All File Changes

v499_base to v500_preview (2026-06-01 to 2026-06-08) v500

• confs/asia.hg.conf
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    7ab07c9ed7ee4fa16601a8ec4b8ba7931ef487be Sun Jun 7 01:11:21 2026 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 1, context: html, text, full: html, text
    7ab07c9ed7ee4fa16601a8ec4b8ba7931ef487be Sun Jun 7 01:11:21 2026 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
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    7ab07c9ed7ee4fa16601a8ec4b8ba7931ef487be Sun Jun 7 01:11:21 2026 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 6, context: html, text, full: html, text
    7ab07c9ed7ee4fa16601a8ec4b8ba7931ef487be Sun Jun 7 01:11:21 2026 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/blastToPsl/blastToPsl.c
  • lines changed 5, context: html, text, full: html, text
    bea3a22e1454e8fee62a026ffcec8c57af4005be Sat Jun 6 13:46:13 2026 -0700
    added -tsv option blastToPsl and blastXmlToPsl to allow parsing scores with other programs
• src/hg/blastToPsl/blastXmlToPsl.c
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    bea3a22e1454e8fee62a026ffcec8c57af4005be Sat Jun 6 13:46:13 2026 -0700
    added -tsv option blastToPsl and blastXmlToPsl to allow parsing scores with other programs
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    051d8d750d9ee269ea2a26575a90a8591fb4cd84 Mon Jun 8 09:34:32 2026 -0700
    added option to get accession with version from blast xml
• src/hg/blastToPsl/pslBuild.c
  • lines changed 4, context: html, text, full: html, text
    bea3a22e1454e8fee62a026ffcec8c57af4005be Sat Jun 6 13:46:13 2026 -0700
    added -tsv option blastToPsl and blastXmlToPsl to allow parsing scores with other programs
• src/hg/blastToPsl/pslBuild.h
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    bea3a22e1454e8fee62a026ffcec8c57af4005be Sat Jun 6 13:46:13 2026 -0700
    added -tsv option blastToPsl and blastXmlToPsl to allow parsing scores with other programs
• src/hg/blastToPsl/tests/expected/hitIdIdTest.psl
  • lines changed 2, context: html, text, full: html, text
    051d8d750d9ee269ea2a26575a90a8591fb4cd84 Mon Jun 8 09:34:32 2026 -0700
    added option to get accession with version from blast xml
• src/hg/blastToPsl/tests/expected/mrna1TsvTest.psl
  • lines changed 12, context: html, text, full: html, text
    bea3a22e1454e8fee62a026ffcec8c57af4005be Sat Jun 6 13:46:13 2026 -0700
    added -tsv option blastToPsl and blastXmlToPsl to allow parsing scores with other programs
• src/hg/blastToPsl/tests/expected/mrna1TsvTest.tsv
  • lines changed 13, context: html, text, full: html, text
    bea3a22e1454e8fee62a026ffcec8c57af4005be Sat Jun 6 13:46:13 2026 -0700
    added -tsv option blastToPsl and blastXmlToPsl to allow parsing scores with other programs
• src/hg/blastToPsl/tests/expected/protMrnaTsvTest.psl
  • lines changed 186, context: html, text, full: html, text
    bea3a22e1454e8fee62a026ffcec8c57af4005be Sat Jun 6 13:46:13 2026 -0700
    added -tsv option blastToPsl and blastXmlToPsl to allow parsing scores with other programs
• src/hg/blastToPsl/tests/expected/protMrnaTsvTest.tsv
  • lines changed 187, context: html, text, full: html, text
    bea3a22e1454e8fee62a026ffcec8c57af4005be Sat Jun 6 13:46:13 2026 -0700
    added -tsv option blastToPsl and blastXmlToPsl to allow parsing scores with other programs
• src/hg/blastToPsl/tests/input/blastn-ncbi-seqs.xml
  • lines changed 118, context: html, text, full: html, text
    a19ed7de71135030a5f88e8bc7098db99fa3e96a Mon Jun 8 09:27:19 2026 -0700
    *** empty log message ***
• src/hg/blastToPsl/tests/makefile
  • lines changed 17, context: html, text, full: html, text
    bea3a22e1454e8fee62a026ffcec8c57af4005be Sat Jun 6 13:46:13 2026 -0700
    added -tsv option blastToPsl and blastXmlToPsl to allow parsing scores with other programs
  • lines changed 7, context: html, text, full: html, text
    051d8d750d9ee269ea2a26575a90a8591fb4cd84 Mon Jun 8 09:34:32 2026 -0700
    added option to get accession with version from blast xml
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 5, context: html, text, full: html, text
    97b76b70f427425072a5b03e7397d076f9f2eebb Wed Jun 3 14:35:33 2026 -0700
    Adding spreadsheet link for SING milestones Year2 and clickable link from timeline
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    da0ead94b78ebd2a515f24aa8261ec65dfacb80a Wed Jun 3 14:38:52 2026 -0700
    SING edit -different grant year cycle (ends 12/31 vs 3/31 for rest of SSPsyGene)
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    211087d88b1c5e2962e8164c13f8dc74c53eb638 Thu Jun 4 12:13:44 2026 -0700
    Adding WUSTL ADGC#7 clickable link to 2026 milestones
  • lines changed 4, context: html, text, full: html, text
    8f89bbd889070be63a5a632b93f4e0e9fd69078b Thu Jun 4 14:43:25 2026 -0700
    Adding UCLA 2026Q4 column _P_ milestones to timeline
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    00334da1123c09a4a857339398546e2eaf94de0f Fri Jun 5 13:06:56 2026 -0700
    Marking Broad/ADGC4 items as active=inprogress per PI Sami email June 2026
• src/hg/hgApi/hgApi.c
  • lines changed 31, context: html, text, full: html, text
    f93b8662afd701763c24634879d05dc08b3178de Fri Jun 5 02:24:16 2026 -0700
    Add exon search: jump to GENE exon N from position box I'm comitting this thinking that the way that we implement searches leads to duplication of code that doesn't look great to me. While this feature looks good, the code duplication across C/JS should probably get reduced with a different approach to the "quick jump" way of the page. We have currently three ways to quick jump, I think: - chr:start-end - rsxxxxx - gene symbol + autosuggest pick - HGVS? They are recognized by both the javascript and the C code with regexes. I think all of these should be probably be only implemented in the C code. The JS only sends the current string to the C code and then gets back if this can be autocompleted and to which position and what to show in the autosuggest area. For example if you type "SOD1<space>e" the C code could send back "Continue typing to jump to exon" and once you're at "SOD1<space>exon 5" the C code sends back "Hit enter to jump to chrX:123123-123213". This would work with any type of identifier and the code would stay in the C code, not more duplication and it would be much clearer to the user what is recognized in the search box. Users can now type "TP53 exon 5" or "TP53:e.5[+/-offset]" in the genome browser position/search box to navigate directly to that exon. The ":e.N" notation follows the VICC Gene Fusion Specification. An optional intronic offset (":e.5+2") lands N bases past the exon boundary, useful for splice site inspection. C (hgFind.c): findGeneExon() resolves the query against the SQL genePred tables listed in the hg.conf "geneTracks" key (default: mane, ncbiRefSeqSelect, knownGene, ncbiRefSeq, ncbiRefSeqHistorical). bigGenePred tracks (e.g. mane) are supported via bigBedOpenExtraIndex. Uses the existing exonToPos() function for strand-aware exon lookup. fixSinglePos() is called so hgp->singlePos is populated for callers. hgApi.c: new cmd=geneExonToPos returns {"pos":"chrom:start-end"} JSON so JS can navigate in place without a full page redirect to hgSearch. Direct URL links (hgTracks?position=GENE+exon+N) also work because findGeneExon() is hooked into hgPositionsFind(). JS: autocomplete.js injects a local "Jump to exon N" suggestion as soon as the exon pattern is detected, or a hint item when the query is still partial ("GENE ex"). Selecting either navigates via hgApi. hgTracks.js routes the two new autocomplete item types to the hgApi call. utils.js adds the two regexes (geneExonExp, geneExonCoordExp). query.html: documents both syntaxes; the :e.N notation links to the VICC Gene Fusion Specification at fusions.cancervariants.org.
• src/hg/hgHubConnect/hooks/pre-finish.c
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    ca23d9f5054fc863beb18d7ef4919b550b2f8d9c Mon Jun 1 10:45:37 2026 -0700
    Allow dot in genome names in hubspace uploads, refs #37665
• src/hg/hgPhyloPlace/debugRecombinantDisplay.c
  • lines changed 8, context: html, text, full: html, text
    92ca35b40020f7b62a7dbd42a7bad7257a4c3eb2 Mon Jun 1 12:15:43 2026 -0700
    Add font size select to recombinant display popup.
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    bfc432194b2d9561227ed39f44593a68d1c90842 Thu Jun 4 22:06:18 2026 -0700
    Recombinant display: show informative only by default.
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 6, context: html, text, full: html, text
    92ca35b40020f7b62a7dbd42a7bad7257a4c3eb2 Mon Jun 1 12:15:43 2026 -0700
    Add font size select to recombinant display popup.
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    bfc432194b2d9561227ed39f44593a68d1c90842 Thu Jun 4 22:06:18 2026 -0700
    Recombinant display: show informative only by default.
• src/hg/hgPublicSessions/hgPublicSessions.c
  • lines changed 5, context: html, text, full: html, text
    48b00fd6aaa85aee01dc7efb2c68374bf980c1a2 Mon Jun 1 15:17:50 2026 -0700
    Fix not html encoding hgPublic sessions output of username, sessionName, db, and searchStr fields, refs #37663
• src/hg/hgSession/backup.c
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    4cffc3eb6f43e109452b5b52d1f760cf1ea6a981 Sun Jun 7 21:47:37 2026 -0700
    Adjusting sessionDb and userDb IDs to be 64-bit in the code, since the database is now ready for it and we're crossing the threshold. refs #33554
• src/hg/hgTables/schema.c
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    7d74f16b6443b2155b8638052919ed4952a6e786 Wed Jun 3 13:00:02 2026 -0700
    Fix table schema button for myVariants tracks, no redmine
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    7d56cd6635651dfd4c9926d062d92ad7b65a3e80 Wed Jun 3 14:52:52 2026 -0700
    More myVariants changes: make the share to accept a comma-sep list of usernames, allow both the read/edit flag and the usernames setting to be editable after creation. When editing usernames, add a confirmation if the field is left blank that this will make the share viewable/editable by anyone with the link, refs #33808
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    cd92ebf69f8471c00837f12c4b3d22b89a1d450c Fri Jun 5 00:08:22 2026 -0700
    Suppress Description link at the top of composite trackUi pages when there's no description, no ticket (email with collaborator)
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    4cffc3eb6f43e109452b5b52d1f760cf1ea6a981 Sun Jun 7 21:47:37 2026 -0700
    Adjusting sessionDb and userDb IDs to be 64-bit in the code, since the database is now ready for it and we're crossing the threshold. refs #33554
• src/hg/hgTracks/bigBedTrack.c
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    5dc1d6e658ab009f27314e192340275a6bb70237 Tue Jun 2 16:20:48 2026 -0700
    Add colorFields trackDb setting for bigBed/bigGenePred color scheme switching Adds a new trackDb statement `colorFields` that renders a "Color by:" dropdown in the track controls page, letting users switch among multiple pre-computed color schemes stored as extra bigBed fields containing R,G,B strings. The `default="label"` key renames the standard itemRgb option in the dropdown. Other entries name extra bigBed fields whose R,G,B values override itemRgb when selected. When a non-default scheme is active, a "(Coloring by: label)" suffix appears in the track long label. Changes: - hui.c/hui.h: new colorFieldsCfgUi() rendered inside bedScoreCfgUi() for bigBed - bigBedTrack.c: colorFieldIdx lookup + per-item filterColor override + longLabel suffix - tagTypes.tab: register colorFields for bigBed and bigGenePred - trackDbLibrary.shtml, trackDbDoc.html, trackDbHub.v3.html, changes.html: documentation refs #26253 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/hgTracks/config.c
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    07e5a2c08f148d8bf31219af8c2218cd2cc893cf Wed Jun 3 09:16:15 2026 -0700
    hgTracks config: pair FreeType font names with their files in one table The configure-page font list lived in two parallel arrays, freeTypeFontNames[] and freeTypeFontFiles[], matched only by position. Nothing tied a name to its file, and maybeNewFonts() looked a name up in the first array and then indexed the second with no bounds check -- so any drift in order or count between the two, or a selected name that matched nothing, silently rendered the wrong font or read past the end of the array. Merge the two arrays into a single struct freeTypeFont[] of {name, file} rows so the two can no longer get out of sync, and make maybeNewFonts() fall back to the bitmap engine when the selected font isn't one we know instead of indexing out of bounds. Same fonts and same name-to-file mapping as before. Also fix faceNames[] to size by element count (ArraySize) rather than byte count (sizeof). refs #37698 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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    60d8399ce8617bf31d27b7752576b66a9f29d9b2 Wed Jun 3 09:20:22 2026 -0700
    hgTracks config: document how to add a new FreeType font Add a "HOW TO ADD A NEW FONT" comment block above the freeTypeFonts[] table explaining the two steps (place the file under freeTypeDir, add a {name, file} row), how freeTypeDir resolves relative to the CGI working directory (so it finds the shared htdocs/urw-fonts even from a per-user sandbox), the name/face/style convention used by the configure-page dropdown, and the gotchas -- notably that variable fonts like InterVariable.ttf render only their default master instance, so a static single-weight file should be used instead. refs #37698 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/hgTracks/hgTracks.c
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    0df5f6317fd6e0033a31aaf56b928f574823075c Wed Jun 3 11:06:54 2026 -0700
    Recommended track sets now can load from a file in htdocs/data/recTrackSets/db/sessionName. The settings are overlayed onto the current cart and no reload of the page is required anymore, refs #37281
• src/hg/hgTracks/hgTracks.h
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    0df5f6317fd6e0033a31aaf56b928f574823075c Wed Jun 3 11:06:54 2026 -0700
    Recommended track sets now can load from a file in htdocs/data/recTrackSets/db/sessionName. The settings are overlayed onto the current cart and no reload of the page is required anymore, refs #37281
• src/hg/hgTracks/myVariantsTrack.c
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    7d56cd6635651dfd4c9926d062d92ad7b65a3e80 Wed Jun 3 14:52:52 2026 -0700
    More myVariants changes: make the share to accept a comma-sep list of usernames, allow both the read/edit flag and the usernames setting to be editable after creation. When editing usernames, add a confirmation if the field is left blank that this will make the share viewable/editable by anyone with the link, refs #33808
