TAG (gwas_norm.metadata.file.GwasFile attribute) CSV_ESCAPE_CHAR_TAG (gwas_norm.metadata.file.GwasFile attribute) csv_kwargs (gwas_norm.metadata.file.GwasFile property) CSV_LINE_TERMINATOR_TAG (gwas_norm.metadata.file.GwasFile attribute) CSV_QUOTE_CHAR_TAG (gwas_norm.metadata.file.GwasFile attribute) CSV_QUOTING_TAG (gwas_norm.metadata.file.GwasFile attribute) CSV_SKIP_INIT_WHITESPACE_TAG (gwas_norm.metadata.file.GwasFile attribute) CSV_STRICT_TAG (gwas_norm.metadata.file.GwasFile attribute) D DATA_TYPE_ATTRIBUTE (gwas_norm.metadata.column.Column attribute) (gwas_norm.metadata.column.MappingColumn attribute) (gwas_norm.metadata.phenotype.Definition attribute) DataSet (class in gwas_norm.variants.constants) dataset_bits() (in module gwas_norm.variants.constants) decode_mapping_flags() (gwas_norm.variants.mapper.BaseMapper class method) (in module gwas_norm.variants.constants) DEFAULT_INTERNAL_DELIMITER (gwas_norm.variants.resolvers.BaseResolver attribute) Definition (class in gwas_norm.metadata.phenotype) definition (gwas_norm.metadata.phenotype.Caveat property) (gwas_norm.metadata.phenotype.Phenotype property) definitions (gwas_norm.metadata.info.Info property) DELETION (in module gwas_norm.variants.constants) delta (gwas_norm.metadata.test.Test.TestResult attribute) description (gwas_norm.variants.constants.MappingFlag attribute) (gwas_norm.variants.vcf_info.So attribute) DETAIL_DELIMITER (in module gwas_norm.config) display_name (gwas_norm.variants.vcf_info.ClinVarOri attribute) (gwas_norm.variants.vcf_info.ClinVarSig attribute) (gwas_norm.variants.vcf_info.So attribute) DNA (in module gwas_norm.variants.constants) DNA_DEL_REGEX (in module gwas_norm.variants.constants) DNA_DEL_STR (in module gwas_norm.variants.constants) DNA_REGEX (gwas_norm.variants.mapper.ScanVcfVariantMapper attribute) (in module gwas_norm.variants.constants) DNA_REGEXP (gwas_norm.variants.mapper.BaseMapper attribute) (gwas_norm.variants.mapper.EnsemblVariantMapper attribute) DNA_STR (in module gwas_norm.variants.constants) DOWNSTREAM (in module gwas_norm.variants.vcf_info) dstruct (gwas_norm.metadata.column.Column property) (gwas_norm.metadata.column.MappingColumn property) (gwas_norm.metadata.phenotype.Definition property) dtype (gwas_norm.metadata.column.Column property) (gwas_norm.metadata.column.MappingColumn property) (gwas_norm.metadata.phenotype.Definition property) E EFFECT_ALLELE_TAG (gwas_norm.metadata.test.Test attribute) EFFECT_SIZE_DELTA (gwas_norm.metadata.test.Test attribute) EFFECT_SIZE_TAG (gwas_norm.metadata.test.Test attribute) effect_type (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.file.FileHolderMixin property) (gwas_norm.metadata.study.StudyFile property) EFFECT_TYPE_TAG (gwas_norm.metadata.analysis.AnalysisFile attribute) (gwas_norm.metadata.file.FileHolderMixin attribute) (gwas_norm.metadata.study.StudyFile attribute) (gwas_norm.metadata.test.Test attribute) ENCODING_TAG (gwas_norm.metadata.file.GwasFile attribute) END (in module gwas_norm.variants.constants), [1] end_anchor (gwas_norm.common.ChrPosSpec attribute), [1] ENS_ID_REGEX (in module gwas_norm.variants.constants) ENS_ID_STR (in module gwas_norm.variants.constants) ENSEMBL_DELETION (in module gwas_norm.variants.constants) EnsemblRefNorm (class in gwas_norm.variants.norm) EnsemblResolver (class in gwas_norm.variants.resolvers) EnsemblVariantMapper (class in gwas_norm.variants.mapper) equals() (gwas_norm.metadata.column.Column method) (gwas_norm.metadata.column.MappingColumn method) (gwas_norm.metadata.phenotype.Definition method) ERROR (in module gwas_norm.variants.constants) error_on_empty() (in module gwas_norm.common), [1] errors (gwas_norm.variants.constants.MappingResult attribute) expand_relative_path() (in module gwas_norm.common), [1] expected_idx (gwas_norm.variants.constants.Column attribute) expected_value (gwas_norm.metadata.test.Test.TestResult attribute) extract_alt_allele() (gwas_norm.variants.mapper.ScanVcfVariantMapper method) extract_cadd() (gwas_norm.variants.resolvers.MappingFileResolver method) extract_datasets() (gwas_norm.variants.resolvers.MappingFileResolver static method) extract_hierarchy_aaf_counts() (gwas_norm.variants.resolvers.PopulationResolver static method) extract_hierarchy_aaf_freq() (gwas_norm.variants.resolvers.PopulationResolver static method) extract_id() (gwas_norm.variants.resolvers.MappingFileResolver static method) extract_mean_aaf_counts() (gwas_norm.variants.resolvers.PopulationResolver static method) extract_mean_aaf_freq() (gwas_norm.variants.resolvers.PopulationResolver static method) extract_metadata() (gwas_norm.variants.resolvers.BaseResolver method) (gwas_norm.variants.resolvers.EnsemblResolver method) (gwas_norm.variants.resolvers.MappingFileResolver method) extract_no_aaf() (gwas_norm.variants.resolvers.PopulationResolver static method) extract_nothing() (gwas_norm.variants.mapper.ScanVcfVariantMapper method) extract_pops() (gwas_norm.variants.resolvers.MappingFileResolver static method) extract_positive_strand() (gwas_norm.variants.mapper.ScanVcfVariantMapper method) extract_strand() (gwas_norm.variants.mapper.ScanVcfVariantMapper method) extract_summary_metadata_row() (gwas_norm.variants.resolvers.BaseResolver class method) (gwas_norm.variants.resolvers.EnsemblResolver class method) (gwas_norm.variants.resolvers.MappingFileResolver class method) extract_var_id() (gwas_norm.variants.mapper.ScanVcfVariantMapper method) extract_vep() (gwas_norm.variants.resolvers.MappingFileResolver method) F FEAT_TRUNCATION (in module gwas_norm.variants.vcf_info) FEATURE (in module gwas_norm.variants.vcf_info) FEATURE_ELONGATION (in module gwas_norm.variants.vcf_info) FEATURE_TYPE (in module