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Created with Raphaël 2.2.029Apr232117151397231Mar27262524231917161211224Feb191716131211109230Jan2726232221161514131298723Dec191615121110985432128Nov2726252422201817141211430Oct2928272322211614131098762129Sep23221918109854129Aug2827262221201918151211107130Jul24222117151093230Jun26251918163230May292321191514228Apr2423221614987428Mar2524211914131110327Feb26252119181714131210765431Jan3029282724232221201817removed deprecated ExternalData modulesMerge pull request #65 from arnaudxk/masterUpdate xref_config.iniENSCORESW-1311: replace ExternalData modules with IO modulesMerge pull request #63 from thomasmaurel/masterMerge pull request #64 from james-monkeyshines/masterENSCORESW-1240: new go_xref entries should be linked to the newly created object_xref with best_ensembl_id, not old ensembl_idAllow 'special' attributes (e.g. Dbxref, Ontology_term) to be specified as a list and written as a single comma-separated valueENSCORESW-1303: logic_name should be lower caseENSCORESW-1193: is_empty should be 0 if there is datarelease/79 upst…release/79 upstream/release/79ENSCORESW-1193: is_empty should be 0 if there is dataIf an executable is wrong or missing from the PATH variable, the script won't attempt to find it using locate anymore. The locate command was sometime returning wrong executable locationENSCORESW-1300: gene names can have spaces, include in regexENSCORESW-1297: early exit if staging, livemirror or core is used when creating the xref databaseupdated config to latest release 80 databasesMerge branch 'master' of https://github.com/Ensembl/ensemblENSCORESW-1294: make sure we fetch the gene we want even if more genes are added to test dataMerge pull request #60 from ens-carlos/masterDelete from all alt-allele-related tables when deleting alt alleles.Merge branch 'experimental/fasterfasta'ENSCORESW-1287: meta keys should be identical between patch and main schema, check both waysMerge branch 'master' of https://github.com/Ensembl/ensemblENSCORESW-1289: add store method for karyotype bandsAllow zero length setting in FASTA to prevent any linefeeds but those required for validity. Limits tweaked.Fix bug with fetch_all_by_outward_search max_range check, and add defaults.Fix bug in fetch_nearest methods whereby one equal winner by distance could be missed out in certain circumstances.ignore object_xrefs that have either been selected for dumping or already dismissed by ProcessPriorities stepENSCORESW-1240: correctly process dependents of dependentsENSCORESW-1284: do not import gene level xrefs via Uniprot, as proteins can be sharedMerge branch 'experimental/cure_gtf'.Update test cases to accommodate shiny new test gene for gtf.Documentation+++Merge branch 'master' of https://github.com/Ensembl/ensemblDocumentation++Update Exon phase warning to include Exon stable ID where possible.Adjust treatment of stop codon detection to consider phase, rather than take three bases every time.assign different priorities for different sources for the same dataClean up debug, remove attempts to find shorter stop codons, as they are filtered out earlier. Also fix problem with no stop codon annotation leading to no start codon either.Patching test databases with the latest patch (genome_statistics.value from INT to BIGINT).add meta entries for new patches