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    d8900846fdae9183808ccd57864191ee48fca00e Fri Jun 5 10:07:25 2026 -0700
    myVariants: fix item display and HGVS gene-track lookup on GenArk hubs, refs #33808 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
• src/hg/hgTracks/recTrackSets.c
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    0df5f6317fd6e0033a31aaf56b928f574823075c Wed Jun 3 11:06:54 2026 -0700
    Recommended track sets now can load from a file in htdocs/data/recTrackSets/db/sessionName. The settings are overlayed onto the current cart and no reload of the page is required anymore, refs #37281
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    3b6659d987c9b7afd53828faf7a6a3487bbc751a Fri Jun 5 13:17:35 2026 -0700
    Update where recTrackSets pulls the .tab files from, refs #32768
• src/hg/hgc/ccdsClick.c
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    1f88a89d5bb7bada7c52ad89f910c6796d1340ed Tue Jun 2 12:26:10 2026 -0700
    Add note on quickLifted CCDS pages explaining the data is from the source assembly, refs #36125 When a user clicks the CCDS link on a quickLifted gene track, the CCDS page necessarily loads from the source assembly (hg38), since CCDS tables exist only there. Mark the click with a one-shot quickLiftCcds CGI var carrying the destination assembly, and on the CCDS page print a note explaining that the CCDS gene model and coordinates shown are from the source assembly, not the destination assembly the user was browsing. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
• src/hg/hgc/hgc.c
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    1f88a89d5bb7bada7c52ad89f910c6796d1340ed Tue Jun 2 12:26:10 2026 -0700
    Add note on quickLifted CCDS pages explaining the data is from the source assembly, refs #36125 When a user clicks the CCDS link on a quickLifted gene track, the CCDS page necessarily loads from the source assembly (hg38), since CCDS tables exist only there. Mark the click with a one-shot quickLiftCcds CGI var carrying the destination assembly, and on the CCDS page print a note explaining that the CCDS gene model and coordinates shown are from the source assembly, not the destination assembly the user was browsing. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
• src/hg/hgc/myVariantsClick.c
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    40b4fc89ec72c22cae51bf9a8b9a7e8dd887eebf Thu Jun 4 15:34:16 2026 -0700
    Show MANE-relative HGVS terms on myVariants SNV detail pages, refs #33808 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/data/recTrackSets/hg19/BRCA1_BRCA2_ENIGMA_hg19
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    89150a8298312f2cc4b69809a65a947cd80a2035 Fri Jun 5 10:14:23 2026 -0700
    Seed the remaining 12 Recommended Track Set files under htdocs/data/recTrackSets/ for Chris's file-based loader. All fetched from RR via rtsUpdate fetch with the final scrub list (eaa7ebfc733). Per-session counts (source vars -> kept after scrub): hg19 CNVs%20Clinical 701->615, Non%20coding%20SNVs 630->572, Exon_Relevance_hg19 977->891, Problematic%20Regions 241->189, BRCA1_BRCA2_ENIGMA_hg19 759->672 (includes the stray ' hgsid=' artifact now caught by the whitespace-key check), insightVcepHg19 210->182; hg38 Clinical_SNVs_hg38 707->625, Clinical_CNVs_hg38 723->640, Exon_Relevance_hg38 962->879, Problematic_Regions_hg38 311->272, BRCA1_BRCA2_ENIGMA_hg38 808->721, insightVcepHg38 266->240. With this, every entry in recTrackSets.{hg19,hg38}.tab has a corresponding file; the namedSessionDb fallback path is no longer needed for these sessions. refs #32768
• src/hg/htdocs/data/recTrackSets/hg19/CNVs%20Clinical
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    89150a8298312f2cc4b69809a65a947cd80a2035 Fri Jun 5 10:14:23 2026 -0700
    Seed the remaining 12 Recommended Track Set files under htdocs/data/recTrackSets/ for Chris's file-based loader. All fetched from RR via rtsUpdate fetch with the final scrub list (eaa7ebfc733). Per-session counts (source vars -> kept after scrub): hg19 CNVs%20Clinical 701->615, Non%20coding%20SNVs 630->572, Exon_Relevance_hg19 977->891, Problematic%20Regions 241->189, BRCA1_BRCA2_ENIGMA_hg19 759->672 (includes the stray ' hgsid=' artifact now caught by the whitespace-key check), insightVcepHg19 210->182; hg38 Clinical_SNVs_hg38 707->625, Clinical_CNVs_hg38 723->640, Exon_Relevance_hg38 962->879, Problematic_Regions_hg38 311->272, BRCA1_BRCA2_ENIGMA_hg38 808->721, insightVcepHg38 266->240. With this, every entry in recTrackSets.{hg19,hg38}.tab has a corresponding file; the namedSessionDb fallback path is no longer needed for these sessions. refs #32768
• src/hg/htdocs/data/recTrackSets/hg19/Exon_Relevance_hg19
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    89150a8298312f2cc4b69809a65a947cd80a2035 Fri Jun 5 10:14:23 2026 -0700
    Seed the remaining 12 Recommended Track Set files under htdocs/data/recTrackSets/ for Chris's file-based loader. All fetched from RR via rtsUpdate fetch with the final scrub list (eaa7ebfc733). Per-session counts (source vars -> kept after scrub): hg19 CNVs%20Clinical 701->615, Non%20coding%20SNVs 630->572, Exon_Relevance_hg19 977->891, Problematic%20Regions 241->189, BRCA1_BRCA2_ENIGMA_hg19 759->672 (includes the stray ' hgsid=' artifact now caught by the whitespace-key check), insightVcepHg19 210->182; hg38 Clinical_SNVs_hg38 707->625, Clinical_CNVs_hg38 723->640, Exon_Relevance_hg38 962->879, Problematic_Regions_hg38 311->272, BRCA1_BRCA2_ENIGMA_hg38 808->721, insightVcepHg38 266->240. With this, every entry in recTrackSets.{hg19,hg38}.tab has a corresponding file; the namedSessionDb fallback path is no longer needed for these sessions. refs #32768
• src/hg/htdocs/data/recTrackSets/hg19/Non%20coding%20SNVs
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    89150a8298312f2cc4b69809a65a947cd80a2035 Fri Jun 5 10:14:23 2026 -0700
    Seed the remaining 12 Recommended Track Set files under htdocs/data/recTrackSets/ for Chris's file-based loader. All fetched from RR via rtsUpdate fetch with the final scrub list (eaa7ebfc733). Per-session counts (source vars -> kept after scrub): hg19 CNVs%20Clinical 701->615, Non%20coding%20SNVs 630->572, Exon_Relevance_hg19 977->891, Problematic%20Regions 241->189, BRCA1_BRCA2_ENIGMA_hg19 759->672 (includes the stray ' hgsid=' artifact now caught by the whitespace-key check), insightVcepHg19 210->182; hg38 Clinical_SNVs_hg38 707->625, Clinical_CNVs_hg38 723->640, Exon_Relevance_hg38 962->879, Problematic_Regions_hg38 311->272, BRCA1_BRCA2_ENIGMA_hg38 808->721, insightVcepHg38 266->240. With this, every entry in recTrackSets.{hg19,hg38}.tab has a corresponding file; the namedSessionDb fallback path is no longer needed for these sessions. refs #32768
• src/hg/htdocs/data/recTrackSets/hg19/Problematic%20Regions
  • lines changed 189, context: html, text, full: html, text
    89150a8298312f2cc4b69809a65a947cd80a2035 Fri Jun 5 10:14:23 2026 -0700
    Seed the remaining 12 Recommended Track Set files under htdocs/data/recTrackSets/ for Chris's file-based loader. All fetched from RR via rtsUpdate fetch with the final scrub list (eaa7ebfc733). Per-session counts (source vars -> kept after scrub): hg19 CNVs%20Clinical 701->615, Non%20coding%20SNVs 630->572, Exon_Relevance_hg19 977->891, Problematic%20Regions 241->189, BRCA1_BRCA2_ENIGMA_hg19 759->672 (includes the stray ' hgsid=' artifact now caught by the whitespace-key check), insightVcepHg19 210->182; hg38 Clinical_SNVs_hg38 707->625, Clinical_CNVs_hg38 723->640, Exon_Relevance_hg38 962->879, Problematic_Regions_hg38 311->272, BRCA1_BRCA2_ENIGMA_hg38 808->721, insightVcepHg38 266->240. With this, every entry in recTrackSets.{hg19,hg38}.tab has a corresponding file; the namedSessionDb fallback path is no longer needed for these sessions. refs #32768
• src/hg/htdocs/data/recTrackSets/hg19/SNVs%20Clinical
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    ef826dbcf8ee0961e27c38050deee74c9870ac05 Tue Jun 2 12:43:26 2026 -0700
    Seed htdocs/data/recTrackSets/ for the upcoming file-based RTS loader: one example RTS per assembly (hg19/SNVs%20Clinical, hg38/Non_Coding_SNVs_hg38), plus copies of the recTrackSets.hg19.tab and recTrackSets.hg38.tab manifests at the top of the new directory. Per-session file format is the same one-key=value-per-line scrubbed cart produced by rtsUpdate. Also refreshes utils/rts/hg19/SNVs%20Clinical via rtsUpdate fetch (676 -> 660 vars after scrub) so both locations agree during the transition. refs #32768
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    ea5553ec83f3f65757c5cc2b1d3b4c676f7f218b Fri Jun 5 10:04:02 2026 -0700
    Retroactively rescrub the two already-seeded RTS files with the expanded verboten.lst from 973632e4fe1. Non_Coding_SNVs_hg38: 574 -> 538 cart vars (drops hgS_*, coord ints, display prefs, lastPosition/oldPosition, virtMode state, rtsLoad, redirect, etc.); SNVs%20Clinical: 660 -> 609 cart vars (same classes). Net effect is RTS files that only contain what the loader should actually apply to user carts. refs #32768
  • lines changed 20, context: html, text, full: html, text
    58e070461663f4d71ce17eb93b17225b20071371 Fri Jun 5 10:12:34 2026 -0700
    Expand verboten.lst with 18 more patterns surfaced during Phase C1 dry-run of the remaining 12 RTS sessions: leaked state from other CGIs (hgg_, hglft_, hgta_, hgHub_do_search), additional hgTracks UI state (hgt_, hgt_configGroupTarget, hgt_doJsCommand, hgt_mdbVal/Var, rulerBaseZoom, hgTracksConfigPage), debris (European, source, sessionTable_length), per-db reverse-complement toggle (complement_<db>), gateway-style position-search input (search), Track Search dialog state (ts*), and single-letter hgc track selector (g). Also drop pairs with empty or whitespace-tainted keys in scrub() to defend against future cart-string corruption (caught a stray ' hgsid=...' from a manually-edited 2021 cart row in BRCA1_BRCA2_ENIGMA_hg19). Re-fetch the 2 already-seeded files so the whole corpus uses the final scrub list. refs #32768
• src/hg/htdocs/data/recTrackSets/hg19/insightVcepHg19
  • lines changed 182, context: html, text, full: html, text
    89150a8298312f2cc4b69809a65a947cd80a2035 Fri Jun 5 10:14:23 2026 -0700
    Seed the remaining 12 Recommended Track Set files under htdocs/data/recTrackSets/ for Chris's file-based loader. All fetched from RR via rtsUpdate fetch with the final scrub list (eaa7ebfc733). Per-session counts (source vars -> kept after scrub): hg19 CNVs%20Clinical 701->615, Non%20coding%20SNVs 630->572, Exon_Relevance_hg19 977->891, Problematic%20Regions 241->189, BRCA1_BRCA2_ENIGMA_hg19 759->672 (includes the stray ' hgsid=' artifact now caught by the whitespace-key check), insightVcepHg19 210->182; hg38 Clinical_SNVs_hg38 707->625, Clinical_CNVs_hg38 723->640, Exon_Relevance_hg38 962->879, Problematic_Regions_hg38 311->272, BRCA1_BRCA2_ENIGMA_hg38 808->721, insightVcepHg38 266->240. With this, every entry in recTrackSets.{hg19,hg38}.tab has a corresponding file; the namedSessionDb fallback path is no longer needed for these sessions. refs #32768
• src/hg/htdocs/data/recTrackSets/hg38/BRCA1_BRCA2_ENIGMA_hg38
  • lines changed 721, context: html, text, full: html, text
    89150a8298312f2cc4b69809a65a947cd80a2035 Fri Jun 5 10:14:23 2026 -0700
    Seed the remaining 12 Recommended Track Set files under htdocs/data/recTrackSets/ for Chris's file-based loader. All fetched from RR via rtsUpdate fetch with the final scrub list (eaa7ebfc733). Per-session counts (source vars -> kept after scrub): hg19 CNVs%20Clinical 701->615, Non%20coding%20SNVs 630->572, Exon_Relevance_hg19 977->891, Problematic%20Regions 241->189, BRCA1_BRCA2_ENIGMA_hg19 759->672 (includes the stray ' hgsid=' artifact now caught by the whitespace-key check), insightVcepHg19 210->182; hg38 Clinical_SNVs_hg38 707->625, Clinical_CNVs_hg38 723->640, Exon_Relevance_hg38 962->879, Problematic_Regions_hg38 311->272, BRCA1_BRCA2_ENIGMA_hg38 808->721, insightVcepHg38 266->240. With this, every entry in recTrackSets.{hg19,hg38}.tab has a corresponding file; the namedSessionDb fallback path is no longer needed for these sessions. refs #32768
• src/hg/htdocs/data/recTrackSets/hg38/Clinical_CNVs_hg38
  • lines changed 640, context: html, text, full: html, text
    89150a8298312f2cc4b69809a65a947cd80a2035 Fri Jun 5 10:14:23 2026 -0700
    Seed the remaining 12 Recommended Track Set files under htdocs/data/recTrackSets/ for Chris's file-based loader. All fetched from RR via rtsUpdate fetch with the final scrub list (eaa7ebfc733). Per-session counts (source vars -> kept after scrub): hg19 CNVs%20Clinical 701->615, Non%20coding%20SNVs 630->572, Exon_Relevance_hg19 977->891, Problematic%20Regions 241->189, BRCA1_BRCA2_ENIGMA_hg19 759->672 (includes the stray ' hgsid=' artifact now caught by the whitespace-key check), insightVcepHg19 210->182; hg38 Clinical_SNVs_hg38 707->625, Clinical_CNVs_hg38 723->640, Exon_Relevance_hg38 962->879, Problematic_Regions_hg38 311->272, BRCA1_BRCA2_ENIGMA_hg38 808->721, insightVcepHg38 266->240. With this, every entry in recTrackSets.{hg19,hg38}.tab has a corresponding file; the namedSessionDb fallback path is no longer needed for these sessions. refs #32768
• src/hg/htdocs/data/recTrackSets/hg38/Clinical_SNVs_hg38
  • lines changed 625, context: html, text, full: html, text
    89150a8298312f2cc4b69809a65a947cd80a2035 Fri Jun 5 10:14:23 2026 -0700
    Seed the remaining 12 Recommended Track Set files under htdocs/data/recTrackSets/ for Chris's file-based loader. All fetched from RR via rtsUpdate fetch with the final scrub list (eaa7ebfc733). Per-session counts (source vars -> kept after scrub): hg19 CNVs%20Clinical 701->615, Non%20coding%20SNVs 630->572, Exon_Relevance_hg19 977->891, Problematic%20Regions 241->189, BRCA1_BRCA2_ENIGMA_hg19 759->672 (includes the stray ' hgsid=' artifact now caught by the whitespace-key check), insightVcepHg19 210->182; hg38 Clinical_SNVs_hg38 707->625, Clinical_CNVs_hg38 723->640, Exon_Relevance_hg38 962->879, Problematic_Regions_hg38 311->272, BRCA1_BRCA2_ENIGMA_hg38 808->721, insightVcepHg38 266->240. With this, every entry in recTrackSets.{hg19,hg38}.tab has a corresponding file; the namedSessionDb fallback path is no longer needed for these sessions. refs #32768
• src/hg/htdocs/data/recTrackSets/hg38/Exon_Relevance_hg38
  • lines changed 879, context: html, text, full: html, text
    89150a8298312f2cc4b69809a65a947cd80a2035 Fri Jun 5 10:14:23 2026 -0700
    Seed the remaining 12 Recommended Track Set files under htdocs/data/recTrackSets/ for Chris's file-based loader. All fetched from RR via rtsUpdate fetch with the final scrub list (eaa7ebfc733). Per-session counts (source vars -> kept after scrub): hg19 CNVs%20Clinical 701->615, Non%20coding%20SNVs 630->572, Exon_Relevance_hg19 977->891, Problematic%20Regions 241->189, BRCA1_BRCA2_ENIGMA_hg19 759->672 (includes the stray ' hgsid=' artifact now caught by the whitespace-key check), insightVcepHg19 210->182; hg38 Clinical_SNVs_hg38 707->625, Clinical_CNVs_hg38 723->640, Exon_Relevance_hg38 962->879, Problematic_Regions_hg38 311->272, BRCA1_BRCA2_ENIGMA_hg38 808->721, insightVcepHg38 266->240. With this, every entry in recTrackSets.{hg19,hg38}.tab has a corresponding file; the namedSessionDb fallback path is no longer needed for these sessions. refs #32768
