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Created with Raphaël 2.2.014Mar131110327Feb26252119181714131210765431Jan302928272423222120181715131097318Dec171211109654328Nov26252322181514121187531Oct302925242321181715121110987432130Sep27262523191817131211109653230Aug29272322201916151298765231Jul302926252423221918171615111043228Jun272624212019ENSCORESW-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.Corrections for reverse-stranded comparisons, more tests. Still doesn't work for distance calculations on neighbouring assembly segments.All cases working, some tested, lots of documentation. Still needs the sign to be inverted on distances.Slippery sigils.[ENSCORESW-840]. The extent of the region spanned by transcripts is …alculated taken into accountLast change got wrongly mixed somehow. Reverting to previous commitDocumentation updates and explanatory notes.Working rewrite of fetch_all_nearest_by_Feature using the API rather than SQL statements. Partially tested but needs some finessing and comments.Mr Tab has proven to be quite an adversary.removing unwanted print outusing biotype group directly rather than list of biotypes belonging to said groupdealing with extra cases where contigs are mapped but not for the same regionBonus debug tests.s/tab/in the eye/[ENSCORESW-840]. The extent of the region spanned by transcripts is calculated taken into accountadded production database connection parameters in ConversionSupport[ENSCORESW-840]. seq region boundaries are fetched from the db (for slices stored in the db) in case[ENSCORESW-840]. seq_region_start from db in case of circular chromosomeinclude non_reference chromosomes for mapping stats