EMBL parser (Kieron): getSequence getAccessions getDescription getKeywords getSpecies getClassification getRawID getRawAccessions getRawDescription getRawKeywords getRawDate getRawSpecies getRawClassification getRawReferences getRawFeatures getRawComments getRawAssemblyHeader getRawAssembly getRawContig -------------------------------------- TrackBased parser (Anne) - common metadata for the following formats: BED, PSL, WIG get_browser_switches get_metadata_value BED parser (Anne): get_raw_seqname get_seqname get_raw_start get_start get_raw_end get_end get_raw_name get_name get_raw_score get_score get_raw_strand get_strand get_raw_thickStart get_thickStart get_raw_thickEnd get_thickEnd get_raw_itemRgb get_itemRgb get_raw_blockCount get_blockCount get_raw_blockSizes get_blockSizes get_raw_blockStarts get_blockStarts PSL parser (Anne) get_raw_Matches get_matches get_raw_misMatches get_misMatches get_raw_repMatches get_repMatches get_raw_nCount get_nCount get_raw_qNumInsert get_qNumInsert get_raw_qBaseInsert get_qBaseInsert get_raw_tNumInsert get_tNumInsert get_raw_tBaseInsert get_tBaseInsert get_raw_strand get_strand get_raw_qName get_qName get_raw_qSize get_qSize get_raw_qStart get_qStart get_raw_qEnd get_qEnd get_raw_tName get_tName get_raw_tSize get_tSize get_raw_tStart get_tStart get_raw_tEnd get_tEnd get_raw_blockCount get_blockCount get_raw_blockSizes get_blockSizes get_raw_qStarts get_qStarts get_raw_tStarts get_tStarts WIG parser (Anne) Metadata: get_feature_count get_wiggle_type Fields: get_raw_chrom get_seqname get_raw_start get_start get_raw_end get_end get_raw_score get_score -------------------------------------- GVF parser (Laurent): get_metadata_key_list get_gvf_version get_genome_build get_sequence_region_list get_metadata_by_pragma get_raw_seqname get_seqname get_raw_source get_source get_raw_type get_type get_raw_start get_start get_raw_end get_end get_raw_score get_score get_raw_strand get_strand get_raw_phase get_phase get_raw_attributes get_attributes get_ID get_variant_seq get_reference_seq VCF parser (Laurent): get_metadata_key_list get_metadata_by_pragma get_vcf_version get_raw_seqname get_seqname get_raw_start get_start get_raw_end get_end get_outer_start get_inner_start get_inner_end get_outer_end get_raw_IDs get_IDs get_raw_reference get_reference get_raw_alternatives get_alternatives get_alternative_description get_raw_score get_score get_raw_filter_results get_filter_results get_raw_info get_info get_info_description get_raw_formats get_formats get_format_description get_metadata_description get_raw_individuals_info get_individuals_info get_individuals_genotypes --------------------------------- EMF parser (Miguel) get_sequences get_score_types tree format date get_next_column --------------------------------- BigBed Parser (Daniel) get_chrom get_start get_end get_score get_parts get_name get_rgb get_bedFeature BigWig Parser (Daniel) get_chrom get_start get_end get_score