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Created with Raphaël 2.2.029May2321191514228Apr2423221614987428Mar2524211914131110327Feb26252119181714131210765431Jan302928272423222120181715131097318Dec171211109654328Nov26252322181514121187531Oct302925242321181715121110987432130Sep27262523191817131211109653230Aug29272322201916151298765231Jul302926252423No Mr Tab, I expect you to die.[ENSCORESW-816] Patch attempting to fix reused contigs being destroyed as duplicates. Also formatting changes.Removed the duplicate removal detection. We really can have these now. I would prefer a better way to detect them thoughFixing the test suite for the right mappingsAdding the attrib types missingRecreating the multi mapping contig issueMerge pull request #14 from sarahhunt/masterinitial PostgreSQL supportENSCORESW-928: use coding exon overlap score if exists[ENSCORESW-922]. Correct condition for features with negative slice relative coordinates.[ENSCORESW-922]. Correct condition for features with negative slice relative coordinates.[ENSCORESW-922]. Correct condition for features with negative slice relative coordinates.[ENSCORESW-922]. Correct condition for features with negative slice relative coordinates.[ENSCORESW-922]. Problem with circular chromosomes when feature start/end wrt slice are negative.Revert "[ENSCORESW-922]. Can use the same code fragment for both circular/non-circular chromosomes."Revert "[ENSCORESW-922]. Problem with circular chromosomes when feature start/end wrt slice are negative."[ENSCORESW-922]. Can use the same code fragment for both circular/non-circular chromosomes.[ENSCORESW-922]. Problem with circular chromosomes when feature start/end wrt slice are negative.ENSCORESW-926: add update method for sliceAdaptorENSCORESW-914: idesc should really be xref.description fieldENSCORESW-925: ignore non numerical extension to _bak tablesENSCORESW-919: official gene name not transfered onto canonical transcriptcopying API changes from head for new REST endpoints[ENSCORESW-827] a big ID slipped through the net.Revert "when running remove method, run _pre_remove method to update meta_coord table"Revert "when removing features, update meta_coord accordingly"ENSCORESW-909: only map miRBase and RFAM if biotype like '%RNA%'Removing the compression script as dnac has been retired long agoSQLite does not understand SUBSTRING as a function. SUBSTR is okSupport alternative methods of sequence storage & indexing.remove license declaration in test database files[ENSCORESW-827] GFF key IDs must be capitalised to be spec-compliant.[ENSCORESW-827] Switch to a consistently lower case ID fieldadded get_all_Exons test for slice_mask_features method expanded to allow masking of non-repeat featuresadded tests for get_all_Genes_by_source, is_chromosome, has_karyotype, karyotype_rank and forced expand methodstest reformatting, replacing a number of ok tests with isget_all_Introns method also available on gene levelspliced_seq method in Transcript can have soft_mask argumentreformatting test cases, replacing 'ok' tests with 'is'