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Created with Raphaël 2.2.013Aug109876432131Jul3027262524232019181613119543229Jun282726252322212019181514131211876131May30292824232221171615141098632127Apr26252423201918171613121110543130Mar292827242322212019161514621Need to do an alias lookup otherwise our search will fail badlyshould return an array ref, not a sliceif no assembly exception, return all slicesadded separate flow for vega databasesseparate flow for vega databases as does not exist for all speciesadded vega runs in core handover configreturn boolean rather than dieing in lock/unlock. Seems to be moreDon't try to lock or seek on logs to teletypes or pipes. Because you can'tFlock-style locking for log files. Needed to automate parts of the Vegalook for pre dbtype only if dbtype is definedoopsupdated to latest schemaexactly max_run iterations, not moreusing semaphoresusing semaphores nowstarting release cycle 69Improved diagnostic on canonical selection.Missing letter 'd' broke coding/merge/other sorting.Revised version of set_canonical_transcripts.pl that uses the new sorting logic.added max_run option, default set to 100ENSCORESW-232: code does not skip proteins with a *, B, Z and X any moreslices are ordered, better chance of finding the genes on the first slicesdo not store attributes with null valueadded early exit conditions :added method get_total to give an estimate of the total number of features expectedadded gene_display_xref_sourcesusing array reference rather than an arrayupdated transcript_display_xref_sources and added gene_display_xref_sourcesarrays/hashes updatesmethod get_total adds an estimate of maximum number of features expectedadded get_total method which gives an indication of how many features are expectedupdated transcript_display_xref_sources and added gene_display_xref_sourcesupdated transcript_display_xref_sources and added gene_display_xref_sourcesupdated transcript_display_xref_sources and added gene_display_xref_sourcesno need to override method transcript_display_xref_sources - diplay xrefs are done in OfficialNaming.pm for zebrafishadded API support for karyotype attributeTwo commits. First is to use a custom factory to let us default to embl, genbank dumps and allow user override [ENSCORESW-226]. Secondly our pipeline was not RC_NAME friendly. We now inherit the default options from hive generic conf and add our own [ENSCORESW-225]A more "new hive" rc name amenable version[ENSCORESW-224]. Fix for multi-line SQ lines caused by large sequences being pushed through SeqDumper. Brought across from HEAD.cvs/release/ens…cvs/release/ensemblgenomes/15-68[ENSCORESW-224]. Fix for multi-line SQ lines caused by large sequences being pushed through SeqDumper. Was never an issue before as our slices were never big enough. Applied the same fix to Genbank but it should be less of an issue due to it's formatting meaning we need larger slices to cause the issue.