v499 branch 2 (small DDOS fix)

• Convert the bundled HTSlib to a git submodule (src/submodules/htslib) and route remote BAM/VCF/tabix access through HTSlib's hfile scheme-handler mechanism backed by UDC, replacing the legacy knetUdc/knetfile hooks: knetUdcInstall remains as a thin compatibility stub; hfile_add_scheme_handler init order is fixed so kent registers UDC handlers before any hopen; remote .bai/.tbi/.crai index reads now go through UDC instead of being downloaded into the current directory; tabix VCF tests previously gated by a non-existent USE_TABIX make variable are re-enabled; fetchKentSource gains initial submodule-aware checkout; and the outdated UCSC-bundled static libcurl is dropped in favor of system libcurl
• Upgrade session and cookie IDs from 32-bit to 64-bit so the browser keeps working after 4 billion users are served, including robot scripts
• Prepare the myVariants feature for a test/v1 release: fix dialog box sizing and other small UI changes, allow tracks to be renamed, and make each row a type (snv, cnv, or transcript)
• Ongoing development of the lift-over user request system
• hubSpace: allow UI uploads to accept a hub.txt + genomes.txt + trackDb.txt assembly hub, not just a useOneFile-style hub
• New hubtools command-line tool: convert trackDb format to TSV, convert TSV to trackDb format, and create bare-bones hub.txt files from a directory of big* files
• Get the hubtools upload command working now that hubSpace is more stable
• Add a BLAT API call
• hgPhyloPlace: draw a RIVET-like recombination diagram in a pop-up
• Reduce bot abuse by limiting how many IP addresses can present the same hguid in a short timeframe before requiring a captcha re-up, when captcha is enabled
• Stop rejected bot traffic from creating empty session and user records: the browser now loads and creates sessionDb and userDb entries only after the captcha check passes, so visitors that never clear the captcha no longer run up the ID counters on those hgcentral tables
• Avoid a crash at exit when a CGI opened a database connection before carefulMemHandler was set up; sqlCleanupAll now lets the system reclaim that memory instead of freeing a mix of allocation types by hand
• Add a way to toggle the trackDb cache per hgTracks invocation without editing hg.conf, and a harness to compare cached and uncached render times
• Fix hgTracks out-of-memory (11+ GB) and timeout when rendering a window with quickLifted bigBed-style tracks
• Add a way to control the display order of filter and highlight controls on the track configuration page
• Fix hgConvert quickLift re-runs: stop re-lifting tracks that already came from a quickLift hub, append to the existing per-source hub file instead of overwriting it, and add a way to remove an individual track from a quickLift hub
• Fix a quickLifted UCSC RefSeq item detail page where the CCDS link errored against the hub-virtual db, and Get Genomic Sequence Near Gene pulled sequence from the wrong assembly
• Fix a quickLifted bigBed mouseover tooltip that reported the pre-lift source position while the position bar showed the lifted target position, with nothing flagging the discrepancy
• Fix a lolly subtrack item that failed to lift to the target assembly, reusing stale memory, corrupting the subtrack's trackDb pointers, and later surfacing as "Can't find tdb for subtrack ... was getSubtrackTdb called on non-subtrack?"
• Fix a stale lastPosition left behind by a quickLift or hgGateway hop to a new assembly, which triggered a spurious "Unable to resolve lastPosition" banner on the destination assembly
• Fix a genePred crash when flipping strands on records with no exon frames
• Fix the OMIM Genes (omimGene2) detail page failing with a MySQL "Commands out of sync" error
• Free a leaked database connection on the OMIM Genes (omimGene2) detail page
• Fix faceted composite UI supporting-file fetch that broke when a broken hub was attached, by switching to hubFromIdNoAbort
• Fix advanced track search when a select and its parent td share a name, causing track search and file search options to show false 0 counts
• Column titles in the faceted composite UI now respect the capitalization used in the metadata
• Tooltips: fix another spot that wasn't using the data-tooltip attribute; tooltips should now use it everywhere
• Establish a convention that /gbdb file or directory names beginning with an underscore are never synced to hgDownload, reducing admin emails
• Change the hgTrackUi link at the top of the page to "Configure track container" to make it easier to find
• Correct the browser system's bounce email address so bounced user emails are now received
• Enlarge several fixed-size string buffers in web.c that were too small at 128 bytes
• Add an automated lifecycle for the tip, beta, and rel Docker QA browser instances on hgwdev and wire them into the weekly autoBuild
• redmineCli: add support for posting comments, updates, and attachments as Redmine private notes

