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Created with Raphaël 2.2.014Aug13109876432131Jul3027262524232019181613119543229Jun282726252322212019181514131211876131May30292824232221171615141098632127Apr26252423201918171613121110543130Mar2928272423222120191615146We are providing $! information when we have not been able to print to a file handleAdding a "print out what would have happened" script to the checkout; could be rolled into the main script in the future. Also extended the options for DNADB and CCDSDB. We also check if we had a DB which contained DNA as not doing so is a very very very bad thing.Adding Ensembl/Havana merge detectionTest cases now pass, we have a capture warns asserting for known bad scenarios and use the Test::Builder code to see if we want to do to screen warning for test cases. Not sure how un # lines in TAP are dealt with; we may want to substitute STDOUT/STDERR for something which can delegate to Test::Builder for note()Works now ... oddTrying to improve the current test cases. Accidentally caused some issues from rerunning the code multiple times as wellMaking attribute adaptor skip anything that was a false attribute[ENSCORESW-238]. Highlighted by Ken Youens-Clark on dev. We call show_valid_species() without a reference to $selfScript used to decode what canonical assignment says has occured during a run. The script accounts for most issues apart from those nasty ones in which case you must firgure that out yourself.Serious modifications. Dump of changes to file, added SQL commit.Added debug info and exceptionsvalue could be a string, not always a numericNeed 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_sources