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Created with Raphaël 2.2.023Apr221614987428Mar2524211914131110327Feb26252119181714131210765431Jan302928272423222120181715131097318Dec171211109654328Nov26252322181514121187531Oct302925242321181715121110987432130Sep27262523191817131211109653230Aug292723222019161512987652spliced_seq method in Transcript can have soft_mask argumentreformatting test cases, replacing 'ok' tests with 'is'Merge pull request #13 from ens-st3/masterMerge pull request #11 from ens-st3/release/75merged from release/75(i) vega prod db details as part of parse_common_optionsMerge pull request #10 from thomasmaurel/masterAdded missing patch_75_76_c.sql into the meta tableadded remove_feature_type methoddo not specify coord_system version if undefinedRevert "when removing features, update meta_coord accordingly"Revert "when running remove method, run _pre_remove method to update meta_coord table"[ENSCORESW-868] Eliminating all evidence of SplicingEvent objects. Ensembl no longer uses them.ENSCORESW-888: version increment for transcripts if there is a changedbass download csv comes with quotesENSCORESW-883: url updated for DBASS ressourcesSplit FTP get method into one that dumps to memory, and the other that dumps to a file explicitly. This is to avoid ambiguity in downloading and to aid code readability.duplicated declarationENSCORESW-854: added lookup for refseq and ccds models in otherfeatures databaseENSCORESW-882: consistent archiving, archive if there has been a changeENSCORESW-888: transcript version number increment if number of exons changePropagated fix [ENSCORESW-840].Propagated fix [ENSCORESW-840]Merge pull request #8 from danstaines/hotfix/multispecies_genome_statisticsMerge pull request #8 from danstaines/hotfix/multispecies_genome_statisticsMerge pull request #9 from dbolser-ebi/masterAdding a fix for Chromosome 0, makeing code more robust[ENSCORESW-885] fix for get and update to support multispecies databases[ENSCORESW-884]. Code did not check for errors or undefs before passingMerge pull request #7 from Anacode/mg13/travis-sqliteadded EntrezGene to trusted source for gene namesreverting changes implemented in f536f27dharness.sh: skip dbConnection.t under SQLite, as it dies mysteriously on travis.Allow transcript.txt to load under SQLite.harness.sh: skip some tests under SQLite.Travis: install DBD::SQLite.Travis: set up SQLite config; fix matrix.travis.yml: add DB=sqlite to env matrix.circ/core/external_db.txt: SQLite does not cope with embedded CRs.Update SQLite test DBs for splicing_event table and friends.