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Created with Raphaël 2.2.017Dec141312111076543230Nov2928272623222120191817161413129876532131Oct3029262524232218171615121098543128Sep2725242118171413121110654330Aug2924232221201716151413109876432131Jul3027262524232019181613119543229Jun2827262523222120Copy is_patch onto branch 66 now that anacode have moved on. -- ds23cvs/release/ens…cvs/release/ensembl/66 release/66 upstream/release/66Update branch 66 now loutre is on 66 to allow empty params as not missing, asLoutre password is optional onto 66 because loutre is now on 66 schema.Add get_annotrack_params to branch 66 for loutre.Adding a no_error flag to allow for simple single value querying where the number of rows returned could be ambigiousGetting rid of a script which still refers to the contig tableGo through an object and make sure everything is populated once we go through a call of $gene->load().Added the method get_all_StructuralVariationFeatures_by_size_rangeAdding get_all_IntronSupportingEvidence()Adding documentation and also switching to using typeAdding defaultsTwo modules used to check a flat file dump parsersparse annotrack db detailstypogiven two databases of the same species, compares the xrefs used for gene display to describe the statistics of what has changed between databasescvs/attic/Root_…cvs/attic/Root_ensembl_all_allelesApplied wait constraints to all three calls. Could have refactored, but the system calls are fiddly and I'll probably make more mistakes that way.Added a queue waiting command to prevent e.g. Human and Mouse projecting simultaneously when Mouse relies upon Human to be complete and correct.Switching back to hive capacity as the current hive pipeline code isn't making much sense to meSwitch to analysis capacityReplaced � and � with & and ^. At least less can render them.Replaced error symbols �� and �� with && and ^^ that can be rendered and/or typed on native linuxUpdated the display of the list of tables (top of the page) and the header of each group of tables.Zapped icky \t charactersIf PASS is not pulled out into a local variable then passed into DBI we will attempt to connect to a database (DBI->trace() confirms the passing of a password). Perl is very oddUse the actual DB nameDo not clutter screen with unwanted infoSwitch to unique tables and not a global arrayMissed a line breakIf we were doing patterns then obliterate the dbname param letting the code do the right thingCounting features over HAPs/Patches/PARs was not working. Fixed by adding a SQL based filtering stage. The normal code will not use this as it is quite nastyremoved predicted sources as these are no longer usedwarn which non_patch chromosomes might have been excluded[ENSCORESW-315]. Fixing a bug where the bind params need to be reused on subsequent queries. MySQL/DBI/DBD::mysql is really bad at warning us when we submit a query with a single ? and no bind parameters (it compensates). Wish it didn'tRegression testingRegression tests are namespaced accordingly[ENSCORESW-314]. Synonym lookup bug fixed. Passed coord system id into the lookup rather than the actual coord system name. Bad bad bad[ENSCORESW-313]. Adding support for external db id lookup and filtering by them on synonymsMouse is upgraded to mm10 from UCSCDefault user addedPermissions comes through as normal octal notation so no need to do lots of individual ones