v445

Code changes:

• Transparency settings added with the new ghostscript (version >= 9.52). Internal effects gain the ability to use alpha-valued colors in both images and PDF output. This supports highlight effects in things like vcfPhasedTrio tracks. This may be a breaking change for some mirrors with custom code modifications - any hard-coded rgbColor structures will need to be updated to include an alpha specification. (#30569)
• Changed the multiwig solution for logos to use the specified track color rather than hardcoded value (#30828). Brian
• Fixed bug where liftover was interpreting colons in bed names as position format (#30705). Chris
• Added support for Genark genomes to the minuscule tool chromToUcsc (#30454). Max
• Fishing up snakes on bigPsl and chains (added some developer only dotplots). Brian
• Ongoing work on making Recommended Track Sets not trash custom tracks or highlights (#26404). Brian
• Added logos built on-the-fly using a wiggle and an associated MAF track. Brian
• Added support for Google Analytics 4. I am unable to use their new UI though, the new version is very hard to use (#30725). Max
• Added a 'vm' option to gbib's update script that can update the underlying operating system to the next version (#24254). Chris
• Tiny GBIC fix for the brand new Fedora 37 linux which we would have run into with all other linux distros soon (#30578). Max
• Various uniprot track updates (#30701). Max
• More work on the trackDb tableBrowser setting in the hubApi, including added tests. Chris
• Fixed table browser schema page when a non-assembly database table. Chris
• Added a few more domains to the https domain whitelist. Galt
• Fixed crash in chromAlias resolution in hgTracks (#30578). Max
• Continuous GenArk process improvements (#29545). Hiram

Data changes:

• (New) Ported problematic regions track from hg19 to hg38 (#30801). Max
• (New) Added GRCm39 to grcIncident otto job (#30735). Hiram
• Stopped printing out the "Variant Review Status" on the clinVar Submissions hgc page. Brian
• Continuous GenArk updates and liftOver files generation. (#29545). Hiram
• Improvements to wuhCor1 big tree build process. Angie