gwas_norm.variants.vcf_info) file_check (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.file.FileHolderMixin property) (gwas_norm.metadata.gwas_data.GwasData property) (gwas_norm.metadata.study.Study property) (gwas_norm.metadata.study.StudyFile property) FILE_CLASS (gwas_norm.metadata.analysis.AnalysisFile attribute) (gwas_norm.metadata.file.FileHolderMixin attribute) (gwas_norm.metadata.study.StudyFile attribute) file_repr_attr_str() (gwas_norm.metadata.analysis.AnalysisFile method) (gwas_norm.metadata.file.FileHolderMixin method) (gwas_norm.metadata.study.StudyFile method) FileHolderMixin (class in gwas_norm.metadata.file) files (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.file.FileHolderMixin property) (gwas_norm.metadata.study.StudyFile property) find_in_header() (in module gwas_norm.utils.genome_chunks) FIVE_PRIME_UTR (in module gwas_norm.variants.vcf_info) fix_vcf_split_counts() (in module gwas_norm.variants.downloads.fix_split_counts) FLAGS (in module gwas_norm.variants.constants) flat_definition (gwas_norm.metadata.phenotype.And property) (gwas_norm.metadata.phenotype.Caveat property) (gwas_norm.metadata.phenotype.Definition property) (gwas_norm.metadata.phenotype.Or property) (gwas_norm.metadata.phenotype.Phenotype property) (gwas_norm.metadata.phenotype.Synonym property) FRAMESHIFT (in module gwas_norm.variants.vcf_info) freq_pops (gwas_norm.metadata.cohort.CaseControlPopulation property) (gwas_norm.metadata.cohort.Population property) (gwas_norm.metadata.cohort.SamplePopulation property) FreqReference (class in gwas_norm.metadata.cohort) from_xml() (gwas_norm.metadata.analysis.AnalysisFile class method) (gwas_norm.metadata.analysis.KeyAnalysis class method) (gwas_norm.metadata.cohort.CaseControlCohort class method) (gwas_norm.metadata.cohort.CaseControlPopulation class method) (gwas_norm.metadata.cohort.Cohort class method) (gwas_norm.metadata.cohort.FreqReference class method) (gwas_norm.metadata.cohort.LdReference class method) (gwas_norm.metadata.cohort.Population class method) (gwas_norm.metadata.cohort.SampleCohort class method) (gwas_norm.metadata.cohort.SamplePopulation class method) (gwas_norm.metadata.column.Column class method) (gwas_norm.metadata.column.MappingColumn class method) (gwas_norm.metadata.file.GwasFile class method) (gwas_norm.metadata.gwas_data.GwasData class method) (gwas_norm.metadata.info.Info class method) (gwas_norm.metadata.phenotype.And class method) (gwas_norm.metadata.phenotype.Caveat class method) (gwas_norm.metadata.phenotype.Definition class method) (gwas_norm.metadata.phenotype.Or class method) (gwas_norm.metadata.phenotype.Phenotype class method) (gwas_norm.metadata.phenotype.Synonym class method) (gwas_norm.metadata.study.Study class method) (gwas_norm.metadata.study.StudyFile class method) (gwas_norm.metadata.test.Test class method) G GENE (in module gwas_norm.variants.vcf_info) get_alt_allele_freq() (gwas_norm.variants.resolvers.EnsemblResolver method) get_analysis_by_name() (gwas_norm.metadata.gwas_data.GwasData method) (gwas_norm.metadata.study.Study method) (gwas_norm.metadata.study.StudyFile method) get_attributes() (gwas_norm.metadata.column.Column class method) (gwas_norm.metadata.column.MappingColumn class method) (gwas_norm.metadata.phenotype.Definition class method) get_buffer_sort_key() (gwas_norm.variants.mapper.ScanVcfVariantMapper method) get_chain_file() (gwas_norm.config.GwasNormConfig method) get_chunks() (in module gwas_norm.utils.genome_chunks) get_class() (gwas_norm.metadata.analysis.AnalysisFile class method) (gwas_norm.metadata.analysis.KeyAnalysis class method) (gwas_norm.metadata.cohort.CaseControlCohort class method) (gwas_norm.metadata.cohort.CaseControlPopulation class method) (gwas_norm.metadata.cohort.Cohort class method) (gwas_norm.metadata.cohort.FreqReference class method) (gwas_norm.metadata.cohort.LdReference class method) (gwas_norm.metadata.cohort.Population class method) (gwas_norm.metadata.cohort.SampleCohort class method) (gwas_norm.metadata.cohort.SamplePopulation class method) (gwas_norm.metadata.column.Column class method) (gwas_norm.metadata.column.MappingColumn class method) (gwas_norm.metadata.file.GwasFile class method) (gwas_norm.metadata.gwas_data.GwasData class method) (gwas_norm.metadata.info.Info class method) (gwas_norm.metadata.phenotype.And class method) (gwas_norm.metadata.phenotype.Caveat class method) (gwas_norm.metadata.phenotype.Definition class method) (gwas_norm.metadata.phenotype.Or class method) (gwas_norm.metadata.phenotype.Phenotype class method) (gwas_norm.metadata.phenotype.Synonym class method) (gwas_norm.metadata.study.Study class method) (gwas_norm.metadata.study.StudyFile class method) (gwas_norm.metadata.test.Test class method) get_column_name() (in module gwas_norm.common), [1] get_config_file() (in module gwas_norm.config) get_defaults() (gwas_norm.config.GwasNormConfig class method) get_end_pos() (in module gwas_norm.utils.genome_chunks) (in module gwas_norm.variants.common) get_file_name() (in module gwas_norm.common), [1] get_mapping_coords() (in module gwas_norm.variants.mapper) get_mapping_error() (gwas_norm.variants.mapper.BaseMapper class method) (gwas_norm.variants.resolvers.BaseResolver class method) get_mapping_file() (gwas_norm.config.GwasNormConfig method) get_mapping_join_key() (gwas_norm.variants.mapper.ScanVcfVariantMapper method) get_mapping_var_id() (gwas_norm.variants.mapper.BaseMapper class method) (gwas_norm.variants.mapper.EnsemblVariantMapper class method) (gwas_norm.variants.mapper.ScanVcfVariantMapper static method) (gwas_norm.variants.mapper.TabixVcfVariantMapper class method) get_minimal_alleles() (gwas_norm.variants.norm.RefNorm static