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Created with Raphaël 2.2.07Oct6543230Sep29282726232221201615141312987652131Aug302625242322191817161512111098542129Jul28272625222120141312118654130Jun282724232221201716141310986532126May252423191817161312111098654328Apr262019181514131187131Mar30292824232221181615141110987432re-instated variation id dumpingadded release info for new refseq sourceschanged refseq_dna to refseq_mRNA and Refseq_ncRNADrop external_db_id from call to get_synonyms() as it is notIn map_stable_ids(): Only add mapping events if the stable ID hasadded another ignore sql statement for Uniprot/SPTREMBL priority_description protein_evidence_gt_3update ignore hashupdate ignore sql statement for EntrezGeneFixed ignore sql that was broken for ignoring entrezgene names if they came via refseq_predictedupdated ignore hashadded another ignore sql statement for Uniprot/SPTREMBL priority_description protein_evidence_gt_3added another ignore sql statement for Uniprot/SPTREMBL priority_description protein_evidence_gt_3parsing protein evidence codeAdded new source for Uniprot/SPTREMBL with protein evidence codes > 3added distinct to select_sth sql - we can have multiple rows with the same child parent and relation_id since adding INTERSECTION tagsBacking out stable_id merging changes until databases are patchedBacking out stable_id merging changes until databases are patchedBacking out stable_id merging changes until databases are patchedRemove options 'do_project_to_common_cs' and 'do_similarity_scoring'.Remove the options for turning off exonerate and for not doing theNo functional changes, apart from reporting the number of exons scoresIn slice_names():release_file is not mandatorytwo types of refseq now to differentiate betwen those mapped via sequence and those directlydie instead of croak to get stack traceset info type to UNMAPPEd for those unmappedCheck the result of the print and die if we have an error. Bits of flatfiles have been missing so hopefully these will now be caughtuncommented patch identifierstable_id merging changesstable_id merge changesThe synteny framework only needs 10 minutes, not 30.No functional changes.Mostly reformatting.Updated schema version to 65Moved the warning about the cache not being on back into the constructor & simplified the construction method for the cache. If someone doesn't inherit from this correctly they'll loose the warning but that is all.Ensembl core is now at v65. Patches to work with flat file handles in core like databases and supporting checksum derived xrefsStable_id table merged with main object tablestable_id table merged with main object tableStable_id table merged with main object tablefixed bug where class is not found and now uses the default one