v413

Code changes:

• Add trackDb variable to switch into density coverage mode when window is more than N bases (maxWindowCoverage) (#27079). Brian
• blatServersCheck support for dynamic servers added (#26658). Galt
• blatPing.csh now filters out dynamic blatServers (#26658). Galt
• Better error messages for hgBlat and gfClient when errors happen in dynamic blat service (#26658). Hiram
• Make the use of FreeType fonts be the default, assume fonts are in htdocs. Brian
• Fix problem where hub composite tracks were duplicated on use of refresh button (#27254). Brian
• GBiC now updates its hgcentral (#27301). Max
• Add GbiC support for Ubuntu20 with mysql 8 (#27070). Max
• Make hgHubConnect use the pipeline library to run hubCheck instead of popen() (#27274). Chris
• Fix missing call to hReplaceGbdb so wuhCor1 vcf tracks work on GbiBs (#27172). Chris
• Fixing link error in clang, found by mbargull on github (https://github.com/ucscGenomeBrowser/kent/pull/54) (#27303). Chris
• Add medical disclaimer to Recommended Track Sets dialog (#25601). Kate
• Allow click-throughs of chain tracks that connect native assemblies with assembly hubs. Brian
• Add gbdb remote-failover (redirect) logging switch to hg.conf (#27121). Max
• Additional fixes for hgc outlink click tracking (#21916). Max
• Utils vcfRenameAndPrune, vcfFilter: support VCF with > million columns. Angie
• hgPhyloPlace. Angie
  • Add links from single-subtree Auspice JSON to sample subtree JSON views.
  • Show amino acid back-mutations, not only amino acid differences from reference.
  • Add nearest neighbor & lineage to sample TSV output.
  • Auspice JSON: add option to label branches by Spike mutations only.
  • ASCII tree in summary: add nearest neighbor & lineage for each sample.

Data changes:

• (New) Vaccines track on wuhCor1 browser (#27312). Hiram
• (New) VM26 gene models for mm39. Brian
• Added makeDb/doc files for partially completed GRCh38.p13 patch work (#25091). Angie
• Remove trackDb cache after trackDb build (#23699). Brian
• Uniprot pipeline updates for ottomatic updates, adding filters (#27069). Max
• Removed '.' characters from Variants of Concern track names; they were causing hgTables and hgTracks.js bugs (#27289). Angie
• hg38 vs. Rembouillet sheep GCF_002742125.1 lastz/chain/net per user request (#27231). Hiram
• Ongoing tweaks to SARS-CoV-2 tree updating pipeline. Angie