method) get_no_data_mapping() (gwas_norm.variants.mapper.BaseMapper class method) (gwas_norm.variants.resolvers.BaseResolver class method) get_norm_assembly_name() (gwas_norm.config.GwasNormConfig method) get_old_analysis_id() (in module gwas_norm.common), [1] get_open_method() (in module gwas_norm.common), [1] get_ref_assembly() (gwas_norm.config.GwasNormConfig method) get_ref_end_pos() (in module gwas_norm.utils.genome_chunks) get_source_join_key() (gwas_norm.variants.mapper.ScanVcfVariantMapper method) get_study_by_name() (gwas_norm.metadata.gwas_data.GwasData method) get_tmp_file() (in module gwas_norm.common), [1] get_uni_id() (in module gwas_norm.variants.common) gwas_norm.common module, [1] gwas_norm.config module gwas_norm.metadata.analysis module gwas_norm.metadata.cohort module gwas_norm.metadata.column module gwas_norm.metadata.file module gwas_norm.metadata.gwas_data module gwas_norm.metadata.info module gwas_norm.metadata.phenotype module gwas_norm.metadata.study module gwas_norm.metadata.test module gwas_norm.utils.genome_chunks module gwas_norm.variants.common module gwas_norm.variants.constants module gwas_norm.variants.mapper module gwas_norm.variants.norm module gwas_norm.variants.resolvers module gwas_norm.variants.vcf_info module GwasData (class in gwas_norm.metadata.gwas_data) GwasFile (class in gwas_norm.metadata.file) GwasNormConfig (class in gwas_norm.config) H has_caveat (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.analysis.KeyAnalysis property) has_header (gwas_norm.metadata.file.GwasFile property) HAS_HEADER_TAG (gwas_norm.metadata.file.GwasFile attribute) has_phenotype (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.analysis.KeyAnalysis property) has_test() (gwas_norm.metadata.analysis.AnalysisFile method) (gwas_norm.metadata.analysis.KeyAnalysis method) header (gwas_norm.metadata.file.GwasFile property) (gwas_norm.variants.mapper.ScanVcfVariantMapper property) header_is_known (gwas_norm.metadata.file.GwasFile property) HIER_AAF (gwas_norm.variants.resolvers.PopulationResolver attribute) I id (gwas_norm.variants.vcf_info.So attribute) ID (in module gwas_norm.variants.constants), [1] impact (gwas_norm.variants.vcf_info.So attribute) impute_alt_allele() (gwas_norm.variants.resolvers.BaseResolver method) (gwas_norm.variants.resolvers.EnsemblResolver method) (gwas_norm.variants.resolvers.MappingFileResolver method) INCOMPLETE_TERMINAL_CODON (in module gwas_norm.variants.vcf_info) index() (gwas_norm.metadata.test.Test.TestResult method) Info (class in gwas_norm.metadata.info) info (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.analysis.KeyAnalysis property) (gwas_norm.metadata.column.Column property) (gwas_norm.metadata.column.MappingColumn property) (gwas_norm.metadata.file.GwasFile property) (gwas_norm.metadata.phenotype.Definition property) (gwas_norm.metadata.study.Study property) (gwas_norm.metadata.study.StudyFile property) INFO_ATTRIBUTE (gwas_norm.metadata.column.Column attribute) (gwas_norm.metadata.column.MappingColumn attribute) (gwas_norm.metadata.file.GwasFile attribute) (gwas_norm.metadata.phenotype.Definition attribute) info_columns (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.analysis.KeyAnalysis property) (gwas_norm.metadata.file.GwasFile property) info_defs (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.analysis.KeyAnalysis property) (gwas_norm.metadata.phenotype.Caveat property) (gwas_norm.metadata.phenotype.Phenotype property) INFRAME_DEL (in module gwas_norm.variants.vcf_info) INFRAME_INS (in module gwas_norm.variants.vcf_info) init_file_attr() (gwas_norm.metadata.analysis.AnalysisFile method) (gwas_norm.metadata.file.FileHolderMixin method) (gwas_norm.metadata.study.StudyFile method) init_info_values() (gwas_norm.metadata.column.Column method) (gwas_norm.metadata.column.MappingColumn method) (gwas_norm.metadata.phenotype.Definition method) init_mapping_file() (gwas_norm.variants.mapper.ScanVcfVariantMapper method) init_source_file() (gwas_norm.variants.mapper.ScanVcfVariantMapper method) INSERTION (in module gwas_norm.variants.constants) int (gwas_norm.variants.vcf_info.ClinVarOri attribute) (gwas_norm.variants.vcf_info.ClinVarSig attribute) INTERGENIC (in module gwas_norm.variants.vcf_info) INTRON (in module gwas_norm.variants.vcf_info) invalidate() (gwas_norm.metadata.analysis.AnalysisFile method) (gwas_norm.metadata.analysis.KeyAnalysis method) (gwas_norm.metadata.file.GwasFile method) (gwas_norm.metadata.study.Study method) (gwas_norm.metadata.study.StudyFile method) invalidate_analyses() (gwas_norm.metadata.study.Study method) (gwas_norm.metadata.study.StudyFile method) is_checked (gwas_norm.metadata.file.GwasFile property) IS_PALINDROMIC (in module gwas_norm.variants.constants) is_validated (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.analysis.KeyAnalysis property) (gwas_norm.metadata.file.GwasFile property) (gwas_norm.metadata.study.Study property) (gwas_norm.metadata.study.StudyFile property) K key_name (gwas_norm.variants.vcf_info.CaddKeys attribute) (gwas_norm.variants.vcf_info.ClinVarKeys attribute) (gwas_norm.variants.vcf_info.VepKeys attribute) KEY_TAG (gwas_norm.metadata.analysis.KeyAnalysis attribute) KeyAnalysis (class in gwas_norm.metadata.analysis) keys (gwas_norm.metadata.analysis.KeyAnalysis property) (gwas_norm.metadata.file.GwasFile property) KEYS_TAG (gwas_norm.metadata.file.GwasFile attribute) L ld_pops (gwas_norm.metadata.cohort.CaseControlPopulation property) (gwas_norm.metadata.cohort.Population property) (gwas_norm.metadata.cohort.SamplePopulation property) LdReference (class in gwas_norm.metadata.cohort) list_populations() (gwas_norm.variants.resolvers.EnsemblResolver