• src/hg/htdocs/data/recTrackSets/hg38/Non_Coding_SNVs_hg38
  • lines changed 574, context: html, text, full: html, text
    ef826dbcf8ee0961e27c38050deee74c9870ac05 Tue Jun 2 12:43:26 2026 -0700
    Seed htdocs/data/recTrackSets/ for the upcoming file-based RTS loader: one example RTS per assembly (hg19/SNVs%20Clinical, hg38/Non_Coding_SNVs_hg38), plus copies of the recTrackSets.hg19.tab and recTrackSets.hg38.tab manifests at the top of the new directory. Per-session file format is the same one-key=value-per-line scrubbed cart produced by rtsUpdate. Also refreshes utils/rts/hg19/SNVs%20Clinical via rtsUpdate fetch (676 -> 660 vars after scrub) so both locations agree during the transition. refs #32768
  • lines changed 48, context: html, text, full: html, text
    ea5553ec83f3f65757c5cc2b1d3b4c676f7f218b Fri Jun 5 10:04:02 2026 -0700
    Retroactively rescrub the two already-seeded RTS files with the expanded verboten.lst from 973632e4fe1. Non_Coding_SNVs_hg38: 574 -> 538 cart vars (drops hgS_*, coord ints, display prefs, lastPosition/oldPosition, virtMode state, rtsLoad, redirect, etc.); SNVs%20Clinical: 660 -> 609 cart vars (same classes). Net effect is RTS files that only contain what the loader should actually apply to user carts. refs #32768
  • lines changed 3, context: html, text, full: html, text
    58e070461663f4d71ce17eb93b17225b20071371 Fri Jun 5 10:12:34 2026 -0700
    Expand verboten.lst with 18 more patterns surfaced during Phase C1 dry-run of the remaining 12 RTS sessions: leaked state from other CGIs (hgg_, hglft_, hgta_, hgHub_do_search), additional hgTracks UI state (hgt_, hgt_configGroupTarget, hgt_doJsCommand, hgt_mdbVal/Var, rulerBaseZoom, hgTracksConfigPage), debris (European, source, sessionTable_length), per-db reverse-complement toggle (complement_<db>), gateway-style position-search input (search), Track Search dialog state (ts*), and single-letter hgc track selector (g). Also drop pairs with empty or whitespace-tainted keys in scrub() to defend against future cart-string corruption (caught a stray ' hgsid=...' from a manually-edited 2021 cart row in BRCA1_BRCA2_ENIGMA_hg19). Re-fetch the 2 already-seeded files so the whole corpus uses the final scrub list. refs #32768
• src/hg/htdocs/data/recTrackSets/hg38/Problematic_Regions_hg38
  • lines changed 272, context: html, text, full: html, text
    89150a8298312f2cc4b69809a65a947cd80a2035 Fri Jun 5 10:14:23 2026 -0700
    Seed the remaining 12 Recommended Track Set files under htdocs/data/recTrackSets/ for Chris's file-based loader. All fetched from RR via rtsUpdate fetch with the final scrub list (eaa7ebfc733). Per-session counts (source vars -> kept after scrub): hg19 CNVs%20Clinical 701->615, Non%20coding%20SNVs 630->572, Exon_Relevance_hg19 977->891, Problematic%20Regions 241->189, BRCA1_BRCA2_ENIGMA_hg19 759->672 (includes the stray ' hgsid=' artifact now caught by the whitespace-key check), insightVcepHg19 210->182; hg38 Clinical_SNVs_hg38 707->625, Clinical_CNVs_hg38 723->640, Exon_Relevance_hg38 962->879, Problematic_Regions_hg38 311->272, BRCA1_BRCA2_ENIGMA_hg38 808->721, insightVcepHg38 266->240. With this, every entry in recTrackSets.{hg19,hg38}.tab has a corresponding file; the namedSessionDb fallback path is no longer needed for these sessions. refs #32768
• src/hg/htdocs/data/recTrackSets/hg38/insightVcepHg38
  • lines changed 240, context: html, text, full: html, text
    89150a8298312f2cc4b69809a65a947cd80a2035 Fri Jun 5 10:14:23 2026 -0700
    Seed the remaining 12 Recommended Track Set files under htdocs/data/recTrackSets/ for Chris's file-based loader. All fetched from RR via rtsUpdate fetch with the final scrub list (eaa7ebfc733). Per-session counts (source vars -> kept after scrub): hg19 CNVs%20Clinical 701->615, Non%20coding%20SNVs 630->572, Exon_Relevance_hg19 977->891, Problematic%20Regions 241->189, BRCA1_BRCA2_ENIGMA_hg19 759->672 (includes the stray ' hgsid=' artifact now caught by the whitespace-key check), insightVcepHg19 210->182; hg38 Clinical_SNVs_hg38 707->625, Clinical_CNVs_hg38 723->640, Exon_Relevance_hg38 962->879, Problematic_Regions_hg38 311->272, BRCA1_BRCA2_ENIGMA_hg38 808->721, insightVcepHg38 266->240. With this, every entry in recTrackSets.{hg19,hg38}.tab has a corresponding file; the namedSessionDb fallback path is no longer needed for these sessions. refs #32768
• src/hg/htdocs/data/recTrackSets/recTrackSets.hg19.tab
  • lines changed 17, context: html, text, full: html, text
    ef826dbcf8ee0961e27c38050deee74c9870ac05 Tue Jun 2 12:43:26 2026 -0700
    Seed htdocs/data/recTrackSets/ for the upcoming file-based RTS loader: one example RTS per assembly (hg19/SNVs%20Clinical, hg38/Non_Coding_SNVs_hg38), plus copies of the recTrackSets.hg19.tab and recTrackSets.hg38.tab manifests at the top of the new directory. Per-session file format is the same one-key=value-per-line scrubbed cart produced by rtsUpdate. Also refreshes utils/rts/hg19/SNVs%20Clinical via rtsUpdate fetch (676 -> 660 vars after scrub) so both locations agree during the transition. refs #32768
• src/hg/htdocs/data/recTrackSets/recTrackSets.hg38.tab
  • lines changed 17, context: html, text, full: html, text
    ef826dbcf8ee0961e27c38050deee74c9870ac05 Tue Jun 2 12:43:26 2026 -0700
    Seed htdocs/data/recTrackSets/ for the upcoming file-based RTS loader: one example RTS per assembly (hg19/SNVs%20Clinical, hg38/Non_Coding_SNVs_hg38), plus copies of the recTrackSets.hg19.tab and recTrackSets.hg38.tab manifests at the top of the new directory. Per-session file format is the same one-key=value-per-line scrubbed cart produced by rtsUpdate. Also refreshes utils/rts/hg19/SNVs%20Clinical via rtsUpdate fetch (676 -> 660 vars after scrub) so both locations agree during the transition. refs #32768
• src/hg/htdocs/goldenPath/help/facetedComposite.html
  • lines changed 163, context: html, text, full: html, text
    706d4aa403071faaf6646c05affbcfe896d427bd Mon Jun 1 16:32:25 2026 -0700
    Moving to a more tab-style for selected/all decision in faceted composite UI, plus some improvements to the docs. refs #36320
• src/hg/htdocs/goldenPath/help/query.html
  • lines changed 30, context: html, text, full: html, text
    f93b8662afd701763c24634879d05dc08b3178de Fri Jun 5 02:24:16 2026 -0700
    Add exon search: jump to GENE exon N from position box I'm comitting this thinking that the way that we implement searches leads to duplication of code that doesn't look great to me. While this feature looks good, the code duplication across C/JS should probably get reduced with a different approach to the "quick jump" way of the page. We have currently three ways to quick jump, I think: - chr:start-end - rsxxxxx - gene symbol + autosuggest pick - HGVS? They are recognized by both the javascript and the C code with regexes. I think all of these should be probably be only implemented in the C code. The JS only sends the current string to the C code and then gets back if this can be autocompleted and to which position and what to show in the autosuggest area. For example if you type "SOD1<space>e" the C code could send back "Continue typing to jump to exon" and once you're at "SOD1<space>exon 5" the C code sends back "Hit enter to jump to chrX:123123-123213". This would work with any type of identifier and the code would stay in the C code, not more duplication and it would be much clearer to the user what is recognized in the search box. Users can now type "TP53 exon 5" or "TP53:e.5[+/-offset]" in the genome browser position/search box to navigate directly to that exon. The ":e.N" notation follows the VICC Gene Fusion Specification. An optional intronic offset (":e.5+2") lands N bases past the exon boundary, useful for splice site inspection. C (hgFind.c): findGeneExon() resolves the query against the SQL genePred tables listed in the hg.conf "geneTracks" key (default: mane, ncbiRefSeqSelect, knownGene, ncbiRefSeq, ncbiRefSeqHistorical). bigGenePred tracks (e.g. mane) are supported via bigBedOpenExtraIndex. Uses the existing exonToPos() function for strand-aware exon lookup. fixSinglePos() is called so hgp->singlePos is populated for callers. hgApi.c: new cmd=geneExonToPos returns {"pos":"chrom:start-end"} JSON so JS can navigate in place without a full page redirect to hgSearch. Direct URL links (hgTracks?position=GENE+exon+N) also work because findGeneExon() is hooked into hgPositionsFind(). JS: autocomplete.js injects a local "Jump to exon N" suggestion as soon as the exon pattern is detected, or a hint item when the query is still partial ("GENE ex"). Selecting either navigates via hgApi. hgTracks.js routes the two new autocomplete item types to the hgApi call. utils.js adds the two regexes (geneExonExp, geneExonCoordExp). query.html: documents both syntaxes; the :e.N notation links to the VICC Gene Fusion Specification at fusions.cancervariants.org.
  • lines changed 4, context: html, text, full: html, text
    9b842af51fa1fa6ebe403f397ce52fc4448b9807 Fri Jun 5 03:32:12 2026 -0700
    docs
  • lines changed 1, context: html, text, full: html, text
    6f429cb567c6a0245bb1f8b98c68071739562f1b Mon Jun 8 05:49:53 2026 -0700
    query.html: fix serial comma and quote style in exon search docs no redmine Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/trackDb/changes.html
  • lines changed 12, context: html, text, full: html, text
    5dc1d6e658ab009f27314e192340275a6bb70237 Tue Jun 2 16:20:48 2026 -0700
    Add colorFields trackDb setting for bigBed/bigGenePred color scheme switching Adds a new trackDb statement `colorFields` that renders a "Color by:" dropdown in the track controls page, letting users switch among multiple pre-computed color schemes stored as extra bigBed fields containing R,G,B strings. The `default="label"` key renames the standard itemRgb option in the dropdown. Other entries name extra bigBed fields whose R,G,B values override itemRgb when selected. When a non-default scheme is active, a "(Coloring by: label)" suffix appears in the track long label. Changes: - hui.c/hui.h: new colorFieldsCfgUi() rendered inside bedScoreCfgUi() for bigBed - bigBedTrack.c: colorFieldIdx lookup + per-item filterColor override + longLabel suffix - tagTypes.tab: register colorFields for bigBed and bigGenePred - trackDbLibrary.shtml, trackDbDoc.html, trackDbHub.v3.html, changes.html: documentation refs #26253 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 9, context: html, text, full: html, text
    ce17d11af0cc02a8aef4f0588a92ac6ff9c0e14d Mon Jun 1 16:53:29 2026 -0700
    Code review edits: closing <A name> anchor tags in the filter and highlight section of trackDbDoc.html. refs #37674
  • lines changed 7, context: html, text, full: html, text
    5dc1d6e658ab009f27314e192340275a6bb70237 Tue Jun 2 16:20:48 2026 -0700
    Add colorFields trackDb setting for bigBed/bigGenePred color scheme switching Adds a new trackDb statement `colorFields` that renders a "Color by:" dropdown in the track controls page, letting users switch among multiple pre-computed color schemes stored as extra bigBed fields containing R,G,B strings. The `default="label"` key renames the standard itemRgb option in the dropdown. Other entries name extra bigBed fields whose R,G,B values override itemRgb when selected. When a non-default scheme is active, a "(Coloring by: label)" suffix appears in the track long label. Changes: - hui.c/hui.h: new colorFieldsCfgUi() rendered inside bedScoreCfgUi() for bigBed - bigBedTrack.c: colorFieldIdx lookup + per-item filterColor override + longLabel suffix - tagTypes.tab: register colorFields for bigBed and bigGenePred - trackDbLibrary.shtml, trackDbDoc.html, trackDbHub.v3.html, changes.html: documentation refs #26253 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 7, context: html, text, full: html, text
    5dc1d6e658ab009f27314e192340275a6bb70237 Tue Jun 2 16:20:48 2026 -0700
    Add colorFields trackDb setting for bigBed/bigGenePred color scheme switching Adds a new trackDb statement `colorFields` that renders a "Color by:" dropdown in the track controls page, letting users switch among multiple pre-computed color schemes stored as extra bigBed fields containing R,G,B strings. The `default="label"` key renames the standard itemRgb option in the dropdown. Other entries name extra bigBed fields whose R,G,B values override itemRgb when selected. When a non-default scheme is active, a "(Coloring by: label)" suffix appears in the track long label. Changes: - hui.c/hui.h: new colorFieldsCfgUi() rendered inside bedScoreCfgUi() for bigBed - bigBedTrack.c: colorFieldIdx lookup + per-item filterColor override + longLabel suffix - tagTypes.tab: register colorFields for bigBed and bigGenePred - trackDbLibrary.shtml, trackDbDoc.html, trackDbHub.v3.html, changes.html: documentation refs #26253 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 39, context: html, text, full: html, text
    5dc1d6e658ab009f27314e192340275a6bb70237 Tue Jun 2 16:20:48 2026 -0700
    Add colorFields trackDb setting for bigBed/bigGenePred color scheme switching Adds a new trackDb statement `colorFields` that renders a "Color by:" dropdown in the track controls page, letting users switch among multiple pre-computed color schemes stored as extra bigBed fields containing R,G,B strings. The `default="label"` key renames the standard itemRgb option in the dropdown. Other entries name extra bigBed fields whose R,G,B values override itemRgb when selected. When a non-default scheme is active, a "(Coloring by: label)" suffix appears in the track long label. Changes: - hui.c/hui.h: new colorFieldsCfgUi() rendered inside bedScoreCfgUi() for bigBed - bigBedTrack.c: colorFieldIdx lookup + per-item filterColor override + longLabel suffix - tagTypes.tab: register colorFields for bigBed and bigGenePred - trackDbLibrary.shtml, trackDbDoc.html, trackDbHub.v3.html, changes.html: documentation refs #26253 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/htdocs/index.html
  • lines changed 1, context: html, text, full: html, text
    dcd410bcd2c37a5892bdb139475fdf10dac14bcd Tue Jun 2 14:38:32 2026 -0700
    Update home page meta description tag with a longer, descriptive value. refs #37335 The previous tag was too short for Google to use, so it synthesized its own search snippet. Replaces it with a richer, broad-audience description while avoiding numbers that fall out of date.
  • lines changed 1, context: html, text, full: html, text
    dfb3100aaa82418024b6006ba4fccd3cf0f3b1b0 Wed Jun 3 11:35:19 2026 -0700
    Update home page meta description to the team-approved human-focused wording. refs #37335 Per discussion on the ticket, Max approved leading with the human genome rather than emphasizing thousands of species, since the large majority of users are on human assemblies.
