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Created with Raphaël 2.2.04Apr3130Mar29282724232221201916151462129Feb282726242322212017161514131098762131Jan3025242319181716131211109654323Dec22212019141312987652130Nov292524232221181715121110987432131Oct2827262524212019181714131211107654Bad DDLWrong db usedUse taxon not dbnameMove tables and viewsDo not add views to tablesFixed capitalisation of BAMAdaptorDid not switch to DBConnect to db for flushRanks would not workAdding support for other meta keys and aliasesRenamingFormattingConfiguring a backupSorting out optsDo not allow us to search for a taxonomy link using the production db name; always use the taxon idupdated ignore statementchanges to accommodate multiple ensembl stable ids linking to the same vega stable idupdated ignore statementsrevert back to selecting all source statuses and all object linkage types to populate display xrefsmissing semicolonAdding the ability to flush the targetZapped one more print(STDERR ...). Information messages goes to stdout.Changes:Allow for using dbhost, dbport etc. as options, and set default valueReplacing the 6 coordinate methods with versions which can operate on transcripts which have not been persisted to a database. The DBID is still used for caching purposesorder by orientation to avoid merging rows with different strandsBad method nameMore canis_lupus_familiaris entriesdon't store digits in typeCanis_familiaris refseq url has gone trinomial to canis_lupus_familiarisdeleted extra quotename column changed to common_name in species tableReclassified pseudogenes into 'pseudogene' category instead of 'short non-coding'attribute_type table does not exist. attrib_type doesAdded a --dropbak/-dB option for dropping the backup table before the script exits.updated ccds and lrg documentationupdate direct xref documentationchanges for xrefs with evidence > 2select transcripts only to get rid of duplicate sql query resultsescape underscores so they are not treated as a wildcard character