v499 branch

• Convert the bundled HTSlib to a git submodule (src/submodules/htslib) and route remote BAM/VCF/tabix access through HTSlib's hfile scheme-handler mechanism backed by UDC, replacing the legacy knetUdc/knetfile hooks: knetUdcInstall remains as a thin compatibility stub; hfile_add_scheme_handler init order is fixed so kent registers UDC handlers before any hopen; remote .bai/.tbi/.crai index reads now go through UDC instead of being downloaded into the current directory; tabix VCF tests previously gated by a non-existent USE_TABIX make variable are re-enabled; fetchKentSource gains initial submodule-aware checkout; and the outdated UCSC-bundled static libcurl is dropped in favor of system libcurl
• Upgrade session and cookie IDs from 32-bit to 64-bit so the browser keeps working after 4 billion users are served, including robot scripts
• Prepare the myVariants feature for a test/v1 release: fix dialog box sizing and other small UI changes, allow tracks to be renamed, and make each row a type (snv, cnv, or transcript)
• Ongoing development of the lift-over user request system
• hubSpace: allow UI uploads to accept a hub.txt + genomes.txt + trackDb.txt assembly hub, not just a useOneFile-style hub
• New hubtools command-line tool: convert trackDb format to TSV, convert TSV to trackDb format, and create bare-bones hub.txt files from a directory of big* files
• Get the hubtools upload command working now that hubSpace is more stable
• Add a BLAT API call
• hgPhyloPlace: draw a RIVET-like recombination diagram in a pop-up
• Reduce bot abuse by limiting how many IP addresses can present the same hguid in a short timeframe before requiring a captcha re-up, when captcha is enabled
• Avoid a crash at exit when a CGI opened a database connection before carefulMemHandler was set up; sqlCleanupAll now lets the system reclaim that memory instead of freeing a mix of allocation types by hand
• Add a way to toggle the trackDb cache per hgTracks invocation without editing hg.conf, and a harness to compare cached and uncached render times
• Fix hgTracks out-of-memory (11+ GB) and timeout when rendering a window with quickLifted bigBed-style tracks
• Add a way to control the display order of filter and highlight controls on the track configuration page
• Fix hgConvert quickLift re-runs: stop re-lifting tracks that already came from a quickLift hub, append to the existing per-source hub file instead of overwriting it, and add a way to remove an individual track from a quickLift hub
• Fix a quickLifted UCSC RefSeq item detail page where the CCDS link errored against the hub-virtual db, and Get Genomic Sequence Near Gene pulled sequence from the wrong assembly
• Fix a quickLifted bigBed mouseover tooltip that reported the pre-lift source position while the position bar showed the lifted target position, with nothing flagging the discrepancy
• Fix a lolly subtrack item that failed to lift to the target assembly, reusing stale memory, corrupting the subtrack's trackDb pointers, and later surfacing as "Can't find tdb for subtrack ... was getSubtrackTdb called on non-subtrack?"
• Fix a stale lastPosition left behind by a quickLift or hgGateway hop to a new assembly, which triggered a spurious "Unable to resolve lastPosition" banner on the destination assembly
• Fix a genePred crash when flipping strands on records with no exon frames
• Fix the OMIM Genes (omimGene2) detail page failing with a MySQL "Commands out of sync" error
• Free a leaked database connection on the OMIM Genes (omimGene2) detail page
• Fix faceted composite UI supporting-file fetch that broke when a broken hub was attached, by switching to hubFromIdNoAbort
• Fix advanced track search when a select and its parent td share a name, causing track search and file search options to show false 0 counts
• Column titles in the faceted composite UI now respect the capitalization used in the metadata
• Tooltips: fix another spot that wasn't using the data-tooltip attribute; tooltips should now use it everywhere
• Establish a convention that /gbdb file or directory names beginning with an underscore are never synced to hgDownload, reducing admin emails
• Change the hgTrackUi link at the top of the page to "Configure track container" to make it easier to find
• Correct the browser system's bounce email address so bounced user emails are now received
• Enlarge several fixed-size string buffers in web.c that were too small at 128 bytes
• Add an automated lifecycle for the tip, beta, and rel Docker QA browser instances on hgwdev and wire them into the weekly autoBuild
• redmineCli: add support for posting comments, updates, and attachments as Redmine private notes