method) (gwas_norm.variants.resolvers.MappingFileResolver method) (gwas_norm.variants.resolvers.PopulationResolver method) LOG10_PVALUE_DELTA (gwas_norm.metadata.test.Test attribute) M main() (in module gwas_norm.variants.constants) map_bits (gwas_norm.variants.constants.MappingResult attribute) map_data_frame() (in module gwas_norm.variants.mapper) map_row (gwas_norm.variants.constants.MappingResult attribute) map_to (gwas_norm.metadata.column.Column property) (gwas_norm.metadata.column.MappingColumn property) (gwas_norm.metadata.phenotype.Definition property) MAP_TO_ATTRIBUTE (gwas_norm.metadata.column.Column attribute) (gwas_norm.metadata.column.MappingColumn attribute) (gwas_norm.metadata.file.GwasFile attribute) (gwas_norm.metadata.phenotype.Definition attribute) map_variant() (gwas_norm.variants.mapper.BaseMapper method) (gwas_norm.variants.mapper.EnsemblVariantMapper method) (gwas_norm.variants.mapper.ScanVcfVariantMapper method) (gwas_norm.variants.mapper.TabixVcfVariantMapper method) MapCoord (class in gwas_norm.variants.constants) mapping_coords (gwas_norm.variants.constants.MappingResult attribute) mapping_correct() (gwas_norm.variants.mapper.ScanVcfVariantMapper class method) MAPPING_DECODE (in module gwas_norm.variants.constants) MAPPING_DECODE_STR (in module gwas_norm.variants.constants) MAPPING_FILE_SECTION (in module gwas_norm.config) MAPPING_FILE_TYPE (gwas_norm.variants.mapper.ScanVcfVariantMapper attribute) MappingColumn (class in gwas_norm.metadata.column) MappingFileResolver (class in gwas_norm.variants.resolvers) MappingFlag (class in gwas_norm.variants.constants) MappingResult (class in gwas_norm.variants.constants) MATURE_MIRNA (in module gwas_norm.variants.vcf_info) md5_chksum (gwas_norm.metadata.file.GwasFile property) md5_file() (in module gwas_norm.common), [1] MD5_TAG (gwas_norm.metadata.file.GwasFile attribute) MEAN_AAF (gwas_norm.variants.resolvers.PopulationResolver attribute) merge_cadd_files() (in module gwas_norm.variants.downloads.merge_cadd) merge_count_files() (in module gwas_norm.variants.downloads.merge_counts) METADATA_SUMMARY_ROW_HEADER (gwas_norm.variants.resolvers.BaseResolver attribute) (gwas_norm.variants.resolvers.EnsemblResolver attribute) (gwas_norm.variants.resolvers.MappingFileResolver attribute) (gwas_norm.variants.resolvers.PopulationResolver attribute) metafile_abspath (gwas_norm.metadata.study.Study property) (gwas_norm.metadata.study.StudyFile property) METAFILE_TAG (gwas_norm.metadata.study.Study attribute) (gwas_norm.metadata.study.StudyFile attribute) metafiles (gwas_norm.metadata.study.Study property) (gwas_norm.metadata.study.StudyFile property) MIN_ALT_IMPUTE_EVIDENCE (gwas_norm.variants.resolvers.BaseResolver attribute) MISSENSE (in module gwas_norm.variants.vcf_info) module gwas_norm.common, [1] gwas_norm.config gwas_norm.metadata.analysis gwas_norm.metadata.cohort gwas_norm.metadata.column gwas_norm.metadata.file gwas_norm.metadata.gwas_data gwas_norm.metadata.info gwas_norm.metadata.phenotype gwas_norm.metadata.study gwas_norm.metadata.test gwas_norm.utils.genome_chunks gwas_norm.variants.common gwas_norm.variants.constants gwas_norm.variants.mapper gwas_norm.variants.norm gwas_norm.variants.resolvers gwas_norm.variants.vcf_info Msg (class in gwas_norm.common), [1] msg_args() (gwas_norm.common.Msg method), [1] msg_prog() (gwas_norm.common.Msg method), [1] N n_analyses (gwas_norm.metadata.gwas_data.GwasData property) n_cases (gwas_norm.metadata.cohort.CaseControlCohort property) (gwas_norm.metadata.cohort.CaseControlMixin property) (gwas_norm.metadata.cohort.CaseControlPopulation property) N_CASES_TAG (gwas_norm.metadata.cohort.CaseControlCohort attribute) (gwas_norm.metadata.cohort.CaseControlMixin attribute) (gwas_norm.metadata.cohort.CaseControlPopulation attribute) n_controls (gwas_norm.metadata.cohort.CaseControlCohort property) (gwas_norm.metadata.cohort.CaseControlMixin property) (gwas_norm.metadata.cohort.CaseControlPopulation property) N_CONTROLS_TAG (gwas_norm.metadata.cohort.CaseControlCohort attribute) (gwas_norm.metadata.cohort.CaseControlMixin attribute) (gwas_norm.metadata.cohort.CaseControlPopulation attribute) n_file_holders() (gwas_norm.metadata.study.Study method) (gwas_norm.metadata.study.StudyFile method) n_files (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.file.FileHolderMixin property) (gwas_norm.metadata.study.StudyFile property) n_samples (gwas_norm.metadata.cohort.CaseControlCohort property) (gwas_norm.metadata.cohort.CaseControlMixin property) (gwas_norm.metadata.cohort.CaseControlPopulation property) (gwas_norm.metadata.cohort.Cohort property) (gwas_norm.metadata.cohort.SampleCohort property) (gwas_norm.metadata.cohort.SamplePopulation property) (gwas_norm.metadata.cohort.SampleSizeMixin property) N_SAMPLES_TAG (gwas_norm.metadata.cohort.SampleCohort attribute) (gwas_norm.metadata.cohort.SamplePopulation attribute) (gwas_norm.metadata.cohort.SampleSizeMixin attribute) n_studies (gwas_norm.metadata.gwas_data.GwasData property) n_tests (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.analysis.KeyAnalysis property) name (gwas_norm.config.GwasNormConfig property) (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.analysis.KeyAnalysis property) (gwas_norm.metadata.cohort.CaseControlCohort property) (gwas_norm.metadata.cohort.Cohort property) (gwas_norm.metadata.cohort.FreqReference property) (gwas_norm.metadata.cohort.LdReference property) (gwas_norm.metadata.cohort.SampleCohort property) (gwas_norm.metadata.column.Column property) (gwas_norm.metadata.column.MappingColumn property) (gwas_norm.metadata.study.Study property) (gwas_norm.metadata.study.StudyFile property) (gwas_norm.variants.constants.Column