v315

Code changes:

• Allow ORFeome and MGC synthetic mRNAs even when there is no Genbank entry (#15184). Mark
• Changed genome-euro redirect to be opt-in, rather than opt-out (#15110). Brian
• Added several new feature types to gff3ToGenePred (rRNA, ncRNA, primary_transcript). Brian
• Fixed a problem with '.' in hub track names (#15182). Brian
• Created hg.conf variables to specify a different userDb and/or sessionDb table name. Brian
• Changed UDC to allow: (1) load bigDataUrls from a specific local directory, configured in hg.conf. This is useful in GBIB and mirrors where lots of time and space is wasted on loading local files via the http protocol. (2) deactivate the udc cache. This is useful on OSX which doesn't support sparse files and so quickly fills any harddisk with hundreds of gigabytes of files full of zeros. Max
• Handle tags in VCF's INFO column that appear to have |-separated columns in both description and data by formatting the contents as HTML table for readability (#14379). Angie
• Polished support for bigDataUrl-only tracks by: (1) hgTrackDb: don't lose bigDataUrl-only tracks in -strict mode. (2) hgTables: fixed schema page and field selection for bigDataUrl-only tracks (#14379, #15059). Angie
• Added extra column for gene symbol for UCSC Genes output from hgVai and hgIntegrator (#11752, #14579). Angie
• Updated usage message in utils that now support URL for chrom.sizes (#14857). Angie
• Ongoing work on hgIntegrator: (1) don't offer "All Tables", and don't offer "All Tracks" except for a track assembly hub with no groups. (2) fixed loss of defaultPos for track hubs. (3) improved message displayed when a position/search term can't be found (#14579). Angie

Data changes:

• Created track for GENCODE V22 for hg38 (#15115). Mark
• New assembly browser for Golden Eagle, aquChr2 (#15096). Hiram
• Created 20-species alignment for tarsier, tarSyr2 (#15112). Hiram
• Created 20-species alignment for hg38 (#15413). Hiram
• Added NCBI RefGene track for hg38, mm10, danRer10, and rn6 (#13673). Brian
• Created new version of UCSC genes for mm10 (#15145). Brian
• Created ExAC release 0.3 variants + calling regions tracks (#14379). Angie
• Turn off exon-numbering feature for DGV track (#7474). Angie
• Automated the update of the ClinVar track for hg19. Max