v498 branch

• Initial commit of myVariants feature: users can now create custom track items on the fly using a form that supports colors, descriptions, names, ref and alt alleles, custom fields, and item sharing
• hubSpace now supports assembly hub upload, limited to one assembly per hub
• Initial support for ripples recombinant search in usher-sampled-server on hgPhyloPlace
• Replace subtrackUrl setting for faceted composites with subtrackUrls, supporting outlinks in multiple fields
• Limit the amount of setting data that can be added to a cart in a single POST request to mitigate cart-stuffing robots
• Fix mdbSearch URL construction so the Advanced tab in track search makes valid hgApi queries
• Push trackDbHub anchor jumps below the search box so the first content under the anchor is no longer hidden
• On-going development of the lift-over user request system
• Reset the assembly request form to verify user authentication with the Cloudflare credentials
• Fortify the GenArk build system for use with cron jobs
• Fix bug in maf track item clicks to correctly link out to the other assemblies in the alignment when they are GenArk browsers
• Render the filter UI on track-collection configuration pages with Submit and Reset to defaults; fix a pre-existing bigGenePred duplicate-filter bug surfaced during the work
• Reduce the gap between the Filters heading and the first filter row on track-collection configuration pages
• Composite hgTrackUi: the global [-] button now hides the composite dropdown, and [-]/[+] remembers previous visibility instead of reverting to pack
• Fixup zoom to exon/codon right-click option for genePreds, bigGenePreds, and bigBeds
• Add simpleTracks mouseover exon length
• Restructure the /docs/ landing page for new users with a sticky sidebar table of contents
• Add a chromAlias info icon next to the chromosome position, with mouseover usage description and docs link
• Added chainToMaf command
• Switch GENCODE versions in all.joiner to use macros instead of growing every release
• New mafToBigMafSummary utility producing bed3+4 input for bedToBigBed -as=mafSummary.as, replacing the documented hgLoadMafSummary -test | cut -f2- | sort hack; also fixes errAbort on plain hg38.chrY-style master src names
• Make assumesHub-from-assembly-hub session portability work across hosts: remap db cart variable and db-keyed cart vars alongside the hub__* track settings that were already being renamed
• Make quickLifted GENCODE tracks usable: click details, position links, Get DNA flow, and coding/non-coding coloring
• Make quickLifted refGene and NCBI RefSeq clicks fully functional: rich RefSeq fields, Predicted Protein and CDS FASTA links, Ctrl/Cmd+drag zoom, and "Select all subtracks" before quickLifting; also keep hidden composite siblings in the lift hub
• hgGene clicks on quickLifted knownGene items no longer segfault: all sections, GeneReviews, and Methods page render
• Remap bigBed search hits from source to destination coordinates on quickLifted hub tracks so search result links resolve correctly
• hgc bigBed click: skip intervals that fail quickLift remap instead of errAborting the page, and only emit BR / set found after passing filters
• Populate the quickLift source track description on details and config pages when the source assembly is a hub or GenArk
• Let quickLift tracks join the hgTracks parallel-fetch worker pool, saving roughly 5 seconds of serial main-thread time per track
• Route parallel-loaded bigDataUrls through hReplaceGbdb so gbdbLoc1/gbdbLoc2 rewrites apply to bigBed, bigWig, and bamWig tracks
• hgTracks no longer SIGBUSes mid-render when /dev/shm is full (notably under Docker's 64 MB default tmpfs); the Docker image now stores the trackDb cache on a persistent path outside /dev/shm
• Resolve the $D macro in quickLifted ClinVar dataVersion paths, rather than displaying the literal $D on the config page
• hgConvert "failed to lift" composite warning now lists only user-visible non-liftable subtracks, while still bringing hidden liftable siblings across
• Exclude quickLifted tracks from hgTables and hgIntegrator output paths where they would produce wrong results: block hgTables output, hide QuickLift groups from both dropdowns, avoid SQL connect to the hub assembly, and stop the hgIntegrator "Choose fields" hang
• New quickLiftBench harness: saved-session comparisons, per-phase timing, parallel-fetch regression case with phase assertions; hgTracks also emits per-track timing on the trackImgOnly=1 fast path
• Move the parseQuickLiftLogs log-crawl helper into the kent source tree
• redmineCli: add --file-list-add to append paths idempotently
• redmineCli: let create accept --tracker and --status by name; fix --status integer-default crash in the resolver

