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Created with Raphaël 2.2.024Mar211914131110327Feb26252119181714131210765431Jan302928272423222120181715131097318Dec171211109654328Nov26252322181514121187531Oct302925242321181715121110987432130Sep27262523191817131211109653230Aug29272322201916151298765231Jul302926252423221918171615111043228Jun27262421[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.dbEntries.t: correct offset in SQLite auto-increment munging.exon.t: ignore 'datatype mismatch' bind errors on floating point for SQLite.homo_sapiens/patch/transcript.txt: SQLite does not like header.when checking a boolean, checkif true, not if definedFlyBase priority descriptions were too long for xref source table. Must always have been truncated, but now shortened in case your mysql server doesn't do automatic truncation.ENSCORESW-875: include HGNC prefix in HGNC download, downstream updates to match the new idsENSCORESW-873: for uniprot, label should be the same as accessionENSCORESW-852 & ENSCORESW-373:[ENSCORESW-836]. Completed method to find and add species_id attribute.[ENSCORESW-836]. Add species id based on constructor flag and on whether species is provided.[ENSCORESW-836]. Support for automatically loading the species_id.ENSCORESW-861: initialize driver before testing itENSCORESW-861: initialize driver before testing itENSCORESW-855: exons are shared across several transcripts, cannot be uniquemore sanity checks for the GFFSerializerupdate to gff3 output format:patch ontology databases to release 76update test databases to release 76ENSCORESW-866: allow NULL as default value for karyotype and stain[ENSCORESW-543]. Version is left undef to match the healthchecks expected behaviour (null instead of empty).Minor updates to xref config for some metazoansRemoved functionality to get INSDC xrefs from FlyBase; these are better determined with the xref pipeline, which attaches them to translations rather than genes.Minor updates to xref config for some metazoansRemoved functionality to get INSDC xrefs from FlyBase; these are better determined with the xref pipeline, which attaches them to translations rather than genes.do not overwrite transcript description with xref description[ENSCORESW-834] Pass on slice to verifying code, so that it can catch rare circular cases.[ENSCORESW-820] Retiring obsolete canonical transcript script. Use select_canonical_transcripts.pl instead.Final change made to correctly compute cross-seq-region distances, a few more tests.