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Created with Raphaël 2.2.03Apr2121Mar2019181287125Feb21191815141312118729Jan24151615141311104223Dec1918177614Nov13127626Oct2524221918171615126Sep252411754331Aug30282422201715139876331Jul25242320191810643229Jun28262522212019131211764111May98430Apr2725241913965329Mar272623191615141312852128Feb272623222120191615141312Merge remote-tracking branch 'origin/bugfix/e97_testdb_patches_master' into feature/stop_codon_readthrough_editPatch test databases for release 97, part 2Patch test databases for release 97, part 2ENSCORESW-3110- Code to handle stop codon readthrough in 12 transcripts. The code edits the amino acid sequence to display the stop codon readthrough with an XMerge pull request #371 from Ensembl/feature/rna-productsTranscriptAdaptor::fetch_by_rnaproduct_id(): do not return explicit undefChange the RNAProduct stable-ID prefix from ENSM to ENSStable.sql: Add stable_id_event.type enum extension to the docstringRNAProductAdaptor::fetch_all_by_external_name(): add some spaces, for readabilityTry to make some SQL statements more readableRNAProductAdaptor: reduce indentation of new_fast() callDocument the use of ## no critic in commentsAdd missing descriptions to RNAProduct.pm and MicroRNA.pmDocumentation of private methods is now in PODs rather than commentss/rnaproduct/RNAProduct/ in commentsGet rid of no-longer-needed FIXME notesAvoid using unless and the postfix form of ifConvert stray tabs to spacesExtend the copyright notice on new RNAProduct filessliceAdaptor.t: account for the new slice added by rnaproduct test dataPatch test databases for RNAPRoduct testsSchema updatesRNAPRoduct: exon supportRNAProductAdaptor: exon support in storingRNAProductAdaptor: exon support in retrievalrnaProduct.t: partial compliance with perlcritic level 2rnaproduct exon testsAnnual copyright updateRNAProductAdaptor: implement store() and remove()RNAProduct: implement synchronise_attributes()MicroRNA: having multiple mirna_arms in the DB is now fatalAttributeAdaptor: add store_on_RNAProduct() and remove_from_RNAProduct()RNAProduct: add store/remove tests + some cosmeticsRNAProduct test suite: use type mapper instead of hardcoded valuesRNAProduct test suite: use correct dbname for miRBase xrefsRNAProduct::get_all_Attributes(): do not throw when data unavailableRNAProduct: mark genomic_start() and genomic_end() stableRNAProductAdaptor: replace fetch_all_by_type_id() with fetch_all_by_type()Transcript: get_all_RNAProducts() now uses type codes instead of IDsRNAProduct: objects now hold type code rather than type ID