• src/hg/htdocs/liftRequest.html
  • lines changed 1, context: html, text, full: html, text
    fc7664f673106948bb09c9f03ce8d10746f66d24 Thu Jun 4 14:32:25 2026 -0700
    should be simple include of gbPageStart.html not the gbPageStartHardcoded.html refs #31811
• src/hg/htdocs/style/facetedComposite.css
  • lines changed 59, context: html, text, full: html, text
    706d4aa403071faaf6646c05affbcfe896d427bd Mon Jun 1 16:32:25 2026 -0700
    Moving to a more tab-style for selected/all decision in faceted composite UI, plus some improvements to the docs. refs #36320
  • lines changed 15, context: html, text, full: html, text
    c44fed5433b4c6c083eca0c0dcbdb49ee253a721 Mon Jun 1 21:54:30 2026 -0700
    Fix for metadata tables in faceted composites stretching past the width of the screen. They should now get a horizontal scroll bar. refs #36320
• src/hg/hubApi/apiUtils.c
  • lines changed 4, context: html, text, full: html, text
    6861403ca8a731be04bb0dc4be79f7272a35b73f Mon Jun 1 10:52:06 2026 -0700
    using otto profile to talk to hgcentral refs #31811liftOver.c
  • lines changed 1, context: html, text, full: html, text
    146388a6797bd5eae6a0be47eb976007fce54358 Thu Jun 4 16:03:49 2026 -0700
    correctly disconnect from hgcentraltest refs #31811
• src/hg/hubApi/blat.c
  • lines changed 12, context: html, text, full: html, text
    6af4f6e10518d33db653c55dadab86b3ed4617ec Wed Jun 3 05:39:35 2026 -0700
    hubApi/blat: fix duplicate itemsReturned, missing target strand, weak default penalty Three QA issues from Gerardo on #36315: - writeJsonOutput() emitted "itemsReturned" twice -- apiFinishOutput() already prints it from the global -- so drop the explicit jsonWriteNumber(). - Protein and translated queries came back with single-char strand because gfOutput only writes the target-strand character when reportTargetStrand is set; hgBlat sets it for translated queries, the API path didn't. Set it when bt.isTx so pslLoad sees the full two-char strand. - blatDelayFractionDefault was 0.3 -- QA's 40-request burst only added ~2.4s. Bumped to 3.0 for ~24s under the same burst; still tunable in hg.conf via hubApi.blatDelayFraction=. refs #36315 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/hubApi/liftOver.c
  • lines changed 51, context: html, text, full: html, text
    623b40a3d4c25c552af92d88aed99c5427446f36 Mon Jun 1 12:12:37 2026 -0700
    avoid race condition using INSERT WHERE NOT EXISTS refs #31811
  • lines changed 15, context: html, text, full: html, text
    fe99a2d141b3f2d33e8706c1061d59015e0c571d Thu Jun 4 14:39:19 2026 -0700
    correct detection of login status and correct use of local hgcentraltest when not on one of the RR servers refs #31811
• src/hg/hubApi/tests/makefile
  • lines changed 13, context: html, text, full: html, text
    53af7110db60ea93d61684c2e3ebb52dc3c73680 Tue Jun 2 11:47:02 2026 -0700
    Fix hubApi blat01 test so the QA cron passes from internal IPs. refs #36315 The apiKey gate on /blat is bypassed for bottleneck.except IPs (which includes hgwdev, where the QA cron runs against genome-test), so a no-apiKey request returns a live blat[] result rather than the apiKey error the test expected. Accept either valid outcome (apiKey gate error or blat[] result). Also query /cgi-bin/hubApi/blat/dna directly as a temporary workaround: the Apache rewrite for the bare /blat/ path is not yet deployed, so /blat/dna returns 404. Revert to the bare path once the rewrite rule is in place.
• src/hg/inc/cart.h
  • lines changed 7, context: html, text, full: html, text
    0df5f6317fd6e0033a31aaf56b928f574823075c Wed Jun 3 11:06:54 2026 -0700
    Recommended track sets now can load from a file in htdocs/data/recTrackSets/db/sessionName. The settings are overlayed onto the current cart and no reload of the page is required anymore, refs #37281
  • lines changed 2, context: html, text, full: html, text
    4cffc3eb6f43e109452b5b52d1f760cf1ea6a981 Sun Jun 7 21:47:37 2026 -0700
    Adjusting sessionDb and userDb IDs to be 64-bit in the code, since the database is now ready for it and we're crossing the threshold. refs #33554
• src/hg/inc/cartDb.h
  • lines changed 2, context: html, text, full: html, text
    4cffc3eb6f43e109452b5b52d1f760cf1ea6a981 Sun Jun 7 21:47:37 2026 -0700
    Adjusting sessionDb and userDb IDs to be 64-bit in the code, since the database is now ready for it and we're crossing the threshold. refs #33554
• src/hg/inc/hgHgvs.h
  • lines changed 9, context: html, text, full: html, text
    40b4fc89ec72c22cae51bf9a8b9a7e8dd887eebf Thu Jun 4 15:34:16 2026 -0700
    Show MANE-relative HGVS terms on myVariants SNV detail pages, refs #33808 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/inc/hui.h
  • lines changed 4, context: html, text, full: html, text
    5dc1d6e658ab009f27314e192340275a6bb70237 Tue Jun 2 16:20:48 2026 -0700
    Add colorFields trackDb setting for bigBed/bigGenePred color scheme switching Adds a new trackDb statement `colorFields` that renders a "Color by:" dropdown in the track controls page, letting users switch among multiple pre-computed color schemes stored as extra bigBed fields containing R,G,B strings. The `default="label"` key renames the standard itemRgb option in the dropdown. Other entries name extra bigBed fields whose R,G,B values override itemRgb when selected. When a non-default scheme is active, a "(Coloring by: label)" suffix appears in the track long label. Changes: - hui.c/hui.h: new colorFieldsCfgUi() rendered inside bedScoreCfgUi() for bigBed - bigBedTrack.c: colorFieldIdx lookup + per-item filterColor override + longLabel suffix - tagTypes.tab: register colorFields for bigBed and bigGenePred - trackDbLibrary.shtml, trackDbDoc.html, trackDbHub.v3.html, changes.html: documentation refs #26253 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/inc/jksql.h
  • lines changed 4, context: html, text, full: html, text
    4cffc3eb6f43e109452b5b52d1f760cf1ea6a981 Sun Jun 7 21:47:37 2026 -0700
    Adjusting sessionDb and userDb IDs to be 64-bit in the code, since the database is now ready for it and we're crossing the threshold. refs #33554
• src/hg/inc/myVariantsShare.h
  • lines changed 17, context: html, text, full: html, text
    7d56cd6635651dfd4c9926d062d92ad7b65a3e80 Wed Jun 3 14:52:52 2026 -0700
    More myVariants changes: make the share to accept a comma-sep list of usernames, allow both the read/edit flag and the usernames setting to be editable after creation. When editing usernames, add a confirmation if the field is left blank that this will make the share viewable/editable by anyone with the link, refs #33808
• src/hg/inc/trackHub.h
  • lines changed 3, context: html, text, full: html, text
    d8900846fdae9183808ccd57864191ee48fca00e Fri Jun 5 10:07:25 2026 -0700
    myVariants: fix item display and HGVS gene-track lookup on GenArk hubs, refs #33808 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
• src/hg/js/autocomplete.js
  • lines changed 56, context: html, text, full: html, text
    f93b8662afd701763c24634879d05dc08b3178de Fri Jun 5 02:24:16 2026 -0700
    Add exon search: jump to GENE exon N from position box I'm comitting this thinking that the way that we implement searches leads to duplication of code that doesn't look great to me. While this feature looks good, the code duplication across C/JS should probably get reduced with a different approach to the "quick jump" way of the page. We have currently three ways to quick jump, I think: - chr:start-end - rsxxxxx - gene symbol + autosuggest pick - HGVS? They are recognized by both the javascript and the C code with regexes. I think all of these should be probably be only implemented in the C code. The JS only sends the current string to the C code and then gets back if this can be autocompleted and to which position and what to show in the autosuggest area. For example if you type "SOD1<space>e" the C code could send back "Continue typing to jump to exon" and once you're at "SOD1<space>exon 5" the C code sends back "Hit enter to jump to chrX:123123-123213". This would work with any type of identifier and the code would stay in the C code, not more duplication and it would be much clearer to the user what is recognized in the search box. Users can now type "TP53 exon 5" or "TP53:e.5[+/-offset]" in the genome browser position/search box to navigate directly to that exon. The ":e.N" notation follows the VICC Gene Fusion Specification. An optional intronic offset (":e.5+2") lands N bases past the exon boundary, useful for splice site inspection. C (hgFind.c): findGeneExon() resolves the query against the SQL genePred tables listed in the hg.conf "geneTracks" key (default: mane, ncbiRefSeqSelect, knownGene, ncbiRefSeq, ncbiRefSeqHistorical). bigGenePred tracks (e.g. mane) are supported via bigBedOpenExtraIndex. Uses the existing exonToPos() function for strand-aware exon lookup. fixSinglePos() is called so hgp->singlePos is populated for callers. hgApi.c: new cmd=geneExonToPos returns {"pos":"chrom:start-end"} JSON so JS can navigate in place without a full page redirect to hgSearch. Direct URL links (hgTracks?position=GENE+exon+N) also work because findGeneExon() is hooked into hgPositionsFind(). JS: autocomplete.js injects a local "Jump to exon N" suggestion as soon as the exon pattern is detected, or a hint item when the query is still partial ("GENE ex"). Selecting either navigates via hgApi. hgTracks.js routes the two new autocomplete item types to the hgApi call. utils.js adds the two regexes (geneExonExp, geneExonCoordExp). query.html: documents both syntaxes; the :e.N notation links to the VICC Gene Fusion Specification at fusions.cancervariants.org.
• src/hg/js/facetedComposite.js
  • lines changed 40, context: html, text, full: html, text
    706d4aa403071faaf6646c05affbcfe896d427bd Mon Jun 1 16:32:25 2026 -0700
    Moving to a more tab-style for selected/all decision in faceted composite UI, plus some improvements to the docs. refs #36320
  • lines changed 16, context: html, text, full: html, text
    fa0fdadb2fe50750c9a4087c59711039174ba5c2 Mon Jun 1 21:57:25 2026 -0700
    Part of making metadata tables in faceted composites get a horizontal scrollbar, refs #36320
• src/hg/js/hgMyData.js
  • lines changed 4, context: html, text, full: html, text
    ca23d9f5054fc863beb18d7ef4919b550b2f8d9c Mon Jun 1 10:45:37 2026 -0700
    Allow dot in genome names in hubspace uploads, refs #37665
  • lines changed 29, context: html, text, full: html, text
    bd91a935679eda68e6bf59ee40e480f3cbd0f6e3 Fri Jun 5 12:48:09 2026 -0700
    Fix hubSpace genome selection committing the wrong genome to hub.txt, refs #37713 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/js/hgPhyloPlace.js
  • lines changed 33, context: html, text, full: html, text
    92ca35b40020f7b62a7dbd42a7bad7257a4c3eb2 Mon Jun 1 12:15:43 2026 -0700
    Add font size select to recombinant display popup.
  • lines changed 17, context: html, text, full: html, text
    413a24fc542e90894efde6c3d73f84d85761e1ad Thu Jun 4 22:40:42 2026 -0700
    @FedeGueli request: also highlight mutations unique to the recombinant
• src/hg/js/hgTracks.js
  • lines changed 23, context: html, text, full: html, text
    7a2dbf6721582d73ac9665d9231ffd7fdb703d3a Wed Jun 3 15:04:56 2026 -0700
    Add a link to create a myVariants item to the menu bar under My Data, refs #33808
  • lines changed 47, context: html, text, full: html, text
    f93b8662afd701763c24634879d05dc08b3178de Fri Jun 5 02:24:16 2026 -0700
    Add exon search: jump to GENE exon N from position box I'm comitting this thinking that the way that we implement searches leads to duplication of code that doesn't look great to me. While this feature looks good, the code duplication across C/JS should probably get reduced with a different approach to the "quick jump" way of the page. We have currently three ways to quick jump, I think: - chr:start-end - rsxxxxx - gene symbol + autosuggest pick - HGVS? They are recognized by both the javascript and the C code with regexes. I think all of these should be probably be only implemented in the C code. The JS only sends the current string to the C code and then gets back if this can be autocompleted and to which position and what to show in the autosuggest area. For example if you type "SOD1<space>e" the C code could send back "Continue typing to jump to exon" and once you're at "SOD1<space>exon 5" the C code sends back "Hit enter to jump to chrX:123123-123213". This would work with any type of identifier and the code would stay in the C code, not more duplication and it would be much clearer to the user what is recognized in the search box. Users can now type "TP53 exon 5" or "TP53:e.5[+/-offset]" in the genome browser position/search box to navigate directly to that exon. The ":e.N" notation follows the VICC Gene Fusion Specification. An optional intronic offset (":e.5+2") lands N bases past the exon boundary, useful for splice site inspection. C (hgFind.c): findGeneExon() resolves the query against the SQL genePred tables listed in the hg.conf "geneTracks" key (default: mane, ncbiRefSeqSelect, knownGene, ncbiRefSeq, ncbiRefSeqHistorical). bigGenePred tracks (e.g. mane) are supported via bigBedOpenExtraIndex. Uses the existing exonToPos() function for strand-aware exon lookup. fixSinglePos() is called so hgp->singlePos is populated for callers. hgApi.c: new cmd=geneExonToPos returns {"pos":"chrom:start-end"} JSON so JS can navigate in place without a full page redirect to hgSearch. Direct URL links (hgTracks?position=GENE+exon+N) also work because findGeneExon() is hooked into hgPositionsFind(). JS: autocomplete.js injects a local "Jump to exon N" suggestion as soon as the exon pattern is detected, or a hint item when the query is still partial ("GENE ex"). Selecting either navigates via hgApi. hgTracks.js routes the two new autocomplete item types to the hgApi call. utils.js adds the two regexes (geneExonExp, geneExonCoordExp). query.html: documents both syntaxes; the :e.N notation links to the VICC Gene Fusion Specification at fusions.cancervariants.org.
• src/hg/js/hui.js
  • lines changed 115, context: html, text, full: html, text
    7d56cd6635651dfd4c9926d062d92ad7b65a3e80 Wed Jun 3 14:52:52 2026 -0700
    More myVariants changes: make the share to accept a comma-sep list of usernames, allow both the read/edit flag and the usernames setting to be editable after creation. When editing usernames, add a confirmation if the field is left blank that this will make the share viewable/editable by anyone with the link, refs #33808
• src/hg/js/utils.js
  • lines changed 5, context: html, text, full: html, text
    f93b8662afd701763c24634879d05dc08b3178de Fri Jun 5 02:24:16 2026 -0700
    Add exon search: jump to GENE exon N from position box I'm comitting this thinking that the way that we implement searches leads to duplication of code that doesn't look great to me. While this feature looks good, the code duplication across C/JS should probably get reduced with a different approach to the "quick jump" way of the page. We have currently three ways to quick jump, I think: - chr:start-end - rsxxxxx - gene symbol + autosuggest pick - HGVS? They are recognized by both the javascript and the C code with regexes. I think all of these should be probably be only implemented in the C code. The JS only sends the current string to the C code and then gets back if this can be autocompleted and to which position and what to show in the autosuggest area. For example if you type "SOD1<space>e" the C code could send back "Continue typing to jump to exon" and once you're at "SOD1<space>exon 5" the C code sends back "Hit enter to jump to chrX:123123-123213". This would work with any type of identifier and the code would stay in the C code, not more duplication and it would be much clearer to the user what is recognized in the search box. Users can now type "TP53 exon 5" or "TP53:e.5[+/-offset]" in the genome browser position/search box to navigate directly to that exon. The ":e.N" notation follows the VICC Gene Fusion Specification. An optional intronic offset (":e.5+2") lands N bases past the exon boundary, useful for splice site inspection. C (hgFind.c): findGeneExon() resolves the query against the SQL genePred tables listed in the hg.conf "geneTracks" key (default: mane, ncbiRefSeqSelect, knownGene, ncbiRefSeq, ncbiRefSeqHistorical). bigGenePred tracks (e.g. mane) are supported via bigBedOpenExtraIndex. Uses the existing exonToPos() function for strand-aware exon lookup. fixSinglePos() is called so hgp->singlePos is populated for callers. hgApi.c: new cmd=geneExonToPos returns {"pos":"chrom:start-end"} JSON so JS can navigate in place without a full page redirect to hgSearch. Direct URL links (hgTracks?position=GENE+exon+N) also work because findGeneExon() is hooked into hgPositionsFind(). JS: autocomplete.js injects a local "Jump to exon N" suggestion as soon as the exon pattern is detected, or a hint item when the query is still partial ("GENE ex"). Selecting either navigates via hgApi. hgTracks.js routes the two new autocomplete item types to the hgApi call. utils.js adds the two regexes (geneExonExp, geneExonCoordExp). query.html: documents both syntaxes; the :e.N notation links to the VICC Gene Fusion Specification at fusions.cancervariants.org.
