v488

Code changes:

• Added a search bar to the track hub definition documentation page (#35618). Chris
• Adding "c h" shortcut to hgTracks to quick-connect a track hub (#35667). Max
• Adding a "hide all" button in the group blue bar (#36354). Max
• Make it obvious to users that identifiers, filters, and intersections have been created and will affect the table browser output using color (#22159). Galt
• Remove 0-length characters from input when searching on hgGateway,hgTracks, and hgSearch (#36387). Chris
• Fixed bug where we didn’t find normalization options for hic files that don't annotate the first chromosome (#36389). Jonathan
• Have gff3ToGenePred indicate which GFF3 errors can be optionally treated as warnings. Mark
• Show proper links to download server for BAM files on the format description page (#36390). Mark
• Correct display of gene name on RefSeq gene track items (#36206). Hiram
• Fixed problem with lrg track nextExon using the wrong handler (#36318). Galt
• Fixed bigBeds limitWiggle optimization to work properly with multi-region (#35580). Galt
• Upgrading our NodeJS on dev from 0.10 to version 22, after 12 years (#36336). Max
• Upgraded RepeatMasker process to version 4.2.1 and RepeatModeler process to version 2.0.7. New genome assemblies going forward will use these new versions. Hiram
• Ongoing work on quickLift. Brian

Data changes:

• Wild-type SpliceAI scores for hg38 (#35100). Gerardo
• Added over 3,000 new fungi assemblies to the GenArk collection for the BRC project (#34337). Hiram
• Continuous GenArk updates and liftOver file generation (#29545). Hiram