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Created with Raphaël 2.2.01Oct30Sep27262523191817131211109653230Aug29272322201916151298765231Jul302926252423221918171615111043228Jun27262421201918171312111065331May302928232221171514131098732130Apr2927262423221918171615121110953227Mar26252221201918151211654128Feb27262522212019181514131211754130Jan29252422211716151410987421Dec20191714131211107Found more deprecated callsFixes for the alt alleles code. We needed to make sure we used the right variables in the code. Also needed to make sure an array is actually defined during constructionFixing an issue raised by vega and non-standard DBAdaptor group names. Vega use ensembl to denote the ensembl db. We assumed incorrectly that core could always be used. That would always fail the moment a different group name was usedSpecify memory requirements for dependent job [farm3].removed the deprecated callDeprecating a number of calls. Instead we want more API compatible callsMaking this script new alt allele compatibleadded test for fetch_all_by_feature_class methodAdd the missing configuration options for the production database.Add memory resources to job waiting for exonerate to finish. RequiredFarm3 seems to require memory resources on the job that waits on theUpdated for farm3 (unit for bsub's -M switch was changed for new farm).Making consistent through plants species the use of ncRNA_EG source for maintaining ncRNA genes xrefs asscoiated with logic_name ncrna_egadded species-specific refseq_dna and refseq_peptide sources where availableENSCORESW-660: added ChEMBL source as part of the Uniprot dependent xrefsENSCORESW-660: when looking for EMBL, make sure it is not ChEMBLadded more methods:ENSCORESW-677: test updated to include get_all_versions methodENSCORESW-677: added method get_all_versionsCCDS db (human, mouse) updated to 74Ontology db updated to 74ENSCORESW-677: added test for get_default_version methodENSCORESW-677: added method get_default_versionaccording to rules of coding, all these methods are stableupdated seq_region statsENSPROD-55: added GenomeContainer to list of available DBAdaptorsSchema patches and version update to metaSchema version update patch (73 -> 74)replaced snp with more generic short_variation callENSPROD-55: adding test module for genome containerENSPROD-55: removing AssemblyAdaptor, wrong object and should not have been thereMust take the SO terms into a new array as current impl assumed we used shift @_[ENSCORESW-664]. Adding support for multiple variation databases from the Slice object.fixing for the new output format lineWrong file name in header[ENSCORESW-675]. Adding methods for working with AltAlleleGroup members and attribs.Documentation changes worked out with Andyget the licence rightRemoved other unnecessary dependencies.Use SequenceOntologyMapper instead of BiotypeMapper to map features to SO terms.