• src/hg/lib/botDelay.c
  • lines changed 6, context: html, text, full: html, text
    4cffc3eb6f43e109452b5b52d1f760cf1ea6a981 Sun Jun 7 21:47:37 2026 -0700
    Adjusting sessionDb and userDb IDs to be 64-bit in the code, since the database is now ready for it and we're crossing the threshold. refs #33554
• src/hg/lib/cart.c
  • lines changed 19, context: html, text, full: html, text
    4cffc3eb6f43e109452b5b52d1f760cf1ea6a981 Sun Jun 7 21:47:37 2026 -0700
    Adjusting sessionDb and userDb IDs to be 64-bit in the code, since the database is now ready for it and we're crossing the threshold. refs #33554
• src/hg/lib/cartDb.as
  • lines changed 1, context: html, text, full: html, text
    4cffc3eb6f43e109452b5b52d1f760cf1ea6a981 Sun Jun 7 21:47:37 2026 -0700
    Adjusting sessionDb and userDb IDs to be 64-bit in the code, since the database is now ready for it and we're crossing the threshold. refs #33554
• src/hg/lib/cartDb.c
  • lines changed 9, context: html, text, full: html, text
    4cffc3eb6f43e109452b5b52d1f760cf1ea6a981 Sun Jun 7 21:47:37 2026 -0700
    Adjusting sessionDb and userDb IDs to be 64-bit in the code, since the database is now ready for it and we're crossing the threshold. refs #33554
• src/hg/lib/cartDb.sql
  • lines changed 2, context: html, text, full: html, text
    4cffc3eb6f43e109452b5b52d1f760cf1ea6a981 Sun Jun 7 21:47:37 2026 -0700
    Adjusting sessionDb and userDb IDs to be 64-bit in the code, since the database is now ready for it and we're crossing the threshold. refs #33554
• src/hg/lib/hgFind.c
  • lines changed 283, context: html, text, full: html, text
    f93b8662afd701763c24634879d05dc08b3178de Fri Jun 5 02:24:16 2026 -0700
    Add exon search: jump to GENE exon N from position box I'm comitting this thinking that the way that we implement searches leads to duplication of code that doesn't look great to me. While this feature looks good, the code duplication across C/JS should probably get reduced with a different approach to the "quick jump" way of the page. We have currently three ways to quick jump, I think: - chr:start-end - rsxxxxx - gene symbol + autosuggest pick - HGVS? They are recognized by both the javascript and the C code with regexes. I think all of these should be probably be only implemented in the C code. The JS only sends the current string to the C code and then gets back if this can be autocompleted and to which position and what to show in the autosuggest area. For example if you type "SOD1<space>e" the C code could send back "Continue typing to jump to exon" and once you're at "SOD1<space>exon 5" the C code sends back "Hit enter to jump to chrX:123123-123213". This would work with any type of identifier and the code would stay in the C code, not more duplication and it would be much clearer to the user what is recognized in the search box. Users can now type "TP53 exon 5" or "TP53:e.5[+/-offset]" in the genome browser position/search box to navigate directly to that exon. The ":e.N" notation follows the VICC Gene Fusion Specification. An optional intronic offset (":e.5+2") lands N bases past the exon boundary, useful for splice site inspection. C (hgFind.c): findGeneExon() resolves the query against the SQL genePred tables listed in the hg.conf "geneTracks" key (default: mane, ncbiRefSeqSelect, knownGene, ncbiRefSeq, ncbiRefSeqHistorical). bigGenePred tracks (e.g. mane) are supported via bigBedOpenExtraIndex. Uses the existing exonToPos() function for strand-aware exon lookup. fixSinglePos() is called so hgp->singlePos is populated for callers. hgApi.c: new cmd=geneExonToPos returns {"pos":"chrom:start-end"} JSON so JS can navigate in place without a full page redirect to hgSearch. Direct URL links (hgTracks?position=GENE+exon+N) also work because findGeneExon() is hooked into hgPositionsFind(). JS: autocomplete.js injects a local "Jump to exon N" suggestion as soon as the exon pattern is detected, or a hint item when the query is still partial ("GENE ex"). Selecting either navigates via hgApi. hgTracks.js routes the two new autocomplete item types to the hgApi call. utils.js adds the two regexes (geneExonExp, geneExonCoordExp). query.html: documents both syntaxes; the :e.N notation links to the VICC Gene Fusion Specification at fusions.cancervariants.org.
• src/hg/lib/hgHgvs.c
  • lines changed 17, context: html, text, full: html, text
    40b4fc89ec72c22cae51bf9a8b9a7e8dd887eebf Thu Jun 4 15:34:16 2026 -0700
    Show MANE-relative HGVS terms on myVariants SNV detail pages, refs #33808 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
  • lines changed 10, context: html, text, full: html, text
    d8900846fdae9183808ccd57864191ee48fca00e Fri Jun 5 10:07:25 2026 -0700
    myVariants: fix item display and HGVS gene-track lookup on GenArk hubs, refs #33808 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
• src/hg/lib/hguidIpAccess.sql
  • lines changed 12, context: html, text, full: html, text
    27875d655386f07bb3c7bbb848aebee80792bc3e Thu Jun 4 09:14:26 2026 -0700
    Adding a .sql to create the hguidIpAccess table for tracking recent hguid/ip relationships (for managing bot traffic). refs #37494
  • lines changed 1, context: html, text, full: html, text
    4cffc3eb6f43e109452b5b52d1f760cf1ea6a981 Sun Jun 7 21:47:37 2026 -0700
    Adjusting sessionDb and userDb IDs to be 64-bit in the code, since the database is now ready for it and we're crossing the threshold. refs #33554
• src/hg/lib/hui.c
  • lines changed 80, context: html, text, full: html, text
    5dc1d6e658ab009f27314e192340275a6bb70237 Tue Jun 2 16:20:48 2026 -0700
    Add colorFields trackDb setting for bigBed/bigGenePred color scheme switching Adds a new trackDb statement `colorFields` that renders a "Color by:" dropdown in the track controls page, letting users switch among multiple pre-computed color schemes stored as extra bigBed fields containing R,G,B strings. The `default="label"` key renames the standard itemRgb option in the dropdown. Other entries name extra bigBed fields whose R,G,B values override itemRgb when selected. When a non-default scheme is active, a "(Coloring by: label)" suffix appears in the track long label. Changes: - hui.c/hui.h: new colorFieldsCfgUi() rendered inside bedScoreCfgUi() for bigBed - bigBedTrack.c: colorFieldIdx lookup + per-item filterColor override + longLabel suffix - tagTypes.tab: register colorFields for bigBed and bigGenePred - trackDbLibrary.shtml, trackDbDoc.html, trackDbHub.v3.html, changes.html: documentation refs #26253 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
  • lines changed 15, context: html, text, full: html, text
    d8900846fdae9183808ccd57864191ee48fca00e Fri Jun 5 10:07:25 2026 -0700
    myVariants: fix item display and HGVS gene-track lookup on GenArk hubs, refs #33808 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
• src/hg/lib/jksql.c
  • lines changed 13, context: html, text, full: html, text
    4cffc3eb6f43e109452b5b52d1f760cf1ea6a981 Sun Jun 7 21:47:37 2026 -0700
    Adjusting sessionDb and userDb IDs to be 64-bit in the code, since the database is now ready for it and we're crossing the threshold. refs #33554
• src/hg/lib/myVariants.c
  • lines changed 5, context: html, text, full: html, text
    7d56cd6635651dfd4c9926d062d92ad7b65a3e80 Wed Jun 3 14:52:52 2026 -0700
    More myVariants changes: make the share to accept a comma-sep list of usernames, allow both the read/edit flag and the usernames setting to be editable after creation. When editing usernames, add a confirmation if the field is left blank that this will make the share viewable/editable by anyone with the link, refs #33808
• src/hg/lib/myVariantsShare.as
  • lines changed 1, context: html, text, full: html, text
    7d56cd6635651dfd4c9926d062d92ad7b65a3e80 Wed Jun 3 14:52:52 2026 -0700
    More myVariants changes: make the share to accept a comma-sep list of usernames, allow both the read/edit flag and the usernames setting to be editable after creation. When editing usernames, add a confirmation if the field is left blank that this will make the share viewable/editable by anyone with the link, refs #33808
• src/hg/lib/myVariantsShare.c
  • lines changed 80, context: html, text, full: html, text
    7d56cd6635651dfd4c9926d062d92ad7b65a3e80 Wed Jun 3 14:52:52 2026 -0700
    More myVariants changes: make the share to accept a comma-sep list of usernames, allow both the read/edit flag and the usernames setting to be editable after creation. When editing usernames, add a confirmation if the field is left blank that this will make the share viewable/editable by anyone with the link, refs #33808
• src/hg/lib/myVariantsShare.sql
  • lines changed 1, context: html, text, full: html, text
    7d56cd6635651dfd4c9926d062d92ad7b65a3e80 Wed Jun 3 14:52:52 2026 -0700
    More myVariants changes: make the share to accept a comma-sep list of usernames, allow both the read/edit flag and the usernames setting to be editable after creation. When editing usernames, add a confirmation if the field is left blank that this will make the share viewable/editable by anyone with the link, refs #33808
• src/hg/lib/sessionDb.as
  • lines changed 1, context: html, text, full: html, text
    4cffc3eb6f43e109452b5b52d1f760cf1ea6a981 Sun Jun 7 21:47:37 2026 -0700
    Adjusting sessionDb and userDb IDs to be 64-bit in the code, since the database is now ready for it and we're crossing the threshold. refs #33554
• src/hg/lib/sessionDb.sql
  • lines changed 1, context: html, text, full: html, text
    4cffc3eb6f43e109452b5b52d1f760cf1ea6a981 Sun Jun 7 21:47:37 2026 -0700
    Adjusting sessionDb and userDb IDs to be 64-bit in the code, since the database is now ready for it and we're crossing the threshold. refs #33554
• src/hg/lib/trackHub.c
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    d8900846fdae9183808ccd57864191ee48fca00e Fri Jun 5 10:07:25 2026 -0700
    myVariants: fix item display and HGVS gene-track lookup on GenArk hubs, refs #33808 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
• src/hg/lib/userDb.as
  • lines changed 1, context: html, text, full: html, text
    4cffc3eb6f43e109452b5b52d1f760cf1ea6a981 Sun Jun 7 21:47:37 2026 -0700
    Adjusting sessionDb and userDb IDs to be 64-bit in the code, since the database is now ready for it and we're crossing the threshold. refs #33554
• src/hg/lib/userDb.sql
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    4cffc3eb6f43e109452b5b52d1f760cf1ea6a981 Sun Jun 7 21:47:37 2026 -0700
    Adjusting sessionDb and userDb IDs to be 64-bit in the code, since the database is now ready for it and we're crossing the threshold. refs #33554
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
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    ebbf5e4ced6bccc61fd43049a2d33c77a0c7a6e2 Fri Jun 5 11:03:27 2026 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/hg38/encode4.regulation.txt
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    df99c448f8e0386bb718da0044b22752fc145713 Thu Jun 4 00:15:12 2026 -0700
    Updating ENCODE4 Regulation labels and description pages for hg38 and mm10. refs #34923 - Capitalized 363 hg38 Layered organ shortLabels and shortened the over-length TF rPeaks and Indiv. composite longLabels; updated the mm10 TF ChIP container longLabel. - TF rPeaks: added the missing SHOX2 to filterValues.factor (now 912), and updated "911 factors"/"2,502 experiments" to "912"/"2,509". - Supertrack pages: changed Layered bullets from "highlights" to "displays", reworded the histone and CTCF bullets, updated the default-organ note, and updated stale hg38 organ counts to 38/41/26/38/36. - Updated the TF ChIP facet name "Tf" -> "TF" on both description pages. - Makedoc: updated hg38 "911-factor" -> "912-factor" and mm10 RNA-seq Unstranded "26" -> "8".
• src/hg/makeDb/doc/hg38/lrSv.txt
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    c81011d4a8f57db347e15aa1248c501b2c8a6fea Mon Jun 1 13:16:15 2026 -0700
    QA fixes for the lrSv long-read SV supertrack: labels and description cleanups. refs #36258 Trim six subtrack longLabels to the 85-char limit (ga4kSv, hprc2Sv, hgsvc2Sv, chirmade101Sv, cpc1Sv, and lrSvAll; the lrSvAll change is also made in the lrSvMergeAll.py generator so a re-run reproduces it). Standardize the APR dataset name to "Arab Pangenome Reference (APR)" across lrSv.ra, lrSv.html, aprSv.html, and the makeDoc comment (was a mix of "Arabic" and "UAE UPR"). lrSv1kgOnt.html: state per-assembly SV counts (hg38 lifted 148,375 vs hs1 native 161,332, each with its own type breakdown) and encode non-ASCII author names as numeric entities. hgsvc3Sv.html: correct the hg38 counts to match the served bigBed (176,231 DEL+INS, 176,531 total). colorsDbSv.html: use $db in the hgdownload path so it resolves on hs1 as well as hg38. cpc1Sv.html: encode a Unicode minus sign as a numeric entity.