v497 branch

• 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

v496 branch

• 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
• 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
• Added new trackDb statement to run track-specific JavaScript plotting code using data from bigBed extra fields; syntax is detailsScript..
• 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
• Corresponding changes in hgc and hgTrackUi to tolerate the GC on-the-fly track
• 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
• Save position range searches to the recent searches list on hgGateway/hgSearch/hgTracks
• Hide composite when all subtracks are hidden
• Hide superTrack when all subtracks are hidden
• 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
• hubCheck: added detection of tracks that list themselves as their own parent, which previously caused an infinite loop
• hgConvert no longer scores all toDb chains; instead, it selects a default one if the toDb CGI variable is already set
• Force Genark autocomplete results to send their genome identifier, like GC[AF]_XXX, as the db field to the hgGateway back end
• hgTracks' "download data in window" feature now always includes track headers
• 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
• Added the ability to read 2bit files for the faSize command, and added test cases to test the faSize command
• Added the ability to read 2bit files for the faCount command, and added test cases to test the faCount command
• Added a 'genome' argument to the 'ucscGenomes' endpoint in hubAPI
• Fixed a crash that occurred when removing the only highlight present, leading to an empty "highlight" cart variable
• When quickLifting decipherSnvs, use source coordinates to query into the supporting table
• Excluded bigRmsk from canWiggle() to prevent a crash when forceWiggle is triggered
• bigGuessDb now supports VCF files; run it with any bigBed, bigWig, or VCF file to output the assembly name
• Fixed mouseOver wiggles not showing up on page load
• Fixed a problem with composite tracks that have only one child and noParentConfig enabled
• hubCheck: added a warning when track names contain periods
• 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
• Fixed quickLiftChain tracks to not wiggle
• Added genePredCompare, a small tool for comparing two genePred files
• Split the varFreqs superTrack docs page into one page per subtrack

v495_branch.2

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 bigTo 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

