v421

Code changes:

• Changed the primary gene set on hg19 to Gencode V38lift37 (#28241). Brian
• Highlight color now persists in the cart (#28098). Max
• Removed botDelay sleep() until it reaches the warnMs threshold, then use the sleep() and begin issuing the warning message (#28173). Hiram
• Fixed CSS bug where the buttons on the highlight popup jump on mouse over (#28090). Max
• Tweaked folder icon for composites/supertrack on hgTracks (#28108). Max
• Fixed hgTracks configure page bug so now dropdowns change colors appropriately as track visibilities are changed (#26257). Max
• Fixed crash when hgvsParseTerm fails to find a match to a psuedo hgvs term (#28147). Chris
• Added fast search to Gencode V36 archive. Brian
• Fixed code to try to avoid the SNP disambiguation page on search results with rsId's. Brian
• Warning message text improved for 'badBlocks' bed file custom track input (#28131). Hiram
• Fixed up build procedure on Mac OSX to account for new freetype and MariaDb client libraries. Hiram
• Genome Browser now prints related tracks section by default unless an hg.conf variable is present to switch it off (#27550). Chris
• hgPhyloPlace. Angie
  • New branch label option: back-mutations, to highlight problematic nodes.
  • New coloring options: Nextstrain clade & Pango lineage from usher/tree.
  • Get mutations from VCF instead of usher's DEBUG mode output.

Data changes:

• (New) GTEx CAVIAR High-Confidence eQTLs release for hg38 (#27947). Matt
• (Update) MANE 0.95 QA ready (#28141). Brian
• (Update) LRG track ready for QA and otto (#24672). Chris
• Fix duplicated item bug in gnomAD pli and missense tracks. Chris
• Rebuilt V38 mafGene downloads for hg38. Brian
• hgPhyloPlace. Angie
• Ongoing improvements to big tree build process.
• New script to automate making a minimized tree for pangolin.