  • lines changed 39, context: html, text, full: html, text
    038bd0cd3f7c84ee984905608dfdd27d02cc61ec Tue Jun 2 05:19:51 2026 -0700
    [Claude] lrSv1kLin: add 1000 Genomes linear long-read SV subtrack (1,218 samples, hg38+hs1) Two native VCFs from the Eichler lab (GRCh38 and CHM13/T2T-CHM13v2), merged with Truvari v5.2.0 and annotated with population-level AFs (EUR, AMR, EAS, AFR, SAS). Track is alpha-only; not added to lrSvAll -- data not yet published. hg38: 587,779 SVs; hs1: 614,522 SVs. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> , refs #36258
• src/hg/makeDb/doc/hg38/ncOrfs.txt
  • lines changed 62, context: html, text, full: html, text
    55e909c0e98fb50a5cd761f1ce2cb52f9089f5f4 Tue Jun 2 03:05:59 2026 -0700
    [Claude] ncOrfs: add 5ULTRA uORFs subtrack (MANE Select, 22,567 features) Adds fiveUltraUorfs, a new subtrack under the ncOrfs supertrack showing 22,567 ATG-initiated uORFs in MANE Select transcripts from the 5ULTRA pipeline (Chaldebas et al., Am J Hum Genet 2026, PMID 41881026). Features are colored by uORF type (Okabe-Ito palette), have exon/intron structure projected from MANE via addIntrons.py, and carry gene, rank, and Kozak strength as extra bigBed fields. ncOrfs.html summary table updated to include the new track. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> refs #37580
  • lines changed 59, context: html, text, full: html, text
    640ebced50314d2662db498562167e0d21980f78 Tue Jun 2 16:36:43 2026 -0700
    gencNcOrfs: add peptide evidence fields from TransCODE/PeptideAtlas (PMID:42092140) Extends the GENCODE Phase I ncORF bigGenePred (Ribo-seq_ORFs.kozak.peptides.bb, 44 fields) with 14 peptide evidence fields joined from five supplementary tables in Mudge et al. 2025. Introduces the "peptidein" concept — ncORFs confidently detected by mass spectrometry but lacking functional annotation for protein status. Data covers 2,150 of 7,264 Phase I ORFs; the remaining 5,114 carry default empty values. Three color schemes are available via the colorFields dropdown: - Kozak strength (default, pre-existing field 9 colors) - Evidence type: gold=peptidein, blue=HLA only, green=non-HLA only, purple=both - HLA class: blue=class I, crimson=class II, purple=both New filters: isPeptidein, hlaClass, hlaFinalTier, hlaHppCategory, riboseqQuality. Phase II shortLabels: "GENCODE Phase II ncORFs Prim/Compr". Phase I kozakTE filterLimits set to -1:1.5 so ORFs with unavailable context are accessible. Build: peptideSupport/addPeptideEvidence.py AutoSql: Ribo-seq_ORFs.kozak.peptides.as BigBed: /gbdb/hg38/ncOrfs/gencNcOrf/Ribo-seq_ORFs.kozak.peptides.bb Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
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    964998333659e919296441a2e8567a6ef4fff8d6 Tue Jun 2 13:42:29 2026 -0700
    Update hg38 RefSeq Historical track to NCBI RS_2024_08 release. refs #35766
• src/hg/makeDb/doc/hg38/varFreqs.txt
  • lines changed 62, context: html, text, full: html, text
    64a3f9e7813e823cf724ea188c3928a911578286 Thu Jun 4 00:32:22 2026 -0700
    varFreqs: replace All Databases Combined with two phenotype-split tracks Replace the single varFreqsAll combined track (and drop the varFreqsDisease track) with two matched tracks for visual case-vs-background comparison: varFreqsAffected - variants seen in the affected/case arms of disease cohorts (SFARI SPARK WES/WGS ASD probands, SCHEMA cases, GREGoR affected, GA4K); ~130,000 individuals varFreqsBackground - population reference cohorts + the unaffected/control arms of disease cohorts ("all other variants"); ~1.5 million individuals A variant seen in both groups appears in both tracks. Genotyping-array cohorts stay out of both (varFreqsArray unchanged). vcfToBigBed.py gains --split-affected to emit both tracks in one pass; it reads phenotype tags (affected/unaffected/unknown) from populations.tsv and is_disease/disease_role from databases.tsv, and derives the length-filter ranges from the observed data. TOPMed reclassified as a population cohort. SPARK WGS display name changed to SFARI SPARK WGS for consistency with the standalone subtracks. Fixed the trackDb mouseOver $-substitution prefix collision by wrapping fields in ${}. New description pages for both tracks. refs #36642
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
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    330702087f98389c3d5b6a1ec0fd7ad56d3bd563 Thu Jun 4 16:15:48 2026 -0700
    add several per user request and otto testing refs #31811
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 1, context: html, text, full: html, text
    57469ac0b93684608b744610b3c42646f232144c Fri Jun 5 11:59:05 2026 -0700
    fixup a legacy assembly refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    57469ac0b93684608b744610b3c42646f232144c Fri Jun 5 11:59:05 2026 -0700
    fixup a legacy assembly refs #29545
• src/hg/makeDb/doc/mm10.encode4.regulation.txt
  • lines changed 1, context: html, text, full: html, text
    df99c448f8e0386bb718da0044b22752fc145713 Thu Jun 4 00:15:12 2026 -0700
    Updating ENCODE4 Regulation labels and description pages for hg38 and mm10. refs #34923 - Capitalized 363 hg38 Layered organ shortLabels and shortened the over-length TF rPeaks and Indiv. composite longLabels; updated the mm10 TF ChIP container longLabel. - TF rPeaks: added the missing SHOX2 to filterValues.factor (now 912), and updated "911 factors"/"2,502 experiments" to "912"/"2,509". - Supertrack pages: changed Layered bullets from "highlights" to "displays", reworded the histone and CTCF bullets, updated the default-organ note, and updated stale hg38 organ counts to 38/41/26/38/36. - Updated the TF ChIP facet name "Tf" -> "TF" on both description pages. - Makedoc: updated hg38 "911-factor" -> "912-factor" and mm10 RNA-seq Unstranded "26" -> "8".
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    330702087f98389c3d5b6a1ec0fd7ad56d3bd563 Thu Jun 4 16:15:48 2026 -0700
    add several per user request and otto testing refs #31811
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    330702087f98389c3d5b6a1ec0fd7ad56d3bd563 Thu Jun 4 16:15:48 2026 -0700
    add several per user request and otto testing refs #31811
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    330702087f98389c3d5b6a1ec0fd7ad56d3bd563 Thu Jun 4 16:15:48 2026 -0700
    add several per user request and otto testing refs #31811
  • lines changed 1, context: html, text, full: html, text
    07c7876ca4f755b24a430c16208a879de9ae614c Fri Jun 5 11:02:32 2026 -0700
    adding one per user request refs #29545
  • lines changed 1, context: html, text, full: html, text
    57469ac0b93684608b744610b3c42646f232144c Fri Jun 5 11:59:05 2026 -0700
    fixup a legacy assembly refs #29545
• src/hg/makeDb/scripts/barChartReorder/barChartReorder.py
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    0aff2d78b3be1b2bcd0839173cddbe359e4bd379 Tue Jun 2 09:53:24 2026 -0700
    Removing the barChartReorder.py script since Diane rebuilt the Wold Lab public hub with the new tissue order. refs #37001 #37619
• src/hg/makeDb/scripts/eve/eve_heatmap.as
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    b7b279e5f1240419fb3a408fff5c82a998a36e76 Wed Jun 3 08:17:09 2026 -0700
    EVE track QA fixes: fix .as field descriptions, clarify protein count in HTML - thickStart/thickEnd .as descriptions corrected (whole protein span, not start/stop codon) - reserved .as description corrected (always 0, not itemRgb) - HTML Methods section: explain that 2,951 of 3,219 proteins have released VCF scores Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/lrSv/lrSv1kLin1218.as
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    038bd0cd3f7c84ee984905608dfdd27d02cc61ec Tue Jun 2 05:19:51 2026 -0700
    [Claude] lrSv1kLin: add 1000 Genomes linear long-read SV subtrack (1,218 samples, hg38+hs1) Two native VCFs from the Eichler lab (GRCh38 and CHM13/T2T-CHM13v2), merged with Truvari v5.2.0 and annotated with population-level AFs (EUR, AMR, EAS, AFR, SAS). Track is alpha-only; not added to lrSvAll -- data not yet published. hg38: 587,779 SVs; hs1: 614,522 SVs. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> , refs #36258
• src/hg/makeDb/scripts/lrSv/lrSv1kLin1218VcfToBed.py
  • lines changed 131, context: html, text, full: html, text
    038bd0cd3f7c84ee984905608dfdd27d02cc61ec Tue Jun 2 05:19:51 2026 -0700
    [Claude] lrSv1kLin: add 1000 Genomes linear long-read SV subtrack (1,218 samples, hg38+hs1) Two native VCFs from the Eichler lab (GRCh38 and CHM13/T2T-CHM13v2), merged with Truvari v5.2.0 and annotated with population-level AFs (EUR, AMR, EAS, AFR, SAS). Track is alpha-only; not added to lrSvAll -- data not yet published. hg38: 587,779 SVs; hs1: 614,522 SVs. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> , refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py
  • lines changed 2, context: html, text, full: html, text
    c81011d4a8f57db347e15aa1248c501b2c8a6fea Mon Jun 1 13:16:15 2026 -0700
    QA fixes for the lrSv long-read SV supertrack: labels and description cleanups. refs #36258 Trim six subtrack longLabels to the 85-char limit (ga4kSv, hprc2Sv, hgsvc2Sv, chirmade101Sv, cpc1Sv, and lrSvAll; the lrSvAll change is also made in the lrSvMergeAll.py generator so a re-run reproduces it). Standardize the APR dataset name to "Arab Pangenome Reference (APR)" across lrSv.ra, lrSv.html, aprSv.html, and the makeDoc comment (was a mix of "Arabic" and "UAE UPR"). lrSv1kgOnt.html: state per-assembly SV counts (hg38 lifted 148,375 vs hs1 native 161,332, each with its own type breakdown) and encode non-ASCII author names as numeric entities. hgsvc3Sv.html: correct the hg38 counts to match the served bigBed (176,231 DEL+INS, 176,531 total). colorsDbSv.html: use $db in the hgdownload path so it resolves on hs1 as well as hg38. cpc1Sv.html: encode a Unicode minus sign as a numeric entity.
• src/hg/makeDb/scripts/ncOrfs/colorByKozak.py
  • lines changed 3, context: html, text, full: html, text
    640ebced50314d2662db498562167e0d21980f78 Tue Jun 2 16:36:43 2026 -0700
    gencNcOrfs: add peptide evidence fields from TransCODE/PeptideAtlas (PMID:42092140) Extends the GENCODE Phase I ncORF bigGenePred (Ribo-seq_ORFs.kozak.peptides.bb, 44 fields) with 14 peptide evidence fields joined from five supplementary tables in Mudge et al. 2025. Introduces the "peptidein" concept — ncORFs confidently detected by mass spectrometry but lacking functional annotation for protein status. Data covers 2,150 of 7,264 Phase I ORFs; the remaining 5,114 carry default empty values. Three color schemes are available via the colorFields dropdown: - Kozak strength (default, pre-existing field 9 colors) - Evidence type: gold=peptidein, blue=HLA only, green=non-HLA only, purple=both - HLA class: blue=class I, crimson=class II, purple=both New filters: isPeptidein, hlaClass, hlaFinalTier, hlaHppCategory, riboseqQuality. Phase II shortLabels: "GENCODE Phase II ncORFs Prim/Compr". Phase I kozakTE filterLimits set to -1:1.5 so ORFs with unavailable context are accessible. Build: peptideSupport/addPeptideEvidence.py AutoSql: Ribo-seq_ORFs.kozak.peptides.as BigBed: /gbdb/hg38/ncOrfs/gencNcOrf/Ribo-seq_ORFs.kozak.peptides.bb Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/fiveUltraUorfs.as
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    55e909c0e98fb50a5cd761f1ce2cb52f9089f5f4 Tue Jun 2 03:05:59 2026 -0700
    [Claude] ncOrfs: add 5ULTRA uORFs subtrack (MANE Select, 22,567 features) Adds fiveUltraUorfs, a new subtrack under the ncOrfs supertrack showing 22,567 ATG-initiated uORFs in MANE Select transcripts from the 5ULTRA pipeline (Chaldebas et al., Am J Hum Genet 2026, PMID 41881026). Features are colored by uORF type (Okabe-Ito palette), have exon/intron structure projected from MANE via addIntrons.py, and carry gene, rank, and Kozak strength as extra bigBed fields. ncOrfs.html summary table updated to include the new track. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> refs #37580
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    30c1c7161e91d449bf748f1453fe408ffef5b50f Wed Jun 3 05:22:33 2026 -0700
    fixes after AI review, no redmine Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/maneUorfsToBed.py
  • lines changed 39, context: html, text, full: html, text
    55e909c0e98fb50a5cd761f1ce2cb52f9089f5f4 Tue Jun 2 03:05:59 2026 -0700
    [Claude] ncOrfs: add 5ULTRA uORFs subtrack (MANE Select, 22,567 features) Adds fiveUltraUorfs, a new subtrack under the ncOrfs supertrack showing 22,567 ATG-initiated uORFs in MANE Select transcripts from the 5ULTRA pipeline (Chaldebas et al., Am J Hum Genet 2026, PMID 41881026). Features are colored by uORF type (Okabe-Ito palette), have exon/intron structure projected from MANE via addIntrons.py, and carry gene, rank, and Kozak strength as extra bigBed fields. ncOrfs.html summary table updated to include the new track. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> refs #37580
• src/hg/makeDb/scripts/varFreqs/databases.tsv
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    64a3f9e7813e823cf724ea188c3928a911578286 Thu Jun 4 00:32:22 2026 -0700
    varFreqs: replace All Databases Combined with two phenotype-split tracks Replace the single varFreqsAll combined track (and drop the varFreqsDisease track) with two matched tracks for visual case-vs-background comparison: varFreqsAffected - variants seen in the affected/case arms of disease cohorts (SFARI SPARK WES/WGS ASD probands, SCHEMA cases, GREGoR affected, GA4K); ~130,000 individuals varFreqsBackground - population reference cohorts + the unaffected/control arms of disease cohorts ("all other variants"); ~1.5 million individuals A variant seen in both groups appears in both tracks. Genotyping-array cohorts stay out of both (varFreqsArray unchanged). vcfToBigBed.py gains --split-affected to emit both tracks in one pass; it reads phenotype tags (affected/unaffected/unknown) from populations.tsv and is_disease/disease_role from databases.tsv, and derives the length-filter ranges from the observed data. TOPMed reclassified as a population cohort. SPARK WGS display name changed to SFARI SPARK WGS for consistency with the standalone subtracks. Fixed the trackDb mouseOver $-substitution prefix collision by wrapping fields in ${}. New description pages for both tracks. refs #36642
• src/hg/makeDb/scripts/varFreqs/populations.tsv
  • lines changed 13, context: html, text, full: html, text
    64a3f9e7813e823cf724ea188c3928a911578286 Thu Jun 4 00:32:22 2026 -0700
    varFreqs: replace All Databases Combined with two phenotype-split tracks Replace the single varFreqsAll combined track (and drop the varFreqsDisease track) with two matched tracks for visual case-vs-background comparison: varFreqsAffected - variants seen in the affected/case arms of disease cohorts (SFARI SPARK WES/WGS ASD probands, SCHEMA cases, GREGoR affected, GA4K); ~130,000 individuals varFreqsBackground - population reference cohorts + the unaffected/control arms of disease cohorts ("all other variants"); ~1.5 million individuals A variant seen in both groups appears in both tracks. Genotyping-array cohorts stay out of both (varFreqsArray unchanged). vcfToBigBed.py gains --split-affected to emit both tracks in one pass; it reads phenotype tags (affected/unaffected/unknown) from populations.tsv and is_disease/disease_role from databases.tsv, and derives the length-filter ranges from the observed data. TOPMed reclassified as a population cohort. SPARK WGS display name changed to SFARI SPARK WGS for consistency with the standalone subtracks. Fixed the trackDb mouseOver $-substitution prefix collision by wrapping fields in ${}. New description pages for both tracks. refs #36642
• src/hg/makeDb/scripts/varFreqs/vcfToBigBed.py
  • lines changed 347, context: html, text, full: html, text
    64a3f9e7813e823cf724ea188c3928a911578286 Thu Jun 4 00:32:22 2026 -0700
    varFreqs: replace All Databases Combined with two phenotype-split tracks Replace the single varFreqsAll combined track (and drop the varFreqsDisease track) with two matched tracks for visual case-vs-background comparison: varFreqsAffected - variants seen in the affected/case arms of disease cohorts (SFARI SPARK WES/WGS ASD probands, SCHEMA cases, GREGoR affected, GA4K); ~130,000 individuals varFreqsBackground - population reference cohorts + the unaffected/control arms of disease cohorts ("all other variants"); ~1.5 million individuals A variant seen in both groups appears in both tracks. Genotyping-array cohorts stay out of both (varFreqsArray unchanged). vcfToBigBed.py gains --split-affected to emit both tracks in one pass; it reads phenotype tags (affected/unaffected/unknown) from populations.tsv and is_disease/disease_role from databases.tsv, and derives the length-filter ranges from the observed data. TOPMed reclassified as a population cohort. SPARK WGS display name changed to SFARI SPARK WGS for consistency with the standalone subtracks. Fixed the trackDb mouseOver $-substitution prefix collision by wrapping fields in ${}. New description pages for both tracks. refs #36642
• src/hg/makeDb/trackDb/human/aprSv.html
  • lines changed 3, context: html, text, full: html, text
    c81011d4a8f57db347e15aa1248c501b2c8a6fea Mon Jun 1 13:16:15 2026 -0700
    QA fixes for the lrSv long-read SV supertrack: labels and description cleanups. refs #36258 Trim six subtrack longLabels to the 85-char limit (ga4kSv, hprc2Sv, hgsvc2Sv, chirmade101Sv, cpc1Sv, and lrSvAll; the lrSvAll change is also made in the lrSvMergeAll.py generator so a re-run reproduces it). Standardize the APR dataset name to "Arab Pangenome Reference (APR)" across lrSv.ra, lrSv.html, aprSv.html, and the makeDoc comment (was a mix of "Arabic" and "UAE UPR"). lrSv1kgOnt.html: state per-assembly SV counts (hg38 lifted 148,375 vs hs1 native 161,332, each with its own type breakdown) and encode non-ASCII author names as numeric entities. hgsvc3Sv.html: correct the hg38 counts to match the served bigBed (176,231 DEL+INS, 176,531 total). colorsDbSv.html: use $db in the hgdownload path so it resolves on hs1 as well as hg38. cpc1Sv.html: encode a Unicode minus sign as a numeric entity.
