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Created with Raphaël 2.2.017Sep131211109653230Aug29272322201916151298765231Jul302926252423221918171615111043228Jun27262421201918171312111065331May302928232221171514131098732130Apr2927262423221918171615121110953227Mar26252221201918151211654128Feb27262522212019181514131211754130Jan29252422211716151410987421Dec201917141312111076543230Nov2928[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.Added SO terms to be able to perform SequenceOntologyMapper tests.Updates to reflect changes in SequenceOntologyMapper interface.Modified the interface to match the SO part in BiotypeMapper.[ENSCORESW-672]. Creating a transcript_id idx on transcript_intron_supporting_evidence.Better test. Better is. Just betterMaking a note to never ever retire this bit of codeChanged check on method translate arguments, bits of documentation andUpdate to test condition to reflect changes in table Term of ontology test database.Tests for the public method translate.Added SO terms to be able to perform SequenceOntologyMapper tests.Constructor update to avoid warningreplaced 'NULL' string with \N where necessaryTest suite for Bio::EnsEMBL::Utils::SequenceOntologyMapper.Update POD descriptionBasic mapper from Ensembl feature object to sequence ontology term.Comment on file mode restrictions using dump_(embl|genbank)Debugged problem with writing EMBL/Genbank files when opened multiplemethod takes in more than one argument, replaced shift with @_Correction to schema_patcher.pl argumentsreplaced shift with @_ when more than one arguments are read in[ENSCORESW-667]. Return empty anonymous array in case _ise_array attribute is undefined.Tests for subroutines in the Bio::EnsEMBL::Utils::IO module.[ENSCORESW-658]. Added subroutine filter_dir to get the lexicographically sorted and filtered[ENSCORESW-634]. Memory efficient version for dumping Genbank format files.Debugged method dump_embl, wasn't seeking EOF after writing the sequence, hence[ENSCORESW-634]. Memory efficient version for writing EMBL format files.ENSCORESW-544: updated lookup methodENSCORESW-544: updated schema with added archive_id_lookupupdated test cases to check integrity of api once deprecated tables, columns and methods have been removedENSCORESW-554: API updates for release 74set of patches for release 74added test database regular expression to detect species stringallow more than one digit in the auto-incrementrevert changes for metacontainer supportcvs/release/ens…cvs/release/ensemblgenomes/20-73ENSCORESW-611: do not run Orphanet sources for human (ie no species)