attribute) (gwas_norm.variants.constants.DataSet attribute) (gwas_norm.variants.constants.MappingFlag attribute) (gwas_norm.variants.vcf_info.ClinVarOri attribute) (gwas_norm.variants.vcf_info.ClinVarSig attribute) (gwas_norm.variants.vcf_info.So attribute) NAME_TAG (gwas_norm.metadata.cohort.CaseControlCohort attribute) (gwas_norm.metadata.cohort.CaseControlPopulation attribute) (gwas_norm.metadata.cohort.Cohort attribute) (gwas_norm.metadata.cohort.FreqReference attribute) (gwas_norm.metadata.cohort.LdReference attribute) (gwas_norm.metadata.cohort.Population attribute) (gwas_norm.metadata.cohort.SampleCohort attribute) (gwas_norm.metadata.cohort.SamplePopulation attribute) NC_TRANS (in module gwas_norm.variants.vcf_info) NC_TRANS_EXON (in module gwas_norm.variants.vcf_info) NMD_TRANS (in module gwas_norm.variants.vcf_info) NO_DATA (in module gwas_norm.variants.constants) norm_name() (in module gwas_norm.common), [1] normalise_alleles() (gwas_norm.variants.norm.RefNorm method) normalise_multi_alleles() (gwas_norm.variants.norm.RefNorm method) NORMALISED (in module gwas_norm.variants.constants) normaliser (gwas_norm.metadata.file.GwasFile property) nsites (gwas_norm.variants.constants.MappingResult attribute) O observed_value (gwas_norm.metadata.test.Test.TestResult attribute) on_file_added() (gwas_norm.metadata.analysis.AnalysisFile method) (gwas_norm.metadata.study.StudyFile method) on_files_removed() (gwas_norm.metadata.study.StudyFile method) open() (gwas_norm.variants.mapper.BaseMapper method) (gwas_norm.variants.mapper.ScanVcfVariantMapper method) (gwas_norm.variants.mapper.TabixVcfVariantMapper method) (gwas_norm.variants.mapper.VcfIterator method) (gwas_norm.variants.norm.EnsemblRefNorm method) (gwas_norm.variants.norm.RefNorm method) Or (class in gwas_norm.metadata.phenotype) order_mappings() (gwas_norm.variants.mapper.BaseMapper class method) OTHER_ALLELE_TAG (gwas_norm.metadata.test.Test attribute) output_sorted (gwas_norm.variants.mapper.ScanVcfVariantMapper property) P parent (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.analysis.KeyAnalysis property) (gwas_norm.metadata.study.Study property) (gwas_norm.metadata.study.StudyFile property) parse_alfa_vcf() (in module gwas_norm.variants.downloads.format_alfa) parse_bool() (in module gwas_norm.common), [1] parse_caveats() (gwas_norm.metadata.analysis.AnalysisFile class method) (gwas_norm.metadata.analysis.KeyAnalysis class method) parse_chrpos_spec_str() (in module gwas_norm.common), [1] parse_clinvar() (in module gwas_norm.variants.vcf_info) parse_clinvar_dbs() (in module gwas_norm.variants.vcf_info) parse_clinvar_delim() (in module gwas_norm.variants.vcf_info) parse_clinvar_disease_db() (in module gwas_norm.variants.vcf_info) parse_clinvar_origin() (in module gwas_norm.variants.vcf_info) parse_clinvar_significance() (in module gwas_norm.variants.vcf_info) parse_clinvar_var_id() (in module gwas_norm.variants.vcf_info) parse_dbsnp_vcf() (in module gwas_norm.variants.downloads.format_dbsnp) parse_files() (gwas_norm.metadata.analysis.AnalysisFile class method) (gwas_norm.metadata.file.FileHolderMixin class method) (gwas_norm.metadata.study.StudyFile class method) parse_float() (in module gwas_norm.variants.vcf_info) parse_info_data() (gwas_norm.metadata.analysis.AnalysisFile class method) (gwas_norm.metadata.analysis.KeyAnalysis class method) parse_none() (in module gwas_norm.variants.vcf_info) parse_phenotypes() (gwas_norm.metadata.analysis.AnalysisFile class method) (gwas_norm.metadata.analysis.KeyAnalysis class method) parse_return() (in module gwas_norm.variants.vcf_info) parse_snpstats() (in module gwas_norm.variants.downloads.format_snpstats) parse_tests() (gwas_norm.metadata.analysis.AnalysisFile class method) (gwas_norm.metadata.analysis.KeyAnalysis class method) parse_vep_consequence() (in module gwas_norm.variants.vcf_info) parse_xml() (gwas_norm.metadata.analysis.AnalysisFile class method) (gwas_norm.metadata.cohort.CaseControlCohort class method) (gwas_norm.metadata.cohort.CaseControlMixin class method) (gwas_norm.metadata.cohort.CaseControlPopulation class method) (gwas_norm.metadata.cohort.SampleCohort class method) (gwas_norm.metadata.cohort.SamplePopulation class method) (gwas_norm.metadata.cohort.SampleSizeMixin class method) (gwas_norm.metadata.file.FileHolderMixin class method) (gwas_norm.metadata.phenotype.And class method) (gwas_norm.metadata.phenotype.Or class method) (gwas_norm.metadata.study.StudyFile class method) parser (gwas_norm.variants.vcf_info.CaddKeys attribute) (gwas_norm.variants.vcf_info.ClinVarKeys attribute) (gwas_norm.variants.vcf_info.VepKeys attribute) PARTIAL_ALLELE_MATCH (in module gwas_norm.variants.constants), [1] passthrough() (in module gwas_norm.common), [1] Phenotype (class in gwas_norm.metadata.phenotype) phenotype (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.analysis.KeyAnalysis property) POLYPHEN (in module gwas_norm.variants.vcf_info) POP_START_IDX (in module gwas_norm.variants.constants) pops (gwas_norm.metadata.cohort.CaseControlCohort property) (gwas_norm.metadata.cohort.Cohort property) (gwas_norm.metadata.cohort.FreqReference property) (gwas_norm.metadata.cohort.LdReference property) (gwas_norm.metadata.cohort.SampleCohort property) Population (class in gwas_norm.metadata.cohort) PopulationResolver (class in gwas_norm.variants.resolvers) private (gwas_norm.metadata.study.Study property) (gwas_norm.metadata.study.StudyFile property) PRIVATE_ATTRIBUTE (gwas_norm.metadata.study.Study attribute) (gwas_norm.metadata.study.StudyFile attribute) PROPORTION_TYPE (gwas_norm.metadata.cohort.CaseControlCohort attribute) (gwas_norm.metadata.cohort.CaseControlMixin