v494_branch.1

• Added a species search bar to most CGIs and a slight reorganization of hgGateway: new species search bar instead of dropdowns on most cgis. The search bar uses the hubApi to find genomes, allowing connecting to genark assemblies without going through hgGateway or hgHubConnect first. Hide the species tree by default on hgGateway. Save the last 10 used assemblies to localStorage, display them on hgGateway, and set them as default selections in the search bar and the menu bar under 'Genomes'. Chris
• Search changes: special code to add item descriptions to MANE and HGNC search results, need a generic way to do this for bigBeds, fix some bugs with hgSearch as a result of the species selection changes. Chris
• Make users confirm they want to disconnect from a hub on hgTracks, as the button is right next to refresh and can/has been clicked accidentally. Chris
• Fixed assembly hub disconnect bug to also clear the db, org, and genome cart variables, otherwise going back to hgTracks from hgHubConnect results in viewing the genome for the first row of the defaultDb table. Chris
• 'GenArk archive' name changes to 'GenArk repository'. Hiram
• Add bold highlight to new genome search result menu. Hiram
• Adding hub email display to hub error output for public hubs. Max
• Hi-C tracks in arc mode previously included extra whitespace at the top, which became excessive when many arcs were hidden. The whitespace has been removed, and the height of these tracks is now just enough to accommodate the highest arc shown.. Jonathan
• Added HTML page for quickLift alignment differences. Braney
• Fixed an issue with the hubApi that caused a bad cache in trackDb. Brian
• Made a special case for the bigBed loader to only load a bed6 if asked to load a bed7 for backwards compatibility. Braney
• Updates to the faceted UI for composite tracks to support tracks that are on by default and to be more consistent when some subtracks have subsequently been hidden manually (e.g., via right click). Jonathan
• The faceted UI for composites now imposes a limit on the number of subtracks that can be active at once for sanity reasons (the new limit of 1000 is still very high). Jonathan
• When the faceted UI includes data type selectors, it is now possible to provide alternate labels for those checkboxes that don't match the internal names used for subtrack selection. Jonathan
• HubSpace changes: fixed a weird DataTables bug where we double-displayed rows when doing a hubUpload; documented on hgCustom that hubSpace exists; defaulted to the currently open hub name when selecting the upload button; and when viewing a hub's files. Chris
• Fix a Visible Tracks bug when calculating the tracks that are on. Chris
• Updated support for Multi-region exon mode knownGene processing. It now correctly handles the pseudoGenes checkbox in the track settings, all the trackSets including MANE, and also the comma-separated ID-list filtering. Galt
• Restoring static curl in build. Galt
• Adding XSS security fix to hub error printf. Max

v493 branch

New feature: "Visible Tracks" group at the top of the hgTracks group list with the list of currently visible tracks if there are more than 32 tracks displayed (#36609). Chris
Added a strand filter to the short match track (#36984). Max
Allow changes to custom track data, even when uploaded via URL (#35492). Max
Eliminated separate load/draw path for bigBeds with less than 9 fields. Use bigBed header for number of fields ONLY if the number of fields is not specified in trackDb (#36940). Brian
Improved readability of hub error message on hgTracks (#36916). Max
The disconnect button now appears in the group blue bar when a hub encounters an error (#36791). Max
Added hicArcLimit and hicArcLimitEnabled trackDb settings for Hi-C tracks to limit the number of displayed interactions in arc mode. These settings display only the N strongest interactions. This setting is enabled by default for all Hi-C tracks, with a default limit of the top 10000 interactions (#36774). Jonathan
Tweaked the auto-shading scheme for HI-C tracks when more than 1000 interactions are being displayed - ideally, this should result in fewer interactions displaying with a fully-saturated color (#36774). Jonathan
Hubspace: users can overwrite uploaded files and delete hub.txt files without deleting all other files in the hub. warn users about certain actions. Don't add auto-generated trackDb stanzas if the user is uploading a hub.txt and the bigDataUrl for a track in the hub.txt is part of the current upload (hacky reliance on scanning the file, not true trackDb parsing (#36830). Chris
Enabled filters in hgTrackUi for bigBed3 and bigBed4 (#28501). Brian
Creation of a new page to automate chain file requests/delivery (#31811). Hiram
Fixed hubUrl retry button url encoding. Chris
Fixed hubUrl encoding in hubSpace UI (#36936). Chris
Made grey bar icons and hgc popups on by default (#36953). Chris
Made trackHubsCanAddGroups the default setting (#36955). Brian
Encode IDs used by jsOnEventById to prevent cases where IDs contain parentheses, quotes, etc. Now IDs can be used more safely in selectors too (#36841).
Whitelist GenArk in localUrl paths in isValidBigDataUrl() in customFactory.c (#34544). Galt
Added support for vai.pl to accept a GenArk assembly accession as db, and for hgVai to accept a geneTrack without the hub_number_ prefix when db is a hub (#36534). Angie
Moved parsePosition and parseRange routines into common.c. Added callback routines for -bed and -positions shared library bigBedCmdSupport and refactored the utilities to use them. -bed and -positions input are sorted automatically by chrom, start (#28109). Galt
Modified pslMap to remotely access chain psl input file if given a URL. Mark
Added number of aligned bases, alignment span, and strand to pslStats. Mark
CGIs should report when they fail to connect to a bottleneck server, rather than silently dying (#36992). Jonathan
Incorporated changes from Andrew Smith to tidy up the new facetedComposite UI for composite tracks (#36320). Jonathan
Fixed the problem with liftOver with genePreds when the result ends up on a different strand and the exonFrames need to be reversed. Brian
Hide table browser link on hgTrackUi for superTracks as per MarkD request. Max
Increased buffer size for VCF INFO field. Max

