v497

Code changes:

• Add per-track color override with native HTML5 color picker, right-click "Change Track Color" dialog, and palette icon, gated behind hg.conf showColorPicker=on (#20460, #37329). Brian
• Show alternative chromosome names from chromAlias on the hgTracks position line (#29201). Brian
• Add mafAddIRowsStream, a streaming rewrite of mafAddIRows with 5-10x lower peak memory and 100x+ faster runtime, used for VGP 577-way alignments (#34370). Hiram
• gcOnFly track ready to use: hgGcPercent.c reworked to correctly handle end-of-sequence and sub-window-size cases, with a configurable bigWig fallback at large display densities to avoid heavy on-the-fly computation (#35958). Hiram
• Faceted composite UI improvements: dynamically show or hide the parent track based on whether any subtracks are visible, support per-subtrack links to external resources via subtrackUrl, and add a defaultSortField setting for subtrack presentation order (#36320). Jonathan
• Add searchItemLabel hgFindSpec setting for bigBed tracks, with variable substitution as the search-result label (#37299). Chris
• Document and release the detailsScript trackDb setting, which can render arbitrary plots or custom JavaScript in the bigBedExtra fields table (#37273). Max
• bigGuessDb: run on any bigBed, bigWig, or VCF and it prints the assembly used to build the file. Max
• Color tandem-repeat variation (strVar) subtracks by expected heterozygosity (similar to information content) instead of motif period, with light gray for monomorphic loci; suggested by Melissa Gymrek. Also fix hgTrackUi filter-label truncation (#36652). Max
• Fix Get DNA: position text box was ignored when a table was specified, and rejected single-base positions (#10316, #15336, #37325). Brian
• Add cartVersion 10 to re-apply the encodeCcreCombined to cCREs track collection migration for carts saved between cartVersion 9 and the trackDb switch (#37383). Brian
• Document the sampleMetadataFile trackDb setting and warn on column-count mismatches during parsing (#37306, #37334). Max
• Fix composite visibility: prefer pack over full when re-enabling subtracks, and stop the matrix [-] button from being undone by propagateVis (#37182). Max
• Fix hgc user-defined table printing where the per-table data variable was overwritten across iterations, and harden table-title rendering against XSS (#37340). Chris
• Restore xref term in findSpec search result name/description after the batched-query optimization had dropped the id->xrefTerm mapping (#37345). Chris
• Fix bigBed search highlighting on non-name indexes by setting browserName from the name field rather than the searched term (#34866). Chris
• Fix tooltip mouseovers for items without an item name (#37322). Chris
• Clean up bigPsl.as / bigTransMap.as field documentation: say "other sequence" instead of "other chromosome", label fields with their PSL field names (#37155). Brian
• Fix mergeSpannedItems for quickLifted tracks by using lifted coordinates instead of source-assembly coordinates (#36048). Brian
• Fix DECIPHER SNV details on quickLifted assemblies: drop transcript/gene links, fix missing space, show lifted-assembly position (#36061). Brian
• Fix hgc crash on quickLifted GenArk source assemblies by extending the MySQL-connect guard with isGenArk() (#37388). Brian
• Fix hNibForChrom crash for assembly hubs by falling back to trackHubGetGenomeUndecorated before dereferencing the genome pointer (#37356). Brian
• Point users to the assembly request form in the error message shown when a db= URL argument is not a valid assembly (#37305). Max
• Finalize NMD escape track output: fix zero-length items at exon/CDS boundary edge cases (#33737). Max
• Add repeatId field to webstr bigBed for outlinks (#36652). Max
• Add hubCheck regression test for bigBed field-count mismatch (#36833). Brian
• Factor common quickLift SQL load pattern into shared quickLiftResolveTable / quickLiftSqlLoadBeds helpers. Brian
• Add streaming-mafAddIRows test fixtures and add mafAddIRowsStream to the utils makefile (#34370). Hiram
• pairLastz: verify GenArk assemblies exist before proceeding; logs accumulate instead of overwriting (#37380). Hiram
• doXenoRefGene.pl: correctly populate the geneName2 column (#14450). Hiram
• doBlastzChainNet.pl: raise chain-run RAM limit to 64g to prevent OOM crashes. Hiram
• Initial galaxy kegAlign / lastz automation scripts and workflow definition (#31811). Hiram
• Remove context-click and dblclick handlers from the hgSearch jstree (#37293). Chris
• Fix various gbic install-script issues found by external testers and code review. Max
• redmineCli: add relate/watch/users/note subcommands, --target-version flag, version-name resolution fix (#37339, #20460). Brian

Data changes:

• MethBase 2 (hg38): methylation calls and hypomethylated regions across many cell types, presented through the new faceted composite UI (#36320). Jonathan
• MPRA track collection on hg38, in collaboration with Katie Pollard's and Nadav Ahituv's groups (#34284). Max
• 1000 Genomes ONT and 945 Han Chinese variant calls added to the phased variants track collection on hg38 (#37306). Max
• Long-read structural-variant track collection on hg38: nine subtracks covering almost 8,000 long-read genomes (han945Sv, lrSv1kgOnt, tommoJpSv, aou1kSv, ga4kSv, decodeSv, hgsvc3Sv, kwanhoSv, chirmade101Sv) (#36258). Max
• abelSv: 17,795 SVs from CCDG deeply sequenced genomes on hg38 (Abel et al. 2020) (#36258). Max
• Long-read SV additions: cpc1Sv (CPC + HPRC pangenome) and aprSv (Arabic Pangenome Reference) on hg38 and hs1 (#36258). Max
• GA4K (Genomic Answers for Kids) small-variant subtrack of the variant frequencies track collection on hg38 (#36642). Max
• Short variants from ColorsDB (colorsDbSnv) added to the variant frequencies track collection on hg38 and hs1, the first variant-frequencies subtrack rendering natively on hs1 (#36642). Max
• BAC clone tracks from CHORI on hg38 (BCGSC Human BAC Re-Array, 32k set) and danRer11 (BAC End Pairs lifted from danRer4) (#35059). Max
• HPRC V2 chain tracks initial test on hg38 (#35415). Hiram
• VGP 577-way cactus alignment view on hg38 and hs1 (#34370). Hiram
• evaSnp8 contrib track on GenArk browsers (#36957). Hiram
• BRC update (#34337). Hiram
• Catch up orphaned assemblies across birds, fish, fungi, invertebrate, plants, primates, vertebrate, viral, and legacy AsmHubs. Hiram
• Differentiate great vs intermediate fruit-eating bat in mammal/VGP order lists (#29545). Hiram