• src/hg/makeDb/trackDb/human/colorsDbSnv.html
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    68c5b3b5dfc4053ff78a6b1d236bd1ac90251cfa Mon Jun 1 14:40:45 2026 -0700
    varFreqs: description pages for the three combined tracks and "SNV" rename sweep. Add varFreqsDisease.html and varFreqsArray.html so the two new combined tracks have full Description/Display/Methods/Data Access/References. Add a Caveats section on varFreqsArray about chip-data quality vs sequencing. Update varFreqsAll.html and the supertrack varFreqs.html to reflect the three-combined-track family (cross-links between siblings, new "Combined Tracks" section, new table rows, and updated source/variant counts). Add a GoNL row to the supertrack table. Sweep 37 subtrack longLabels and four cross-referencing description pages (colorsDbSnv.html, mei.html, meiSwegen.html, phasedVars.html) from "Variant Frequencies:" to "SNV Frequencies:" to match the supertrack shortLabel. refs #36642
• src/hg/makeDb/trackDb/human/colorsDbSv.html
  • lines changed 3, context: html, text, full: html, text
    c81011d4a8f57db347e15aa1248c501b2c8a6fea Mon Jun 1 13:16:15 2026 -0700
    QA fixes for the lrSv long-read SV supertrack: labels and description cleanups. refs #36258 Trim six subtrack longLabels to the 85-char limit (ga4kSv, hprc2Sv, hgsvc2Sv, chirmade101Sv, cpc1Sv, and lrSvAll; the lrSvAll change is also made in the lrSvMergeAll.py generator so a re-run reproduces it). Standardize the APR dataset name to "Arab Pangenome Reference (APR)" across lrSv.ra, lrSv.html, aprSv.html, and the makeDoc comment (was a mix of "Arabic" and "UAE UPR"). lrSv1kgOnt.html: state per-assembly SV counts (hg38 lifted 148,375 vs hs1 native 161,332, each with its own type breakdown) and encode non-ASCII author names as numeric entities. hgsvc3Sv.html: correct the hg38 counts to match the served bigBed (176,231 DEL+INS, 176,531 total). colorsDbSv.html: use $db in the hgdownload path so it resolves on hs1 as well as hg38. cpc1Sv.html: encode a Unicode minus sign as a numeric entity.
• src/hg/makeDb/trackDb/human/cpc1Sv.html
  • lines changed 1, context: html, text, full: html, text
    c81011d4a8f57db347e15aa1248c501b2c8a6fea Mon Jun 1 13:16:15 2026 -0700
    QA fixes for the lrSv long-read SV supertrack: labels and description cleanups. refs #36258 Trim six subtrack longLabels to the 85-char limit (ga4kSv, hprc2Sv, hgsvc2Sv, chirmade101Sv, cpc1Sv, and lrSvAll; the lrSvAll change is also made in the lrSvMergeAll.py generator so a re-run reproduces it). Standardize the APR dataset name to "Arab Pangenome Reference (APR)" across lrSv.ra, lrSv.html, aprSv.html, and the makeDoc comment (was a mix of "Arabic" and "UAE UPR"). lrSv1kgOnt.html: state per-assembly SV counts (hg38 lifted 148,375 vs hs1 native 161,332, each with its own type breakdown) and encode non-ASCII author names as numeric entities. hgsvc3Sv.html: correct the hg38 counts to match the served bigBed (176,231 DEL+INS, 176,531 total). colorsDbSv.html: use $db in the hgdownload path so it resolves on hs1 as well as hg38. cpc1Sv.html: encode a Unicode minus sign as a numeric entity.
• src/hg/makeDb/trackDb/human/decipher.ra
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    f2ef97844c0973a30cbbc1afcdd01b4096143a69 Wed Jun 3 10:56:07 2026 -0700
    Add date-based dataVersion to composite/superTrack otto containers. refs #36455 Composite and superTrack container pages do not display 'Data last updated at UCSC' (printUpdateTime returns early for them), so a dataVersion file is the only freshness signal a user sees there. Add one to the dbVar (dbVarSv), panelApp, clinGen (clinGenComp) and decipher (decipherContainer) containers. Each otto build script writes a per-assembly 'Last updated <date>' file when it actually updates the data, and the container stanza points to it via dataVersion. clinGen's container date is written by its three displayed feeds (makeDosage, makeGeneValidity, makeClinGenCspec); decipher writes hg38 only (hg19 is frozen).
• src/hg/makeDb/trackDb/human/eve.html
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    b7b279e5f1240419fb3a408fff5c82a998a36e76 Wed Jun 3 08:17:09 2026 -0700
    EVE track QA fixes: fix .as field descriptions, clarify protein count in HTML - thickStart/thickEnd .as descriptions corrected (whole protein span, not start/stop codon) - reserved .as description corrected (always 0, not itemRgb) - HTML Methods section: explain that 2,951 of 3,219 proteins have released VCF scores Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/eve.ra
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    dfe4ce8ecd6ca71b2bc90b98b4f4ac73fad0c9eb Wed Jun 3 06:47:31 2026 -0700
    EVE track QA fixes: longLabel sentence case, dataVersion, relatedTracks cross-links Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/fiveUltraUorfs.html
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    55e909c0e98fb50a5cd761f1ce2cb52f9089f5f4 Tue Jun 2 03:05:59 2026 -0700
    [Claude] ncOrfs: add 5ULTRA uORFs subtrack (MANE Select, 22,567 features) Adds fiveUltraUorfs, a new subtrack under the ncOrfs supertrack showing 22,567 ATG-initiated uORFs in MANE Select transcripts from the 5ULTRA pipeline (Chaldebas et al., Am J Hum Genet 2026, PMID 41881026). Features are colored by uORF type (Okabe-Ito palette), have exon/intron structure projected from MANE via addIntrons.py, and carry gene, rank, and Kozak strength as extra bigBed fields. ncOrfs.html summary table updated to include the new track. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> refs #37580
• src/hg/makeDb/trackDb/human/hg38/gencNcOrfs.html
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    640ebced50314d2662db498562167e0d21980f78 Tue Jun 2 16:36:43 2026 -0700
    gencNcOrfs: add peptide evidence fields from TransCODE/PeptideAtlas (PMID:42092140) Extends the GENCODE Phase I ncORF bigGenePred (Ribo-seq_ORFs.kozak.peptides.bb, 44 fields) with 14 peptide evidence fields joined from five supplementary tables in Mudge et al. 2025. Introduces the "peptidein" concept — ncORFs confidently detected by mass spectrometry but lacking functional annotation for protein status. Data covers 2,150 of 7,264 Phase I ORFs; the remaining 5,114 carry default empty values. Three color schemes are available via the colorFields dropdown: - Kozak strength (default, pre-existing field 9 colors) - Evidence type: gold=peptidein, blue=HLA only, green=non-HLA only, purple=both - HLA class: blue=class I, crimson=class II, purple=both New filters: isPeptidein, hlaClass, hlaFinalTier, hlaHppCategory, riboseqQuality. Phase II shortLabels: "GENCODE Phase II ncORFs Prim/Compr". Phase I kozakTE filterLimits set to -1:1.5 so ORFs with unavailable context are accessible. Build: peptideSupport/addPeptideEvidence.py AutoSql: Ribo-seq_ORFs.kozak.peptides.as BigBed: /gbdb/hg38/ncOrfs/gencNcOrf/Ribo-seq_ORFs.kozak.peptides.bb Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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    30c1c7161e91d449bf748f1453fe408ffef5b50f Wed Jun 3 05:22:33 2026 -0700
    fixes after AI review, no redmine Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/ncOrfs.html
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    55e909c0e98fb50a5cd761f1ce2cb52f9089f5f4 Tue Jun 2 03:05:59 2026 -0700
    [Claude] ncOrfs: add 5ULTRA uORFs subtrack (MANE Select, 22,567 features) Adds fiveUltraUorfs, a new subtrack under the ncOrfs supertrack showing 22,567 ATG-initiated uORFs in MANE Select transcripts from the 5ULTRA pipeline (Chaldebas et al., Am J Hum Genet 2026, PMID 41881026). Features are colored by uORF type (Okabe-Ito palette), have exon/intron structure projected from MANE via addIntrons.py, and carry gene, rank, and Kozak strength as extra bigBed fields. ncOrfs.html summary table updated to include the new track. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> refs #37580
• src/hg/makeDb/trackDb/human/hg38/ncOrfs.ra
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    55e909c0e98fb50a5cd761f1ce2cb52f9089f5f4 Tue Jun 2 03:05:59 2026 -0700
    [Claude] ncOrfs: add 5ULTRA uORFs subtrack (MANE Select, 22,567 features) Adds fiveUltraUorfs, a new subtrack under the ncOrfs supertrack showing 22,567 ATG-initiated uORFs in MANE Select transcripts from the 5ULTRA pipeline (Chaldebas et al., Am J Hum Genet 2026, PMID 41881026). Features are colored by uORF type (Okabe-Ito palette), have exon/intron structure projected from MANE via addIntrons.py, and carry gene, rank, and Kozak strength as extra bigBed fields. ncOrfs.html summary table updated to include the new track. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> refs #37580
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    640ebced50314d2662db498562167e0d21980f78 Tue Jun 2 16:36:43 2026 -0700
    gencNcOrfs: add peptide evidence fields from TransCODE/PeptideAtlas (PMID:42092140) Extends the GENCODE Phase I ncORF bigGenePred (Ribo-seq_ORFs.kozak.peptides.bb, 44 fields) with 14 peptide evidence fields joined from five supplementary tables in Mudge et al. 2025. Introduces the "peptidein" concept — ncORFs confidently detected by mass spectrometry but lacking functional annotation for protein status. Data covers 2,150 of 7,264 Phase I ORFs; the remaining 5,114 carry default empty values. Three color schemes are available via the colorFields dropdown: - Kozak strength (default, pre-existing field 9 colors) - Evidence type: gold=peptidein, blue=HLA only, green=non-HLA only, purple=both - HLA class: blue=class I, crimson=class II, purple=both New filters: isPeptidein, hlaClass, hlaFinalTier, hlaHppCategory, riboseqQuality. Phase II shortLabels: "GENCODE Phase II ncORFs Prim/Compr". Phase I kozakTE filterLimits set to -1:1.5 so ORFs with unavailable context are accessible. Build: peptideSupport/addPeptideEvidence.py AutoSql: Ribo-seq_ORFs.kozak.peptides.as BigBed: /gbdb/hg38/ncOrfs/gencNcOrf/Ribo-seq_ORFs.kozak.peptides.bb Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    aba7745711570d17c8bcc1cc2236eeaaae1857f9 Thu Jun 4 00:27:41 2026 -0700
    Staging the ENCODE4 Regulation track for hg38 and mm10 on hgwbeta, refs #34923
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.html
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    df99c448f8e0386bb718da0044b22752fc145713 Thu Jun 4 00:15:12 2026 -0700
    Updating ENCODE4 Regulation labels and description pages for hg38 and mm10. refs #34923 - Capitalized 363 hg38 Layered organ shortLabels and shortened the over-length TF rPeaks and Indiv. composite longLabels; updated the mm10 TF ChIP container longLabel. - TF rPeaks: added the missing SHOX2 to filterValues.factor (now 912), and updated "911 factors"/"2,502 experiments" to "912"/"2,509". - Supertrack pages: changed Layered bullets from "highlights" to "displays", reworded the histone and CTCF bullets, updated the default-organ note, and updated stale hg38 organ counts to 38/41/26/38/36. - Updated the TF ChIP facet name "Tf" -> "TF" on both description pages. - Makedoc: updated hg38 "911-factor" -> "912-factor" and mm10 RNA-seq Unstranded "26" -> "8".
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.ra
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    df99c448f8e0386bb718da0044b22752fc145713 Thu Jun 4 00:15:12 2026 -0700
    Updating ENCODE4 Regulation labels and description pages for hg38 and mm10. refs #34923 - Capitalized 363 hg38 Layered organ shortLabels and shortened the over-length TF rPeaks and Indiv. composite longLabels; updated the mm10 TF ChIP container longLabel. - TF rPeaks: added the missing SHOX2 to filterValues.factor (now 912), and updated "911 factors"/"2,502 experiments" to "912"/"2,509". - Supertrack pages: changed Layered bullets from "highlights" to "displays", reworded the histone and CTCF bullets, updated the default-organ note, and updated stale hg38 organ counts to 38/41/26/38/36. - Updated the TF ChIP facet name "Tf" -> "TF" on both description pages. - Makedoc: updated hg38 "911-factor" -> "912-factor" and mm10 RNA-seq Unstranded "26" -> "8".
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra
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    4509fab8ce258ede7421c8112edb67f956b96e35 Mon Jun 1 19:23:28 2026 -0700
    Updating ENCODE4 Regulation Indiv. subtrack labels. Removes leading "with " from 818 hg38 longLabels, capitalizes the first letter of 8,559 longLabels, and updates 8,497 shortLabels to end with "Peak" or "Signal". refs #34923
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    df99c448f8e0386bb718da0044b22752fc145713 Thu Jun 4 00:15:12 2026 -0700
    Updating ENCODE4 Regulation labels and description pages for hg38 and mm10. refs #34923 - Capitalized 363 hg38 Layered organ shortLabels and shortened the over-length TF rPeaks and Indiv. composite longLabels; updated the mm10 TF ChIP container longLabel. - TF rPeaks: added the missing SHOX2 to filterValues.factor (now 912), and updated "911 factors"/"2,502 experiments" to "912"/"2,509". - Supertrack pages: changed Layered bullets from "highlights" to "displays", reworded the histone and CTCF bullets, updated the default-organ note, and updated stale hg38 organ counts to 38/41/26/38/36. - Updated the TF ChIP facet name "Tf" -> "TF" on both description pages. - Makedoc: updated hg38 "911-factor" -> "912-factor" and mm10 RNA-seq Unstranded "26" -> "8".
