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Created with Raphaël 2.2.030Jun282724232221201716141310986532126May252423191817161312111098654328Apr262019181514131187131Mar30292824232221181615141110987432128Feb252423222118171615141098743131Jan28272620181413121110765423Dec2117161514131098765432130Nov292524232219181615121110985432better warning for projectionscheck if defined else lots of warning laterremoved use of DBD::mysql which is not needed and stopped other users without this installedUpdate assembly.accession in meta table to supplied -assembly_acc.make sure transcripts and exons are loaded before the are transformedDelete resource files from the current directory before generating new onesUpdated instructions for regenerating LinkOut filesInstructions on updating LinkOut files.added CADRE, AspGD, GeneDB and misc_EG::EG sources. updated TRNASCAN_SE and RNAMMER sources; Updated species config for most of all fungi speciesEnsemblGenomes module, similar to ncRNA_DBParser.pm to maintain xrefs even though there is no parser for them yetAdded RNAMMER and TRANSCAN_SE to the list of sources to move to the gene levelAdded RNAMMEr and TRANSCAN_SE to the list of sources for gene descriptions; added a method called set_source_id_to_external_nameartificial species counter to prevent warnings when making multiple db connectionsTest has been testing the wrong number. Changed test 18 to expect latest stable ID of 3.Need to check aliases but no warning if first timeUpdated patch identifiers in the meta tableUpdated patch identifiers in the meta table.Added reconnect_when_lost subroutinePing the db handle on prepare and do, if reconnect_when_lost is set to 1.Added method 'set_reconnect_when_lost'bug fix for uniprot genename having same display and accessionbug fix for uniprot genename having same display and accessionadd synoyms for dependentsbug fix for uniprot genename having same display and accessionRemoved temporary version of populate_production_db_tables.plDumping backup tables out to a file.Added a test for output directoryNew script for submitting density feature jobsChanges for submit_density_features.pl scriptChanged parameter names in density feature scriptsadded POD for fetch_Iterator_by_Sliceadded POD for fetch_Iterator_by_SliceTest for dependencies on Variation, Funcgen or Compara modules in Core modules.Updated to load GL accession as a synonym of the patch scaffold/supercontig.Added 1000genomes populations, minimumnumber of observations and also includes LRG transcriptsargument verbose was not dereferenced, don't know why it was working beforeUpdated store method to set stable id version to 1 if it's undefined.Updated store method to set stable id version to 1 if it's undefined.look for assembled and component overlapsUpdated store method to set stable id version to 1 if it's undefined.