v446

Code changes:

• Moved the download current track data button to blue bar menu under "Downloads" (#30865). Chris
• Added a little help box with link to new FAQ if hgTracks takes longer than x seconds (-> hg.conf) to load (#30591). Max
• Changed the way we load recommended track sets. We now overlay their contents, no longer obliterating the current session (#28525). Brian
• Added downloadUrl trackDb statement, to show link to GFF files for gene tracks above the docs page, so it cannot be missed anymore (#30904). Max
• Added support for chromAlias to the hubApi (#30544). Hiram
• Fixed up broken support for curated assemblies in the API (#30544). Hiram
• Fixed non-knownCanonical results not showing up in a knownGene search (#25078). Chris
• Turned on phyloP logo for 100 way on hgwdev, phyloP scores are shown as a sequence logo if zoomed in to near base mode. Brian
• Single position search coming from hgGateway now goes directly to hgTracks before drawing any html. Chris
• Fixed dbSnp pipeline for handling clinvar records that had multiple significances (#30617). Galt
• Restored color to the Short Match track, which was being drawn with an alpha of 0 (invisible) after the transparency changes (#30866). Jonathan
• Restored standard color parsing for 3-value colors in BED files, as 255,255,255 (white) was causing an error with full alpha added (the color 0xffffffff has the value -1, which is interpreted as an error instead of a valid color) (#30569). Jonathan
• Highlights should now appear in multi-region mode; they were being ignored due to an error in chromosome name handling (#30833). Jonathan
• In image and PDF output, highlights would be broken by vertical bars from the blue ruler lines in the background. The combination of the two is now handled in the same way as the web display, which looks better (#30833). Jonathan
• Made hubId's portable in newly created sessions by saving away the hubUrl's of attached hubs in the cart (#28525). Brian
• Fixed a bug in trackDb caching that I introduced when saving trackDb parsing errors in each tdb rather than crashing the whole browser (#30881). Brian
• Added download links for gene track GTF files in GenArk assemblies in description pages for tracks, soon to be obsolete by downloadUrl trackDb statement. Hiram
• bigMafToMaf program has been updated to use significantly less memory, allowing large bigMaf files to be converted back to MAF (#28491). Mark
• Made kent-core repo with all MIT-licensed kent-code only see https://github.com/ucscGenomeBrowser/kent-core. Max
• Added a change list to trackDb, see https://genome-test.gi.ucsc.edu/goldenPath/help/trackDb/changes.html. Max
• Continuous GenArk process improvements (#29545). Hiram

Data changes:

• HPRC collection of genomes now available in GenArk. Hiram
• CCGP collection of genomes begins to appear in GenArk. Hiram
• Improvements to wuhCor1 big tree build process. Angie.
• Continuous GenArk updates and liftOver files generation. (#29545). Hiram