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@braneyTall braneyTall released this 30 Apr 18:55
v497_branch.1
1960bd9
  • 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
  • Show alternative chromosome names from chromAlias on the hgTracks position line
  • Add mafAddIRowsStream, a streaming rewrite of mafAddIRows with 5-10x lower peak memory and 100x+ faster runtime, used for VGP 577-way alignments
  • 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
  • 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
  • Add searchItemLabel hgFindSpec setting for bigBed tracks, with variable substitution as the search-result label
  • Document and release the detailsScript trackDb setting, which can render arbitrary plots or custom JavaScript in the bigBedExtra fields table
  • bigGuessDb: run on any bigBed, bigWig, or VCF and it prints the assembly used to build the file
  • 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
  • Fix Get DNA: position text box was ignored when a table was specified, and rejected single-base positions
  • Add cartVersion 10 to re-apply the encodeCcreCombined to cCREs track collection migration for carts saved between cartVersion 9 and the trackDb switch
  • Document the sampleMetadataFile trackDb setting and warn on column-count mismatches during parsing
  • Fix composite visibility: prefer pack over full when re-enabling subtracks, and stop the matrix [-] button from being undone by propagateVis
  • Fix hgc user-defined table printing where the per-table data variable was overwritten across iterations, and harden table-title rendering against XSS
  • Restore xref term in findSpec search result name/description after the batched-query optimization had dropped the id->xrefTerm mapping
  • Fix bigBed search highlighting on non-name indexes by setting browserName from the name field rather than the searched term
  • Fix tooltip mouseovers for items without an item name
  • Clean up bigPsl.as / bigTransMap.as field documentation: say "other sequence" instead of "other chromosome", label fields with their PSL field names
  • Fix mergeSpannedItems for quickLifted tracks by using lifted coordinates instead of source-assembly coordinates
  • Fix DECIPHER SNV details on quickLifted assemblies: drop transcript/gene links, fix missing space, show lifted-assembly position
  • Fix hgc crash on quickLifted GenArk source assemblies by extending the MySQL-connect guard with isGenArk()
  • Fix hNibForChrom crash for assembly hubs by falling back to trackHubGetGenomeUndecorated before dereferencing the genome pointer
  • Point users to the assembly request form in the error message shown when a db= URL argument is not a valid assembly
  • Finalize NMD escape track output: fix zero-length items at exon/CDS boundary edge cases
  • Add repeatId field to webstr bigBed for outlinks
  • Add hubCheck regression test for bigBed field-count mismatch
  • Factor common quickLift SQL load pattern into shared quickLiftResolveTable / quickLiftSqlLoadBeds helpers
  • Add streaming-mafAddIRows test fixtures and add mafAddIRowsStream to the utils makefile
  • pairLastz: verify GenArk assemblies exist before proceeding; logs accumulate instead of overwriting
  • doXenoRefGene.pl: correctly populate the geneName2 column
  • doBlastzChainNet.pl: raise chain-run RAM limit to 64g to prevent OOM crashes
  • Initial galaxy kegAlign / lastz automation scripts and workflow definition
  • Remove context-click and dblclick handlers from the hgSearch jstree
  • Fix various gbic install-script issues found by external testers and code review
  • redmineCli: add relate/watch/users/note subcommands, --target-version flag, version-name resolution fix
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