attribute) (gwas_norm.metadata.cohort.CaseControlPopulation attribute) (gwas_norm.metadata.cohort.SampleCohort attribute) (gwas_norm.metadata.cohort.SamplePopulation attribute) (gwas_norm.metadata.cohort.SampleSizeMixin attribute) PROT_ALTERING (in module gwas_norm.variants.vcf_info) pubmed_id (gwas_norm.metadata.study.Study property) (gwas_norm.metadata.study.StudyFile property) PUBMED_ID_TAG (gwas_norm.metadata.study.Study attribute) (gwas_norm.metadata.study.StudyFile attribute) PVALUE_LOGGED_TAG (gwas_norm.metadata.file.GwasFile attribute) (gwas_norm.metadata.test.Test attribute) PVALUE_TAG (gwas_norm.metadata.test.Test attribute) Q query_allele_freq() (gwas_norm.variants.resolvers.EnsemblResolver method) query_region() (gwas_norm.variants.mapper.EnsemblVariantMapper method) quick_match() (gwas_norm.variants.mapper.BaseMapper class method) R rank (gwas_norm.variants.vcf_info.ClinVarSig attribute) (gwas_norm.variants.vcf_info.So attribute) read() (gwas_norm.metadata.gwas_data.GwasData method) REAL_TYPE (gwas_norm.metadata.cohort.CaseControlCohort attribute) (gwas_norm.metadata.cohort.CaseControlMixin attribute) (gwas_norm.metadata.cohort.CaseControlPopulation attribute) (gwas_norm.metadata.cohort.SampleCohort attribute) (gwas_norm.metadata.cohort.SamplePopulation attribute) (gwas_norm.metadata.cohort.SampleSizeMixin attribute) REF (in module gwas_norm.variants.constants), [1] ref_allele (gwas_norm.variants.constants.MapCoord attribute) ref_assembly_match() (gwas_norm.variants.norm.RefNorm method) REF_FLIP (in module gwas_norm.variants.constants), [1] REF_POP_TAG (gwas_norm.metadata.cohort.FreqReference attribute) (gwas_norm.metadata.cohort.LdReference attribute) reference_string (gwas_norm.metadata.phenotype.And property) (gwas_norm.metadata.phenotype.Caveat property) (gwas_norm.metadata.phenotype.Definition property) (gwas_norm.metadata.phenotype.Or property) (gwas_norm.metadata.phenotype.Phenotype property) (gwas_norm.metadata.phenotype.Synonym property) REFERENCE_STRING_TAG (gwas_norm.metadata.phenotype.Caveat attribute) (gwas_norm.metadata.phenotype.Phenotype attribute) RefNorm (class in gwas_norm.variants.norm) refpops (gwas_norm.metadata.cohort.FreqReference property) (gwas_norm.metadata.cohort.LdReference property) refresh_analysis_data() (gwas_norm.metadata.study.Study method) (gwas_norm.metadata.study.StudyFile method) REG_REGION (in module gwas_norm.variants.vcf_info) REG_REGION_ABLATION (in module gwas_norm.variants.vcf_info) REG_REGION_AMP (in module gwas_norm.variants.vcf_info) relative_path (gwas_norm.metadata.file.GwasFile property) RELATIVE_PATH_TAG (gwas_norm.metadata.file.GwasFile attribute) remove_analysis() (gwas_norm.metadata.study.Study method) (gwas_norm.metadata.study.StudyFile method) remove_column() (gwas_norm.metadata.info.Info method) remove_definition() (gwas_norm.metadata.info.Info method) remove_files() (gwas_norm.metadata.analysis.AnalysisFile method) (gwas_norm.metadata.file.FileHolderMixin method) (gwas_norm.metadata.study.StudyFile method) remove_freq_pop() (gwas_norm.metadata.cohort.CaseControlPopulation method) (gwas_norm.metadata.cohort.Population method) (gwas_norm.metadata.cohort.SamplePopulation method) remove_ld_pop() (gwas_norm.metadata.cohort.CaseControlPopulation method) (gwas_norm.metadata.cohort.Population method) (gwas_norm.metadata.cohort.SamplePopulation method) remove_pop() (gwas_norm.metadata.cohort.FreqReference method) (gwas_norm.metadata.cohort.LdReference method) remove_study() (gwas_norm.metadata.gwas_data.GwasData method) repr_attr_str() (gwas_norm.metadata.analysis.AnalysisFile method) (gwas_norm.metadata.analysis.KeyAnalysis method) (gwas_norm.metadata.study.Study method) (gwas_norm.metadata.study.StudyFile method) reset_freq_pops() (gwas_norm.metadata.cohort.CaseControlPopulation method) (gwas_norm.metadata.cohort.Population method) (gwas_norm.metadata.cohort.SamplePopulation method) reset_ld_pops() (gwas_norm.metadata.cohort.CaseControlPopulation method) (gwas_norm.metadata.cohort.Population method) (gwas_norm.metadata.cohort.SamplePopulation method) reset_pops() (gwas_norm.metadata.cohort.FreqReference method) (gwas_norm.metadata.cohort.LdReference method) reset_seen_values() (gwas_norm.metadata.cohort.CaseControlCohort method) (gwas_norm.metadata.cohort.CaseControlMixin method) (gwas_norm.metadata.cohort.CaseControlPopulation method) (gwas_norm.metadata.cohort.SampleCohort method) (gwas_norm.metadata.cohort.SamplePopulation method) (gwas_norm.metadata.cohort.SampleSizeMixin method) resolve_poor_mapping() (gwas_norm.variants.resolvers.BaseResolver method) (gwas_norm.variants.resolvers.EnsemblResolver method) resolver (gwas_norm.variants.constants.MappingResult attribute) (gwas_norm.variants.mapper.BaseMapper property) return_none() (in module gwas_norm.variants.mapper) reverse_complement() (in module gwas_norm.variants.mapper) root_norm_dir (gwas_norm.metadata.gwas_data.GwasData property) root_source_dir (gwas_norm.metadata.gwas_data.GwasData property) ROOT_TAG (gwas_norm.metadata.analysis.AnalysisFile attribute) (gwas_norm.metadata.analysis.KeyAnalysis attribute) (gwas_norm.metadata.cohort.CaseControlCohort attribute) (gwas_norm.metadata.cohort.CaseControlPopulation attribute) (gwas_norm.metadata.cohort.Cohort attribute) (gwas_norm.metadata.cohort.FreqReference attribute) (gwas_norm.metadata.cohort.LdReference attribute) (gwas_norm.metadata.cohort.Population attribute) (gwas_norm.metadata.cohort.SampleCohort attribute) (gwas_norm.metadata.cohort.SamplePopulation attribute) (gwas_norm.metadata.column.Column attribute) (gwas_norm.metadata.column.MappingColumn attribute) (gwas_norm.metadata.file.GwasFile attribute) (gwas_norm.metadata.gwas_data.GwasData