v403

Code changes:

• Replaced synchronous HTTP requests at page unload with a combination of asynchronous and synchronous requests elsewhere. This means carts should now do a better job of staying updated in the Chrome browser (#25017). Jonathan
• Restoring the suggestion box behaviors where searching for a gene both turns on the default gene track and highlights that gene name within the track (#25703). Jonathan
• hgc VCF details: removed more cases of diploid-specific terms when viewing monoploid data (like SARS-CoV-2) (#25409). Angie
• hgTracks VCF+treeFile custom tracks: added highlightIds setting in preparation for hgPhyloPlace (#25943). Angie
• hgTracks VCF haplotype display: speed up by implifying genotype parsing (#25943). Angie
• hgTracks VCF haplotype display: tolerate IUPAC ambiguous characters. Angie
• All CGIs VCF: support GenBank & RefSeq IDs in VCF for SARS-CoV-2. Angie
• Major update to the generateUsageStats.py script adding options to output individual stats or all at once. Matt
• First steps towards a "related tracks" section in every track docs page (#25721). Max
• transMapPslToGenePred: add report of location of frameshifts for use by Comparative Annotation Tool Kit (CAT). Mark
• Fixed bug in hgLiftOver CGI and liftOver utility reported by a user. The bug caused it to miss some valid mappable exons. Added test cases including BED12 which was missing (#26057). Galt
• Added hg.conf var (browser.recTrackSets) to enable Recommended Track Sets feature (#25601). Kate
• Fixed problem with session links when tiny session URLs are used. Bug introduced with Recommended Track Sets (#26050). Kate
• Don't print hub search tree until we know we have something to populate the tree with (#26013). Christopher
• Fix overly ambitious hgTrackUi link selector which broke track search metadata drop-downs and pagination (#25969) and (#25968). Christopher
• Ongoing work on GENCODE merge. Brian
• Added trackDb variable to disable configuration of parents in composites. Brian

Data changes:

• Add 'tableBrowser off' setting for Nextstrain Variants and SARS-CoV-2 Phylogeny at GISAID's request (#26072). Angie
• Cluster-admin started otto-push for Nextstrain tracks; updated pennant & descriptions. Angie
• Make doc checked in for build procedures taking place on: ambMex2, mm39, canFam5. Hiram
• Changed ORF3b to its SARS-CoV-2 length rather than SARS-CoV and renamed ORF3b-2 to ORF3d. Irwin Jungreis of MIT
• Stage genome in a bottle structural variants and trios on dev (#24349). Christopher
• Update LOVD and DECIPHER to bigBed (#25841). Christopher
• Progress on Franklin-like display. Brian