v496

Code changes:

• Many updates to the faceted composite UI: removed local storage use, began using our server as a proxy for fetching metadata files for hubs on CORS-enabled servers (also local gbdb files), added collapsible facets and UI chips for selected values, and dynamically updated facet counts (#36320). 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 in bigBedCmdSupport.c. Improved error messages for chromStart/chromEnd boundary violations. Added abort behavior when coordinates exceed chromSize, with a new -skipChromCheck option to bypass both chrom name and size validation. Fixed undetected integer overflow issues; now warns when coordinate values are too large rather than silently failing. Expanded coordinate handling in utils and lib to use the full unsigned integer range for chromStart/chromEnd, consistent with the BED standard and .2bit chrom support. Fixed minor overflow in bigBed.c that could exceed the 4 GB address boundary. Changes originated in bigBedToBed.c and were refactored into the six other utilities (#28109). Galt
• Added new trackDb statement to run track-specific JavaScript plotting code using data from bigBed extra fields; syntax is detailsScript.<plotType>.<fieldName> <jsonConfig> (#37273). Max
• Calculation of the GC percent track on-the-fly in the browser to eliminate the disk space waste of the bigWig files for this track (#35958). Hiram
• Corresponding changes in hgc and hgTrackUi to tolerate the GC on-the-fly track (#35958). Hiram
• hgSearch merges search results by track name on the client side, preventing a display bug in the category tree and merging results from different findSpecs for the same track into a single result set (#34334, #37078). Chris
• Save position range searches to the recent searches list on hgGateway/hgSearch/hgTracks (#34588). Chris
• Hide composite when all subtracks are hidden (#37182). Max
• Hide superTrack when all subtracks are hidden (#37282). Max
• hubCheck: added validation of sequence names in 2bit files for illegal characters; names must match [A-Za-z0-9._-], start with a letter or digit, and be at most 254 characters. Added a -noSeqNameCheck flag to disable the check (#37174). Brian
• hubCheck: added detection of tracks that list themselves as their own parent, which previously caused an infinite loop (#35986). Brian
• hgConvert no longer scores all toDb chains; instead, it selects a default one if the toDb CGI variable is already set (#36111). Chris
• Force Genark autocomplete results to send their genome identifier, like GC[AF]_XXX, as the db field to the hgGateway back end (#37276). Chris
• hgTracks' "download data in window" feature now always includes track headers (#36802). Chris
• Fixed a bug in the hgGateway search box to eliminate HTML markup characters in the resulting search answer string that fills the input search form (#18255). Hiram
• Added the ability to read 2bit files for the faSize command, and added test cases to test the faSize command. Hiram
• Added the ability to read 2bit files for the faCount command, and added test cases to test the faCount command. Hiram
• Added a 'genome' argument to the 'ucscGenomes' endpoint in hubAPI (#35972). Hiram
• Fixed a crash that occurred when removing the only highlight present, leading to an empty "highlight" cart variable (#37268). Jonathan
• When quickLifting decipherSnvs, use source coordinates to query into the supporting table (#36061). Brian
• Excluded bigRmsk from canWiggle() to prevent a crash when forceWiggle is triggered (#37229). Brian
• bigGuessDb now supports VCF files; run it with any bigBed, bigWig, or VCF file to output the assembly name (#30316). Max
• Fixed mouseOver wiggles not showing up on page load (#37205). Chris
• Fixed a problem with composite tracks that have only one child and noParentConfig enabled (#37130). Brian
• hubCheck: added a warning when track names contain periods (#37223). Brian
• Added refSeqComposite to the quickLift vetted tracks list and fixed the label checkbox cart variable to use trackHubSkipHubName so it matches regardless of hub name prefix. Brian
• Fixed quickLiftChain tracks to not wiggle (#36514). Brian
• Added genePredCompare, a small tool for comparing two genePred files. Max
• Split the varFreqs superTrack docs page into one page per subtrack (#36642). Max

Data changes:

• Added new MPRA super track (#34284). Max
• Added new gnomAD repeat variation subtrack (#35420). Max
• Added new tandem repeat variation tracks (strVar) with three subtracks (#36652). Max
• Added GREGoR to the varFreqs superTrack and a new merged-all track that combines all databases (#36642). Max
• Added new promoterAi track, Illumina's deleteriousness score for promoters (#37278). Max
• Added new primateAi track, Illumina's deleteriousness score for coding sequences (#37274). Max
• Added new NMD escape superTrack (#33737). Max
• Added ncOrfs superTrack docs page (#37036). Max