v492 Genome Browser Software

This is the v492 release of the UCSC Genome Browser. A summary of the relevant code changes includes:

• Save HGVS searches onto the search history stack.
• HGVS searches use the refSeqSelect table if the transcript is present.
• Do HGVS searches in the auto-suggest position box on hgTracks.
• Fixed hgTrackUi to properly show filters for bigBeds with less than five fields.
• In bigBed click handling, changed error to warning when trackDb type field count differs from the bigBed header.
• Removed the info link for quickLift groups in hgTracks.
• Fixed gene alleles section of hgGene when doing hgGene in the popup on hgTracks.
• Fixed hgTracks tooltips to store the tooltip information in the 'data-tooltip' attribute instead of in the 'title' attribute to preserve the title strings. wait until DOMContentLoaded to actually parse the titles into 'data-tooltip' so the text size variable is presen.
• Fixed default hidden sections in hgGene to properly open when clicked, and fixed the population button in the Common Gene Haplotype Alleles section.
• Fixed PDF output problem in hgTracks. Previously, we had set hgFindMatches = NULL for PDF output to suppress the item search highlight in the generated PDF. But track loading code in bigBedTrack and squishPackyMode both depend on that search term, those routines that need the original search value.
• Added hgTables Summary and intersection buttons for knownCanonical.
• Fixed missing field descriptions for mm39 knownGene.
• Fixed Table Browser to allow bigGenePred to be used like genePred and provide CDS FASTA output.
• Fixed hgTables Sequence output with CDS casing bug that caused introns to be upper case and has existed since 2002.
• Fixed hgLiftOver min match filter with -multiple fixed. It has been allowing too-small regions in the output. Error was in the system since 2013.
• Beginning to import the TOGA V2 annotations. Added a 'hideToggle' class element to hgc description page to allow hide/show of text on the description page for a track item. Function is on the TOGA V2 details page.

v491 Genome Browser Software

This is the v491 release of the UCSC Genome Browser. A summary of the relevant code changes includes:

• Single path for loading bigBeds, and auto-recognizing the bigBed type based on the header.
• Initial import and rework of a new faceted UI for composite tracks, intended for situations where there are too many tracks for the existing composite UI to be usable. The feature was graciously contributed by Andrew Smith at USC.
• Added a checkbox that turns on rearrangement mode automatically for all CTs generated by hgBlat.
• Fixed another jquery-upgrade-induced bug on the composite track UI page.
• Fixed a problem quickLifting between human assemblies.
• Fixed link to hs1 browser from hub management page listing track hub.
• hConnectCentralNoCache can now access remote central servers.
• The right-click menu in hgTracks was listing all visibility options for tracks with an onlyVisibility setting (which is supposed to limit options). It has been made aware of the setting.
• Fixed maf frames caching bug.
• Fixed search bug on assembly hubs with supertracks caused by spurious calls to hubCollectTracks.
• Made listExisting endpoint to hubApi/liftOver respect fromGenome and toGenome arguments, taking precedence over the filter argument. If both fromGenome and toGenome arguments are present, they are ANDed together.
• Explicitly send cookies when doing async cart requests.
• Added option to twoBitMask to allow a bigBed file for masking.
• Fixed mafAddIrows and mafSplit to recognize GenArk GCx... assemblies in MAF files where the problem was the assembly name has dots in the name, and MAF files delineate assembly name and sequence name with a dot.