v466

Code changes:

• Added the number of start/end hard and soft clipped bases to BAM hgc page (#33292). Mark
• Plug trackDbCache into hgc and hgTrackUi (#33787). Brian
• Skip BAM details if the read is very long (#33292). Max
• Added a new baseView track type that will draw something like the base position track given a set of coordinates from a bigBed file. Brian
• Removed the click & drag to scroll tooltip from hgTracks image (#33700). Chris
• Changed "Reset filters" label to "Clear filters" on bigBeds tracks and decorators, as that is really what the button does (#33727). Mark
• Fixed native assemblies not being selectable in hgGateway autocomplete (#33572). Chris
• Search results in hgTables now bold properly (#33731). Chris
• Unify the different color pickers (drag select highlights, track item highlights and track item colors) into hui.js. Ensure the text box and palette selector work (#24507). Chris
• Libify some searching code so checkHgFindSpec can use it. Make checkHgFindSpec use the same code path as hgSearch so it can correctly test the search (#33731). Chris
• Changed hgTracks view DNA link to not have the hgsid twice (#33691). Chris
• Skip screen width auto-detection if hgTracks is run from command line. Max
• Merged blatHuge implementation. This adds a gfServer and blat that search genomes greater than 4 gigbases (#20470). Mark
• Moving to jsdelivr as the CDN as the bootstrap one is slowing us down, we should stop using CDNs altogether. Max
• Added pslSpliceJunctions to gather information in splice junctions for comparative mapping analysis. Mark
• Improved dbDbToHubTxt.c to allow the creation of a curated track hub instead of just a curated assembly hub. Hiram
• Added a script refSeqOnGenBank.py to translate RefSeq genes to the corresponding GenBank assembly. Hiram
• Continuous GenArk process improvements (#29545). Hiram
• New lib module mmHash (memory-mapped hash) for very large lookup tables. Angie
• Util tabToMmHash to make mmHash file from tab-separated file. Angie
• hgPhyloPlace:
  • Use mmHash to speed up name/ID lookups and metadata lookups. Angie
  • New config option anchorSamples: always include certain samples in subtrees. Angie

Data changes:

• HGMD 2023 update (#32001). Max
• Improvements to wuhCor1 big tree build process. Angie.
• Continuous GenArk updates and liftOver file generation (#29545). Hiram