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Created with Raphaël 2.2.027Jul2521201911875128Jun2423171614109732131May2524171611109654329Apr251913118531Mar232118161510225Feb2423191817161512429Jan2625222118151211875418Dec151411108432130Nov272625242320191817161211109228Oct272221201916151386124Sep23222117161514111098432127Aug2012111075432131Jul302827222120171614131076432126Jun2518171511103226May212019181387629Apr232117151397231Mar27262524231917161211224Feb191716131211109230Jan2726232221Tydied up the symlink creation codeAdded source_dir and target_dir parameters allowing copy of databases outside the MySQL default internal directory on Sanger machines /mysql/data_3306/databases/. When target_dir is specified, the script will automatically create a symlink from target_dir to /mysql/data_3306/databases/. This change will allow us to copy databases from and to the new ens-staging3 MySQL servermiRNA was meant to be mRNA, for protein coding transcriptRevert "Fix tests for change in Sequence Ontology"Merge branch 'master' of github.com:Ensembl/ensemblFix tests for change in Sequence OntologyMerge pull request #146 from muffato/compara_test_dbMerge branch 'master' of github.com:Ensembl/ensemblAdding correct Sequence Ontology term for protein_coding => mRNA, used for gff3 serializerensure otherf_dba knows its dna_dbChanging all ens-staging1/2 to ens-staging3, as we'll be using this new host for pipelines until the EBI shift overdatafix: a row was duplicatedAdded the SQLite schemaAdded ensembl-compara to the travis environment, but exclude it from CoverallsAdded tests for Slice::get_all_compara_DnaAlignFeatures()Added tests for Slice::get_all_compara_Syntenies()Added tests for Gene::get_all_homologous_Genes()Patch test database for 86ontology updated for release 86Update to release 86Remove protein_coding -> miRNA in Sequence Ontology Mapper, miRNA are not protein coding, so that's just wrongIt should be seq_region_start and seq_region_end for UTRs, since start/end now are relative to the feature, as with other feature typesIt should be seq_region_start and seq_region_end for UTRs, since start/end now are relative to the feature, as with other feature typesBecause of a fix of a very old bug in the mapper, some Exon features if they're made via a Slice have start() and end() relative to the feature. So in genomic2cdna calls we were using $self->start() and $self->end(), this means we were sometimes using incorrect coordinates. Change to seq_reion_start and seq_region_endENSCORESW-1834 - Fix source for source in summary_tp_hash for Transcript featuresMerge pull request #141 from muffato/masterCorrected annual Copyright updaterMerge pull request #142 from khowe/masterTweak to gene description filtersbugfix: get_all_DBAdaptors() should return an empty list if the species name (alias) does not existMerge pull request #139 from mn1/masterRemoved duplicate lineTrying to restore the copyright to what is on masterSupport for multi letter patchesMerge pull request #138 from Ensembl/ENSCORESW-1834- Fix how UTRs are created, they should be created with start/end relative to the feature, not in genomic coordinatesMerge pull request #137 from Ensembl/ENSCORESW-1834Changes to gtf serializer to deal with offset in codon and utr reginosUpdate xref_config.ini to use revised GO FTP site layoutadded one term to test database