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Created with Raphaël 2.2.018Mar151211654128Feb27262522212019181514131211754130Jan29252422211716151410987421Dec201917141312111076543230Nov2928272623222120191817161413129876532131Oct3029262524232218171615121098543128Sep2725242118171413121110654330Aug2924232221201716151413109876432131Jul30272625Try to tolerate plural examples.New method store_batch_on_ for faster bulk storage of attributes. New modules GeneGCBatch and PepStatsBatch use this method. Updated test to include use of this method.reformatted source with current perltidy settingsAdded fetch_all_by_description with simple testcase.Reformat code and slightly improve the HTML outputnow supporting is_root methodadded test to check if term is_rootAdded some additional documentation to counter cases where Transcripts without Slices were being used, creating garbage mappings. ENSCORESW-208input and return list of values made more consistent between methodstrim end of line white spaces[ENSCORESW-377]. Fixing the seq region synonym as mentioned by Steve S. Also added a test case which looks for synonyms with a coordinate system not as before which only worked when we had no coordinate system)using plain assignment to assigne individual values to a has, rather than the fat comma used in the larger hash declarationAdded constrain_to_seq_region for web rendering reasons, where requested slice->expand were flying off the end of chromosomes.moving logic for slice projection filtering into sliceadaptor so compara have an easier time using it and getting better patch support inadding frozen confs and CLEAN.t to ignore listadding the ontology db adaptorAdded a useful comment for future code archaeologists.adding serialisation code to the adaptors which lets us write the connections out if neededdo not overwrite Uniprot_genename and EntrezGene for pigUpdate the regexp to catch the primary key lineadding external_synonym into the list of backed up tableswhen clearing up, also reset transcript display xrefs and descriptionsJob name was truncated to bsub limits, but previous job name was not. Fixed for all three invocations.updated file to match current latest production database schema on the staging serveranalysis_web_data column db_type should be an enum rather than a setRemoved false implication of rate limiting.adding a quick bit of code to check for bam alignmentsAdding BAM checks which ensure the file is consistent. Can cause issues to the program test run if they are not correct but this means they will not work in productions/n/g/; Copy paste error in wait-state command. Omitted "go projection" implication when previous code referred to "name projection" with an "n"too verboseupdated human ccds to release 71attach dna db to rnaseq dbcvs/release/ens…cvs/release/ensembl/70 release/70 upstream/release/70add dna db for rnaseq databasestweaks to formatting of param list so that they (hopefully) all fit on one line. Don't try to check PATCH seq_region_attribs since it doesn't work with with Ensembl-vega databasesBetter executable bitsRemoving. Incoming with better executable bits onPOD correction for _id_cache that was breaking Doxygen render.Don't check for internal stops in polymorphic pseudogene transcripts.Don't check for internal stops in polymorphic pseudogene transcripts.added udr as an option. udr is a faster rsync