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Created with Raphaël 2.2.027Feb26242322212017161514131098762131Jan3025242319181716131211109654323Dec22212019141312987652130Nov292524232221181715121110987432131Oct28272625242120191817141312111076543230Sep292827262322212016151413129Fixing bug due to overzelous _ removal. Caused issues for patch/haplotype regions mostly noticable from the region report tool.cvs/release/ens…cvs/release/ensemblgenomes/13-66We were way too generous with the _ cleanup. Applied to numbers onlyNeed to chomp the checksum output and we missed out on a sum callEnhanced biotype grouping requests. Still really needs to be databased, but such is our legacy.Added more groupings for use in FASTA dumping.BigBed is now available as an external adaptorRemoving supporting evidence adaptorLetting datafiles support more than just one file extensionMissing the documentationLetting datafiles support more than just one file extensionMade the circular slice code compartmentalised to just SliceAdaptor (making cache initalisation code easier) and we now only build circular slices when the seqregion it is based off is flagged as circularAttempting to fix the issues with too many KNOWN status genes appearing in species we should not be seeing them in. UniProtParser now limits to using ACs with an evidence of 1 and 2. We now do not assign KNOWN based upon a depdendent xref when we didn't trust the parent xref. Also the loader & SQL has been edited to allow for LOWEVIDENCE types of sources.Bringing the bit after # back inAnalysis logic_names should be all lower caseSymbolic link was wrong and it's data_files not data_fileSpelt the wrongHave to try to flag them upBad name for data_files dirSkip if it was a userdata DBTitles has gone nowMake sure our error message gives enough info about what it's doingSwitching onquick commit. this has broken the script but so we can test if it worksExtended to report biotypes as belonging to larger groupings.removed the todosAdded direct chunk size and linewidth assignments to constructor.Adding no_ftp_tablewrong file testA symbolic link is a fileNow does webcode checkingRemoving the dead dumper and adding a readme to help with remembering which one is the file we need to work withConflict resolved we think. 1.18 code had very odd hash assignment/caching code which should not have workedAdding the data-files dir into the pathAdded support for the two types of dirs we needLetting users clear the linked caches if they wish to. This is better than users assuming the caches they think they can clearLetting users clear the sequence cache if they wish toBulletproofing and adding docsLess of the verbosity and make sure we can return a typeSkip if name is multi or if species was ancestral