variant_mapper API

• variant_mapper package
  • variant_mapper.mapper module
    • BaseMapper
      • BaseMapper.DNA_REGEXP
      • BaseMapper.best_mapping()
      • BaseMapper.check_ref_alleles()
      • BaseMapper.close()
      • BaseMapper.decode_mapping_flags()
      • BaseMapper.get_mapping_error()
      • BaseMapper.get_mapping_var_id()
      • BaseMapper.get_no_data_mapping()
      • BaseMapper.map_variant()
      • BaseMapper.open()
      • BaseMapper.order_mappings()
      • BaseMapper.quick_match()
      • BaseMapper.resolver
      • BaseMapper.sort_map()
      • BaseMapper.validate_genomic_coords()
      • BaseMapper.validate_resolver()
      • BaseMapper.var_id_match()
    • EnsemblVariantMapper
      • EnsemblVariantMapper.DNA_REGEXP
      • EnsemblVariantMapper.get_mapping_var_id()
      • EnsemblVariantMapper.map_variant()
      • EnsemblVariantMapper.query_region()
    • TabixVcfVariantMapper
      • TabixVcfVariantMapper.close()
      • TabixVcfVariantMapper.get_mapping_var_id()
      • TabixVcfVariantMapper.map_variant()
      • TabixVcfVariantMapper.open()
    • ScanVcfVariantMapper
      • ScanVcfVariantMapper.DNA_REGEX
      • ScanVcfVariantMapper.MAPPING_FILE_TYPE
      • ScanVcfVariantMapper.check_new_chr_name()
      • ScanVcfVariantMapper.check_norm()
      • ScanVcfVariantMapper.check_ref()
      • ScanVcfVariantMapper.close()
      • ScanVcfVariantMapper.extract_alt_allele()
      • ScanVcfVariantMapper.extract_nothing()
      • ScanVcfVariantMapper.extract_positive_strand()
      • ScanVcfVariantMapper.extract_strand()
      • ScanVcfVariantMapper.extract_var_id()
      • ScanVcfVariantMapper.get_buffer_sort_key()
      • ScanVcfVariantMapper.get_mapping_join_key()
      • ScanVcfVariantMapper.get_mapping_var_id()
      • ScanVcfVariantMapper.get_source_join_key()
      • ScanVcfVariantMapper.header
      • ScanVcfVariantMapper.init_mapping_file()
      • ScanVcfVariantMapper.init_source_file()
      • ScanVcfVariantMapper.map_variant()
      • ScanVcfVariantMapper.mapping_correct()
      • ScanVcfVariantMapper.open()
      • ScanVcfVariantMapper.output_sorted
      • ScanVcfVariantMapper.sort_buffer()
      • ScanVcfVariantMapper.source
      • ScanVcfVariantMapper.test_sort_order()
      • ScanVcfVariantMapper.validate_resolver()
    • VcfIterator
      • VcfIterator.close()
      • VcfIterator.open()
  • variant_mapper.resolvers module
    • BaseResolver
      • BaseResolver.DEFAULT_INTERNAL_DELIMITER
      • BaseResolver.METADATA_SUMMARY_ROW_HEADER
      • BaseResolver.MIN_ALT_IMPUTE_EVIDENCE
      • BaseResolver.extract_metadata()
      • BaseResolver.extract_summary_metadata_row()
      • BaseResolver.get_mapping_error()
      • BaseResolver.get_no_data_mapping()
      • BaseResolver.impute_alt_allele()
      • BaseResolver.resolve_poor_mapping()
      • BaseResolver.sort_map()
      • BaseResolver.validate_data_source()
    • PopulationResolver
      • PopulationResolver.ALLOWED_ALLELE_FREQ
      • PopulationResolver.HIER_AAF
      • PopulationResolver.MEAN_AAF
      • PopulationResolver.METADATA_SUMMARY_ROW_HEADER
      • PopulationResolver.extract_hierarchy_aaf_counts()
      • PopulationResolver.extract_hierarchy_aaf_freq()
      • PopulationResolver.extract_mean_aaf_counts()
      • PopulationResolver.extract_mean_aaf_freq()
      • PopulationResolver.extract_no_aaf()
      • PopulationResolver.list_populations()
      • PopulationResolver.validate_population_kwarg()
    • MappingFileResolver
      • MappingFileResolver.METADATA_SUMMARY_ROW_HEADER
      • MappingFileResolver.extract_cadd()
      • MappingFileResolver.extract_datasets()
      • MappingFileResolver.extract_id()
      • MappingFileResolver.extract_metadata()
      • MappingFileResolver.extract_pops()
      • MappingFileResolver.extract_summary_metadata_row()
      • MappingFileResolver.extract_vep()
      • MappingFileResolver.impute_alt_allele()
      • MappingFileResolver.list_populations()
      • MappingFileResolver.validate_cadd_format()
      • MappingFileResolver.validate_data_source()
      • MappingFileResolver.validate_header_format()
      • MappingFileResolver.validate_population_kwarg()
      • MappingFileResolver.validate_populations()
      • MappingFileResolver.validate_vep_format()
    • EnsemblResolver
      • EnsemblResolver.METADATA_SUMMARY_ROW_HEADER
      • EnsemblResolver.cache
      • EnsemblResolver.extract_metadata()
      • EnsemblResolver.extract_summary_metadata_row()
      • EnsemblResolver.get_alt_allele_freq()
      • EnsemblResolver.impute_alt_allele()
      • EnsemblResolver.list_populations()
      • EnsemblResolver.query_allele_freq()
      • EnsemblResolver.resolve_poor_mapping()
      • EnsemblResolver.validate_data_source()
      • EnsemblResolver.validate_populations()
  • variant_mapper.norm module
    • RefNorm
      • RefNorm.cache_ref_assembly_match()
      • RefNorm.close()
      • RefNorm.get_minimal_alleles()
      • RefNorm.is_open
      • RefNorm.normalise_alleles()
      • RefNorm.normalise_multi_alleles()
      • RefNorm.open()
      • RefNorm.ref_assembly_match()
      • RefNorm.search_assembly()
      • RefNorm.valid_ref()
    • EnsemblRefNorm
      • EnsemblRefNorm.close()
      • EnsemblRefNorm.open()
      • EnsemblRefNorm.search_assembly()