v495

Code changes:

• New display for superTracks in hgTrackUi (#36917). Max
• Fixed ideogram range parsing when clicking on the ideogram (#37115). Chris
• Removed the limit of 4096 highlights being active at once (#36895). Jonathan
• Switching green polyA-color to default off for BAM tracks (#37133). Max
• Added an hg.conf-defined 'popular' species list to the search bar as default results on focus, combined with the recents list. Added a chevron indicator next to the search bar. Added popular species support to hgConvert, hgIntegrator, and hgSearch. For hgConvert, filtered the popular genomes list by available liftOver chains and disabled unavailable entries (#36232). Chris
• Fixed the hubApi JSON output for columnTypes when more than one track is requested with /getData/track. Added an option in the hgTracks view menu to include column headers when downloading track data. Changed wig table output to behave like bedGraph (chrom, start, stop, value keyed by track name) instead of having a top-level chromosome key. Limited track download requests to 100 tracks to avoid hubApi timeouts (#36858, #36802). Chris
• Fixed saving UCSC databases to the 'Genomes' menu bar recents list when adding genomes from outside hgGateway. Corrected URLs for GenArk hubs. Made menu bar assembly link clicks add to the recents list. Improved labels for recent genomes in the menu bar and excluded default assemblies (hg38/hg19/mm10/mm39/hs1) that are already present. Fixed handling of non-GenArk assembly hub links to include hubUrl and hub_id. Handled public assembly hubs without BLAT/PCR servers by submitting the form so the backend can display an appropriate message (#36535). Chris
• Refactored chromosome position parsing in hgFind into its own function for reuse. Added a defaultPosition check in hubCheck that verifies the requested chromosome exists for an assembly hub (#37126). Chris
• Adding the genePredCompare tool to the kent repo: compare two genePred files and summarize differences, originally for ncbiRefSeq against refGene, but can be used for any genePred file; useful, e.g., to compare lifted genePreds with native genePreds. Max
• Libified the API key set/revoke methods in hubSpaceKeys so they can be called from other modules (#36517). Chris
• Fixed a crash when the trackDb cache is enabled and one of the tables listed in hg.conf's trackDb setting doesn't exist. Added sqlMayConnect/sqlMayConnectRemote to jksql so hdb.c can gracefully handle a missing database instead of aborting. Brian
• Fixed the hgc detail page for ClinVar submissions track items on chrom index 0 in the bigBed numbering scheme. First fixed an off-by-one, then fixed caching of lastChromId so it doesn't incorrectly skip lookups (#37138). Brian
• Wrapped the printing of each hub in search results with errCatch so that an error in one hub doesn't derail the entire search results page (#37100). Brian
• In the right-click menu, fixed "zoom to transcript" to use the built-in URL parser instead of a regex for parsing coordinates, allowing chromosome names with dots as in GenArk assemblies (#35905). Chris
• Added warning in the download dialog when no tracks are selected (#36802). Chris
• Made the 'cf' keyboard shortcut on hgTracks work even when no track list is present below the image (#34456). Chris
• Fixed species search bugs: removed duplicate hidden form variable in hgConvert, made organism comparison case-insensitive so 'human' matches 'Human' for GenArk results (#36535, #36232). Chris
• Fixed up erratic assembly hub connection failures in the API. Hiram
• Making tableBrowser off warning show up on Table Browser (#37168). Max
• Changed the default trackDb cache directory to /dev/shm/trackDbCache (#35945). Brian
• Removed an unused forward declaration in apiUtils.c (#37085). Brian
• Added tutorial for building heatmap tracks (#36176). Jonathan
• Updated seven big* utilities (bigBedToBed, bigMafToMaf, bigWigToWig, bigWigToBedGraph, bigGenePredToGenePred, bigPslToPsl, bigChainToChain) with support for multiple -range parameters that validate bed and position values, via a new callback function in bigBedCmdSupport.c. Added the ability to quickly check allowed chromosomes so users see an error for incorrect chromosome names, and a new -skipChromCheck option to skip the check. Works with all filter options (#28109, #36925). Galt
• All seven *toBig* and big*To* utilities now properly run their inverse utilities, recreating the original input and verifying correctness. Added the bigWigToWig call to the wigToBigWig test, the bigChainToChain call to the chainToBigChain test, and the genePredToBigGenePred call to the bigGenePredToGenePred test (#28109, #36925). Galt

Data changes:

• Adding gnomAD 3 coverage track for hg38 (#37041). Max
• Continuous GenArk updates and liftOver file generation (#29545). Hiram