v406

Code changes:

• Increased maximum number of barChart bars from 100 to 1000 (#26354). Kate
• Gene Reviews reworked to use bigBed format, to support disease info in mouseOver (#19841). Kate
• Changed the mouseOver for OMIM Gene track (#26221). Brian
• Huge speed improvement of javascript in View, Facets, and Subtracks for hgTrackUi (#26381). Galt
• Huge speed improvement of javascript in Matrix for hgTrackUi (#26398). Galt
• Now refGene shows accessions by default (#26089). Max
• Fixed hgBlat handling only newlines for input and improving hgBlat by moving the gfServer connect to the per-thread routine. (#26285). Galt
• GBIC fix for Centos 8 (#26320). Max
• Work on faToVcf util: added -maskSites option (for SARS-CoV-2 Problematic Sites file). Angie
• Work on vcf lib: bump up limit on number of columns (>100,000 in latest sarascov2phylo). Angie
• New utils vcfRenameAndPrune, phyloRenameAndPrune for renaming & subsetting samples in vcf+tree. Angie
• More google analytics support (#21916). Max
• Ongoing work on allowing the use of Freetype fonts (#25525). Brian
• Under development, not released, wiggle mouse over pop-up with data values (#21980). Hiram
• Switching our makefiles to C99 syntax. Max
• Changed gfServer default timeout to 90 seconds instead of 10 after improving error handling on socket after failure to avoid multiple long timeouts (#26285). Galt
• Improvements in assembly hub construction scripts to correctly manage a bacterial assembly (#23891). Hiram
• Added trackDb settings to control defaults for hic tracks in native, hub, and custom tracks. Available settings include default resolution, track color, and drawing mode (#26312). Jonathan
• Fix bug in ref/alt name shortening in vcfToBed (#25010). Christopher
• Replaced the clusterGenes -minOverlappingBases option with -ignoreBases; -minOverlappingBases did not work correctly and would have required major code changes where -ignoreBases directly address the issue of minor overlap at the ends of transcripts. Mark

Data changes:

• Clinvar Submissions track (#26330). Brian
• IEDB track for wuhCor1 (#26305). Max
• New Phylogeny Public track for SARS-CoV-2. Angie