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Created with Raphaël 2.2.01Mar29Feb282726242322212017161514131098762131Jan3025242319181716131211109654323Dec22212019141312987652130Nov292524232221181715121110987432131Oct28272625242120191817141312111076543230Sep2928272623222120161514this script replaces fix_component_overlaps.plthis script replaces fix_component_gaps.pl*** empty log message ***don't limit seq_region to chromosomes, so the script can be used to fix overlaps in mappings between other coord_systemsprinting out mapping typeDo not clip the host name after the first dot if the host name is inreplaced by fix_cmp_overlaps.plreplaced by merge_cmp_gaps.plAdd command line switches --source and --target to be used when copyingdon't sort chromosomes, this enables the script to work on supercontigs as wellUse "locate -l 1 $exe" to locate the executable when "which $exe" fails.Error checkingapplied 67 patches a & bdrop stable ID viewsschema version updateupdated API version to 67Biotype groupings now including all transcript biotypes.Fixing 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 works