attribute) (gwas_norm.metadata.info.Info attribute) (gwas_norm.metadata.phenotype.And attribute) (gwas_norm.metadata.phenotype.Caveat attribute) (gwas_norm.metadata.phenotype.Definition attribute) (gwas_norm.metadata.phenotype.Or attribute) (gwas_norm.metadata.phenotype.Phenotype attribute) (gwas_norm.metadata.phenotype.Synonym attribute) (gwas_norm.metadata.study.Study attribute) (gwas_norm.metadata.study.StudyFile attribute) (gwas_norm.metadata.test.Test attribute) RS_REGEX (in module gwas_norm.variants.constants) RS_STR (in module gwas_norm.variants.constants) S safe_move() (in module gwas_norm.common), [1] SampleCohort (class in gwas_norm.metadata.cohort) SamplePopulation (class in gwas_norm.metadata.cohort) SampleSizeMixin (class in gwas_norm.metadata.cohort) ScanVcfVariantMapper (class in gwas_norm.variants.mapper) search_assembly() (gwas_norm.variants.norm.EnsemblRefNorm method) (gwas_norm.variants.norm.RefNorm method) SequenceError set_attributes() (gwas_norm.metadata.column.Column method) (gwas_norm.metadata.column.MappingColumn method) (gwas_norm.metadata.phenotype.Definition method) set_file() (gwas_norm.common.Msg method), [1] set_header() (gwas_norm.metadata.file.GwasFile method) set_verbose() (gwas_norm.common.Msg method), [1] SIFT (in module gwas_norm.variants.vcf_info) skip_vcf_header() (in module gwas_norm.variants.common) skiplines (gwas_norm.metadata.file.GwasFile property) SKIPLINES_TAG (gwas_norm.metadata.file.GwasFile attribute) So (class in gwas_norm.variants.vcf_info) sort_buffer() (gwas_norm.variants.mapper.ScanVcfVariantMapper method) sort_map() (gwas_norm.variants.mapper.BaseMapper static method) (gwas_norm.variants.resolvers.BaseResolver static method) source (gwas_norm.variants.mapper.ScanVcfVariantMapper property) source_coords (gwas_norm.variants.constants.MappingResult attribute) source_genome_assembly (gwas_norm.metadata.study.Study property) (gwas_norm.metadata.study.StudyFile property) SOURCE_GENOME_ASSEMLY_TAG (gwas_norm.metadata.study.Study attribute) (gwas_norm.metadata.study.StudyFile attribute) source_row (gwas_norm.variants.constants.MappingResult attribute) spec_columns (gwas_norm.common.ChrPosSpec attribute), [1] SPLICE_ACCEPTOR (in module gwas_norm.variants.vcf_info) SPLICE_DONOR (in module gwas_norm.variants.vcf_info) SPLICE_DONOR_FIFTH_BASE (in module gwas_norm.variants.vcf_info) SPLICE_DONOR_REGION (in module gwas_norm.variants.vcf_info) SPLICE_POLYPRIM_TRACT (in module gwas_norm.variants.vcf_info) SPLICE_REGION (in module gwas_norm.variants.vcf_info) split_alt() (in module gwas_norm.variants.common) split_alts() (in module gwas_norm.variants.mapper) split_mapping_file() (in module gwas_norm.variants.downloads.split_mapping) STANDARD_ERROR_DELTA (gwas_norm.metadata.test.Test attribute) STANDARD_ERROR_TAG (gwas_norm.metadata.test.Test attribute) START (in module gwas_norm.variants.constants), [1] start_anchor (gwas_norm.common.ChrPosSpec attribute), [1] START_LOST (in module gwas_norm.variants.vcf_info) start_pos (gwas_norm.variants.constants.MapCoord attribute) START_POS_TAG (gwas_norm.metadata.test.Test attribute) START_RETAINED (in module gwas_norm.variants.vcf_info) stdopen() (in module gwas_norm.common), [1] STOP_GAINED (in module gwas_norm.variants.vcf_info) STOP_LOST (in module gwas_norm.variants.vcf_info) STOP_RETAINED (in module gwas_norm.variants.vcf_info) strand (gwas_norm.variants.constants.MapCoord attribute) STRAND (in module gwas_norm.variants.constants), [1] STRAND_FLIP (in module gwas_norm.variants.constants), [1] studies (gwas_norm.metadata.gwas_data.GwasData property) Study (class in gwas_norm.metadata.study) study_id (gwas_norm.metadata.study.Study property) (gwas_norm.metadata.study.StudyFile property) STUDY_ID_TAG (gwas_norm.metadata.study.Study attribute) (gwas_norm.metadata.study.StudyFile attribute) study_name (gwas_norm.metadata.study.Study property) (gwas_norm.metadata.study.StudyFile property) STUDY_NAME_TAG (gwas_norm.metadata.study.Study attribute) (gwas_norm.metadata.study.StudyFile attribute) study_norm_absolute_dir (gwas_norm.metadata.study.Study property) (gwas_norm.metadata.study.StudyFile property) study_norm_dir (gwas_norm.metadata.study.Study property) (gwas_norm.metadata.study.StudyFile property) STUDY_NORM_DIR_TAG (gwas_norm.metadata.study.Study attribute) (gwas_norm.metadata.study.StudyFile attribute) study_source_absolute_dir (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.study.Study property) (gwas_norm.metadata.study.StudyFile property) study_source_dir (gwas_norm.metadata.study.Study property) (gwas_norm.metadata.study.StudyFile property) STUDY_SOURCE_DIR_TAG (gwas_norm.metadata.study.Study attribute) (gwas_norm.metadata.study.StudyFile attribute) StudyFile (class in gwas_norm.metadata.study) Synonym (class in gwas_norm.metadata.phenotype) SYNONYMOUS (in module gwas_norm.variants.vcf_info) synonyms (gwas_norm.metadata.phenotype.Synonym property) T TabixVcfVariantMapper (class in gwas_norm.variants.mapper) Test (class in gwas_norm.metadata.test) Test.TestResult (class in gwas_norm.metadata.test) test_chr_name() (gwas_norm.metadata.test.Test method) test_coords() (in module gwas_norm.variants.norm) test_effects() (gwas_norm.metadata.test.Test method) TEST_FAIL (gwas_norm.metadata.test.Test attribute) test_id (gwas_norm.metadata.test.Test.TestResult attribute) test_outcome (gwas_norm.metadata.test.Test.TestResult attribute) TEST_PASS (gwas_norm.metadata.test.Test attribute) test_pvalue() (gwas_norm.metadata.test.Test method) test_row() (gwas_norm.metadata.test.Test method) test_sort_order() (gwas_norm.variants.mapper.ScanVcfVariantMapper method) test_standard_error() (gwas_norm.metadata.test.Test