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Created with Raphaël 2.2.026Apr2019181514131187131Mar30292824232221181615141110987432128Feb252423222118171615141098743131Jan28272620181413121110765423Dec2117161514131098765432130Nov292524232219181615121110985432129Oct2726252221191815141312118654130Sep292724212017161513109872131Aug2726Modified to allow component type 'O' (other sequence) in the .agp file.*** empty log message ***Reorder $slice->is_circular testsReorder $slice->is_circular testReorder test $slice->is_circularReorder test that contain $slice->is_circularAdded procedure file parameter.Changes to is_circular method.Internal method _build_circular_slice_cache addedcommented out problem method for gettting aliasesFix for massive memory usage on snpstatsadded alt allele calls ans moving certain sources to the gene levelalt allele processing addednew process states addedadded ustilago maydis speciesmodule for uniprot genenameBugfix for SqlHelper which caused it to rerun a transaction even if it succeeded; test case added. Bugfix to gene.t which had a syntax error.Test case addition to make sure we don't keep on iterating executing the transaction when its been successfulTypo caused compilation error; fixedMoved to subdirectory link_outScript for generating LinkOut files for the NCBI website.Bugfix which made a successful transaction be executed for the total number of retriesAdded code to fix issue with Corf genes in zebrafish. The gene names were not being modified to look like hsC*orf*-like. This now works.*** empty log message ***Updated the URL for OMIM file.Updated URL for OMIM file.Added an additional check in the transform method. When testing exons, if consecutive exons in the old version of the transcript were on the same strand then the new versions should be on the same strand too. If not, returns undef. Prevents cases being transformed where the transcript's exons map as below:Replaced sub get_hgnc_synonyms with get_ext_synonymsExample code to retrieve Alternative Splicing events from a set of genes.Parser replaced with VegaOfficialNameParser.pmReplace HGNC_ENSTParser.pm, GI_Vega_Parser.pm and ZFIN_DARTParser.pm parsers with VegaOfficialNameParser.pmParser replaced with VegaOfficialNameParser.pmReplaced call to method get_hgnc_synonyms with get_ext_synonymsRemove field dbprimary_acc_linkable from external_db table.ndexing changes for stable ids.Update schema versiondo not check gor logic_name havana if we are looking at teh vega databasechanged the dumped databases entrys from int to enum so changed the values here to match those in the databaseAdd abillity to ignore a black list of genes for dumping. Also new methos to get a hash of the non reference alt_alleleschanged the dumped databases entrys form int to enum so changed the values here to match those in the database