method) test_start_pos() (gwas_norm.metadata.test.Test method) test_type (gwas_norm.metadata.test.Test.TestResult attribute) test_var_id() (gwas_norm.metadata.test.Test method) tests (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.analysis.KeyAnalysis property) TF_BINDING_SITE (in module gwas_norm.variants.vcf_info) TFBS_ABLATION (in module gwas_norm.variants.vcf_info) TFBS_AMP (in module gwas_norm.variants.vcf_info) THREE_PRIME_UTR (in module gwas_norm.variants.vcf_info) to_xml() (gwas_norm.metadata.analysis.AnalysisFile method) (gwas_norm.metadata.analysis.KeyAnalysis method) (gwas_norm.metadata.cohort.CaseControlCohort method) (gwas_norm.metadata.cohort.CaseControlPopulation method) (gwas_norm.metadata.cohort.Cohort method) (gwas_norm.metadata.cohort.FreqReference method) (gwas_norm.metadata.cohort.LdReference method) (gwas_norm.metadata.cohort.Population method) (gwas_norm.metadata.cohort.SampleCohort method) (gwas_norm.metadata.cohort.SamplePopulation method) (gwas_norm.metadata.column.Column method) (gwas_norm.metadata.column.MappingColumn method) (gwas_norm.metadata.file.GwasFile method) (gwas_norm.metadata.gwas_data.GwasData method) (gwas_norm.metadata.info.Info method) (gwas_norm.metadata.phenotype.And method) (gwas_norm.metadata.phenotype.Caveat method) (gwas_norm.metadata.phenotype.Definition method) (gwas_norm.metadata.phenotype.Or method) (gwas_norm.metadata.phenotype.Phenotype method) (gwas_norm.metadata.phenotype.Synonym method) (gwas_norm.metadata.study.Study method) (gwas_norm.metadata.study.StudyFile method) (gwas_norm.metadata.test.Test method) TRANS_ABLATION (in module gwas_norm.variants.vcf_info) TRANS_AMP (in module gwas_norm.variants.vcf_info) TYPE (gwas_norm.metadata.cohort.CaseControlCohort attribute) (gwas_norm.metadata.cohort.CaseControlMixin attribute) (gwas_norm.metadata.cohort.CaseControlPopulation attribute) (gwas_norm.metadata.cohort.Cohort attribute) (gwas_norm.metadata.cohort.Population attribute) (gwas_norm.metadata.cohort.SampleCohort attribute) (gwas_norm.metadata.cohort.SamplePopulation attribute) (gwas_norm.metadata.cohort.SampleSizeMixin attribute) U unbind() (gwas_norm.metadata.analysis.AnalysisFile method) (gwas_norm.metadata.analysis.KeyAnalysis method) (gwas_norm.metadata.file.GwasFile method) (gwas_norm.metadata.study.Study method) (gwas_norm.metadata.study.StudyFile method) UNDEF_TYPE (gwas_norm.metadata.phenotype.Definition attribute) units (gwas_norm.metadata.analysis.AnalysisFile property) (gwas_norm.metadata.file.FileHolderMixin property) (gwas_norm.metadata.study.StudyFile property) UNITS_TAG (gwas_norm.metadata.analysis.AnalysisFile attribute) (gwas_norm.metadata.file.FileHolderMixin attribute) (gwas_norm.metadata.study.StudyFile attribute) UNKNOWN_INDEL (in module gwas_norm.variants.constants) UPSTREAM (in module gwas_norm.variants.vcf_info) URL_TAG (gwas_norm.metadata.study.Study attribute) (gwas_norm.metadata.study.StudyFile attribute) V valid_ref() (gwas_norm.variants.norm.RefNorm method) validate() (gwas_norm.metadata.analysis.AnalysisFile method) (gwas_norm.metadata.analysis.KeyAnalysis method) (gwas_norm.metadata.file.GwasFile method) (gwas_norm.metadata.study.Study method) (gwas_norm.metadata.study.StudyFile method) validate_cadd_format() (gwas_norm.variants.resolvers.MappingFileResolver static method) validate_data_source() (gwas_norm.variants.resolvers.BaseResolver method) (gwas_norm.variants.resolvers.EnsemblResolver method) (gwas_norm.variants.resolvers.MappingFileResolver method) validate_header_format() (gwas_norm.variants.resolvers.MappingFileResolver static method) validate_header_metadata() (in module gwas_norm.variants.vcf_info) validate_population_kwarg() (gwas_norm.variants.resolvers.MappingFileResolver class method) (gwas_norm.variants.resolvers.PopulationResolver class method) validate_populations() (gwas_norm.variants.resolvers.EnsemblResolver method) (gwas_norm.variants.resolvers.MappingFileResolver method) validate_resolver() (gwas_norm.variants.mapper.BaseMapper method) (gwas_norm.variants.mapper.ScanVcfVariantMapper method) validate_vep_format() (gwas_norm.variants.resolvers.MappingFileResolver static method) VALUE_TAG (gwas_norm.metadata.analysis.KeyAnalysis attribute) value_type (gwas_norm.metadata.cohort.CaseControlCohort property) (gwas_norm.metadata.cohort.CaseControlMixin property) (gwas_norm.metadata.cohort.CaseControlPopulation property) (gwas_norm.metadata.cohort.SampleCohort property) (gwas_norm.metadata.cohort.SamplePopulation property) (gwas_norm.metadata.cohort.SampleSizeMixin property) var_id_match() (gwas_norm.variants.mapper.BaseMapper class method) VAR_ID_TAG (gwas_norm.metadata.test.Test attribute) variant_type() (in module gwas_norm.variants.mapper) VCF_FORMAT_IDX (in module gwas_norm.variants.constants) VCF_ID_IDX (in module gwas_norm.variants.constants) VCF_INFO_IDX (in module gwas_norm.variants.constants) VCF_MISSING (in module gwas_norm.variants.vcf_info) vcf_to_ensembl() (in module gwas_norm.variants.mapper) VcfIterator (class in gwas_norm.variants.mapper) VEP_INFO_FIELD (in module gwas_norm.variants.vcf_info) vep_info_parser() (in module gwas_norm.variants.vcf_info) VEP_KEY_LOOKUP (in module gwas_norm.variants.vcf_info) VEP_MAIN_DELIMITER (in module gwas_norm.variants.vcf_info) vep_name (gwas_norm.variants.vcf_info.VepKeys attribute) vep_worst_consequence() (in module gwas_norm.variants.vcf_info) VepKeys (class in gwas_norm.variants.vcf_info) W weight (gwas_norm.metadata.cohort.FreqReference property) (gwas_norm.metadata.cohort.LdReference property) WEIGHT_TAG (gwas_norm.metadata.cohort.FreqReference attribute) (gwas_norm.metadata.cohort.LdReference attribute) write() (gwas_norm.metadata.gwas_data.GwasData method)