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    8069aa69b6f4d04621a7bcae3b43cea2bb6623c5 Thu Jun 4 11:17:27 2026 -0700
    Updating the accession metadata column header to uppercase (Accession) in the six ENCODE4 Regulation faceted composites' primaryKey and subtrackUrls. refs #34923
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.ra
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    4509fab8ce258ede7421c8112edb67f956b96e35 Mon Jun 1 19:23:28 2026 -0700
    Updating ENCODE4 Regulation Indiv. subtrack labels. Removes leading "with " from 818 hg38 longLabels, capitalizes the first letter of 8,559 longLabels, and updates 8,497 shortLabels to end with "Peak" or "Signal". refs #34923
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    8069aa69b6f4d04621a7bcae3b43cea2bb6623c5 Thu Jun 4 11:17:27 2026 -0700
    Updating the accession metadata column header to uppercase (Accession) in the six ENCODE4 Regulation faceted composites' primaryKey and subtrackUrls. refs #34923
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.html
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    df99c448f8e0386bb718da0044b22752fc145713 Thu Jun 4 00:15:12 2026 -0700
    Updating ENCODE4 Regulation labels and description pages for hg38 and mm10. refs #34923 - Capitalized 363 hg38 Layered organ shortLabels and shortened the over-length TF rPeaks and Indiv. composite longLabels; updated the mm10 TF ChIP container longLabel. - TF rPeaks: added the missing SHOX2 to filterValues.factor (now 912), and updated "911 factors"/"2,502 experiments" to "912"/"2,509". - Supertrack pages: changed Layered bullets from "highlights" to "displays", reworded the histone and CTCF bullets, updated the default-organ note, and updated stale hg38 organ counts to 38/41/26/38/36. - Updated the TF ChIP facet name "Tf" -> "TF" on both description pages. - Makedoc: updated hg38 "911-factor" -> "912-factor" and mm10 RNA-seq Unstranded "26" -> "8".
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.ra
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    4509fab8ce258ede7421c8112edb67f956b96e35 Mon Jun 1 19:23:28 2026 -0700
    Updating ENCODE4 Regulation Indiv. subtrack labels. Removes leading "with " from 818 hg38 longLabels, capitalizes the first letter of 8,559 longLabels, and updates 8,497 shortLabels to end with "Peak" or "Signal". refs #34923
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    8069aa69b6f4d04621a7bcae3b43cea2bb6623c5 Thu Jun 4 11:17:27 2026 -0700
    Updating the accession metadata column header to uppercase (Accession) in the six ENCODE4 Regulation faceted composites' primaryKey and subtrackUrls. refs #34923
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfPeaks.html
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    df99c448f8e0386bb718da0044b22752fc145713 Thu Jun 4 00:15:12 2026 -0700
    Updating ENCODE4 Regulation labels and description pages for hg38 and mm10. refs #34923 - Capitalized 363 hg38 Layered organ shortLabels and shortened the over-length TF rPeaks and Indiv. composite longLabels; updated the mm10 TF ChIP container longLabel. - TF rPeaks: added the missing SHOX2 to filterValues.factor (now 912), and updated "911 factors"/"2,502 experiments" to "912"/"2,509". - Supertrack pages: changed Layered bullets from "highlights" to "displays", reworded the histone and CTCF bullets, updated the default-organ note, and updated stale hg38 organ counts to 38/41/26/38/36. - Updated the TF ChIP facet name "Tf" -> "TF" on both description pages. - Makedoc: updated hg38 "911-factor" -> "912-factor" and mm10 RNA-seq Unstranded "26" -> "8".
• src/hg/makeDb/trackDb/human/hgsvc3Sv.html
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    c81011d4a8f57db347e15aa1248c501b2c8a6fea Mon Jun 1 13:16:15 2026 -0700
    QA fixes for the lrSv long-read SV supertrack: labels and description cleanups. refs #36258 Trim six subtrack longLabels to the 85-char limit (ga4kSv, hprc2Sv, hgsvc2Sv, chirmade101Sv, cpc1Sv, and lrSvAll; the lrSvAll change is also made in the lrSvMergeAll.py generator so a re-run reproduces it). Standardize the APR dataset name to "Arab Pangenome Reference (APR)" across lrSv.ra, lrSv.html, aprSv.html, and the makeDoc comment (was a mix of "Arabic" and "UAE UPR"). lrSv1kgOnt.html: state per-assembly SV counts (hg38 lifted 148,375 vs hs1 native 161,332, each with its own type breakdown) and encode non-ASCII author names as numeric entities. hgsvc3Sv.html: correct the hg38 counts to match the served bigBed (176,231 DEL+INS, 176,531 total). colorsDbSv.html: use $db in the hgdownload path so it resolves on hs1 as well as hg38. cpc1Sv.html: encode a Unicode minus sign as a numeric entity.
• src/hg/makeDb/trackDb/human/lrSv.html
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    c81011d4a8f57db347e15aa1248c501b2c8a6fea Mon Jun 1 13:16:15 2026 -0700
    QA fixes for the lrSv long-read SV supertrack: labels and description cleanups. refs #36258 Trim six subtrack longLabels to the 85-char limit (ga4kSv, hprc2Sv, hgsvc2Sv, chirmade101Sv, cpc1Sv, and lrSvAll; the lrSvAll change is also made in the lrSvMergeAll.py generator so a re-run reproduces it). Standardize the APR dataset name to "Arab Pangenome Reference (APR)" across lrSv.ra, lrSv.html, aprSv.html, and the makeDoc comment (was a mix of "Arabic" and "UAE UPR"). lrSv1kgOnt.html: state per-assembly SV counts (hg38 lifted 148,375 vs hs1 native 161,332, each with its own type breakdown) and encode non-ASCII author names as numeric entities. hgsvc3Sv.html: correct the hg38 counts to match the served bigBed (176,231 DEL+INS, 176,531 total). colorsDbSv.html: use $db in the hgdownload path so it resolves on hs1 as well as hg38. cpc1Sv.html: encode a Unicode minus sign as a numeric entity.
• src/hg/makeDb/trackDb/human/lrSv.ra
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    c81011d4a8f57db347e15aa1248c501b2c8a6fea Mon Jun 1 13:16:15 2026 -0700
    QA fixes for the lrSv long-read SV supertrack: labels and description cleanups. refs #36258 Trim six subtrack longLabels to the 85-char limit (ga4kSv, hprc2Sv, hgsvc2Sv, chirmade101Sv, cpc1Sv, and lrSvAll; the lrSvAll change is also made in the lrSvMergeAll.py generator so a re-run reproduces it). Standardize the APR dataset name to "Arab Pangenome Reference (APR)" across lrSv.ra, lrSv.html, aprSv.html, and the makeDoc comment (was a mix of "Arabic" and "UAE UPR"). lrSv1kgOnt.html: state per-assembly SV counts (hg38 lifted 148,375 vs hs1 native 161,332, each with its own type breakdown) and encode non-ASCII author names as numeric entities. hgsvc3Sv.html: correct the hg38 counts to match the served bigBed (176,231 DEL+INS, 176,531 total). colorsDbSv.html: use $db in the hgdownload path so it resolves on hs1 as well as hg38. cpc1Sv.html: encode a Unicode minus sign as a numeric entity.
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    038bd0cd3f7c84ee984905608dfdd27d02cc61ec Tue Jun 2 05:19:51 2026 -0700
    [Claude] lrSv1kLin: add 1000 Genomes linear long-read SV subtrack (1,218 samples, hg38+hs1) Two native VCFs from the Eichler lab (GRCh38 and CHM13/T2T-CHM13v2), merged with Truvari v5.2.0 and annotated with population-level AFs (EUR, AMR, EAS, AFR, SAS). Track is alpha-only; not added to lrSvAll -- data not yet published. hg38: 587,779 SVs; hs1: 614,522 SVs. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> , refs #36258
• src/hg/makeDb/trackDb/human/lrSv1kLin.html
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    038bd0cd3f7c84ee984905608dfdd27d02cc61ec Tue Jun 2 05:19:51 2026 -0700
    [Claude] lrSv1kLin: add 1000 Genomes linear long-read SV subtrack (1,218 samples, hg38+hs1) Two native VCFs from the Eichler lab (GRCh38 and CHM13/T2T-CHM13v2), merged with Truvari v5.2.0 and annotated with population-level AFs (EUR, AMR, EAS, AFR, SAS). Track is alpha-only; not added to lrSvAll -- data not yet published. hg38: 587,779 SVs; hs1: 614,522 SVs. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> , refs #36258
• src/hg/makeDb/trackDb/human/lrSv1kgOnt.html
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    c81011d4a8f57db347e15aa1248c501b2c8a6fea Mon Jun 1 13:16:15 2026 -0700
    QA fixes for the lrSv long-read SV supertrack: labels and description cleanups. refs #36258 Trim six subtrack longLabels to the 85-char limit (ga4kSv, hprc2Sv, hgsvc2Sv, chirmade101Sv, cpc1Sv, and lrSvAll; the lrSvAll change is also made in the lrSvMergeAll.py generator so a re-run reproduces it). Standardize the APR dataset name to "Arab Pangenome Reference (APR)" across lrSv.ra, lrSv.html, aprSv.html, and the makeDoc comment (was a mix of "Arabic" and "UAE UPR"). lrSv1kgOnt.html: state per-assembly SV counts (hg38 lifted 148,375 vs hs1 native 161,332, each with its own type breakdown) and encode non-ASCII author names as numeric entities. hgsvc3Sv.html: correct the hg38 counts to match the served bigBed (176,231 DEL+INS, 176,531 total). colorsDbSv.html: use $db in the hgdownload path so it resolves on hs1 as well as hg38. cpc1Sv.html: encode a Unicode minus sign as a numeric entity.
• src/hg/makeDb/trackDb/human/lrSvAll.ra
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    c81011d4a8f57db347e15aa1248c501b2c8a6fea Mon Jun 1 13:16:15 2026 -0700
    QA fixes for the lrSv long-read SV supertrack: labels and description cleanups. refs #36258 Trim six subtrack longLabels to the 85-char limit (ga4kSv, hprc2Sv, hgsvc2Sv, chirmade101Sv, cpc1Sv, and lrSvAll; the lrSvAll change is also made in the lrSvMergeAll.py generator so a re-run reproduces it). Standardize the APR dataset name to "Arab Pangenome Reference (APR)" across lrSv.ra, lrSv.html, aprSv.html, and the makeDoc comment (was a mix of "Arabic" and "UAE UPR"). lrSv1kgOnt.html: state per-assembly SV counts (hg38 lifted 148,375 vs hs1 native 161,332, each with its own type breakdown) and encode non-ASCII author names as numeric entities. hgsvc3Sv.html: correct the hg38 counts to match the served bigBed (176,231 DEL+INS, 176,531 total). colorsDbSv.html: use $db in the hgdownload path so it resolves on hs1 as well as hg38. cpc1Sv.html: encode a Unicode minus sign as a numeric entity.
• src/hg/makeDb/trackDb/human/mei.html
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    68c5b3b5dfc4053ff78a6b1d236bd1ac90251cfa Mon Jun 1 14:40:45 2026 -0700
    varFreqs: description pages for the three combined tracks and "SNV" rename sweep. Add varFreqsDisease.html and varFreqsArray.html so the two new combined tracks have full Description/Display/Methods/Data Access/References. Add a Caveats section on varFreqsArray about chip-data quality vs sequencing. Update varFreqsAll.html and the supertrack varFreqs.html to reflect the three-combined-track family (cross-links between siblings, new "Combined Tracks" section, new table rows, and updated source/variant counts). Add a GoNL row to the supertrack table. Sweep 37 subtrack longLabels and four cross-referencing description pages (colorsDbSnv.html, mei.html, meiSwegen.html, phasedVars.html) from "Variant Frequencies:" to "SNV Frequencies:" to match the supertrack shortLabel. refs #36642
• src/hg/makeDb/trackDb/human/meiSwegen.html
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    68c5b3b5dfc4053ff78a6b1d236bd1ac90251cfa Mon Jun 1 14:40:45 2026 -0700
    varFreqs: description pages for the three combined tracks and "SNV" rename sweep. Add varFreqsDisease.html and varFreqsArray.html so the two new combined tracks have full Description/Display/Methods/Data Access/References. Add a Caveats section on varFreqsArray about chip-data quality vs sequencing. Update varFreqsAll.html and the supertrack varFreqs.html to reflect the three-combined-track family (cross-links between siblings, new "Combined Tracks" section, new table rows, and updated source/variant counts). Add a GoNL row to the supertrack table. Sweep 37 subtrack longLabels and four cross-referencing description pages (colorsDbSnv.html, mei.html, meiSwegen.html, phasedVars.html) from "Variant Frequencies:" to "SNV Frequencies:" to match the supertrack shortLabel. refs #36642
• src/hg/makeDb/trackDb/human/panelApp.ra
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    f2ef97844c0973a30cbbc1afcdd01b4096143a69 Wed Jun 3 10:56:07 2026 -0700
    Add date-based dataVersion to composite/superTrack otto containers. refs #36455 Composite and superTrack container pages do not display 'Data last updated at UCSC' (printUpdateTime returns early for them), so a dataVersion file is the only freshness signal a user sees there. Add one to the dbVar (dbVarSv), panelApp, clinGen (clinGenComp) and decipher (decipherContainer) containers. Each otto build script writes a per-assembly 'Last updated <date>' file when it actually updates the data, and the container stanza points to it via dataVersion. clinGen's container date is written by its three displayed feeds (makeDosage, makeGeneValidity, makeClinGenCspec); decipher writes hg38 only (hg19 is frozen).
• src/hg/makeDb/trackDb/human/phasedVars.html
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    68c5b3b5dfc4053ff78a6b1d236bd1ac90251cfa Mon Jun 1 14:40:45 2026 -0700
    varFreqs: description pages for the three combined tracks and "SNV" rename sweep. Add varFreqsDisease.html and varFreqsArray.html so the two new combined tracks have full Description/Display/Methods/Data Access/References. Add a Caveats section on varFreqsArray about chip-data quality vs sequencing. Update varFreqsAll.html and the supertrack varFreqs.html to reflect the three-combined-track family (cross-links between siblings, new "Combined Tracks" section, new table rows, and updated source/variant counts). Add a GoNL row to the supertrack table. Sweep 37 subtrack longLabels and four cross-referencing description pages (colorsDbSnv.html, mei.html, meiSwegen.html, phasedVars.html) from "Variant Frequencies:" to "SNV Frequencies:" to match the supertrack shortLabel. refs #36642
• src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
  • lines changed 2, context: html, text, full: html, text
    9169db807b49113b231d35f2beec4e04c2fb1756 Wed Jun 3 08:29:02 2026 -0700
    Add dataVersion to Orphanet and ClinGen dosage tracks to show upstream release. refs #36455 Orphanet: parse the JDBOR release version (e.g. 1.3.42 / 4.1.8 [2025-03-03]) from the downloaded XML and write it to a per-assembly version.txt that the orphadata track points to via dataVersion. ClinGen: write the ClinGen dosage 'results as of' date (e.g. 28 Apr,2026) from the curation list header to a version file shared by the clinGenHaplo and clinGenTriplo subtracks. The other ClinGen feeds publish no dataset-level date, so they are left unversioned. The version file is written per assembly only after that assembly's bigBed is installed, surfacing the source's own release, which can differ from our otto update timestamp.
  • lines changed 1, context: html, text, full: html, text
    f2ef97844c0973a30cbbc1afcdd01b4096143a69 Wed Jun 3 10:56:07 2026 -0700
    Add date-based dataVersion to composite/superTrack otto containers. refs #36455 Composite and superTrack container pages do not display 'Data last updated at UCSC' (printUpdateTime returns early for them), so a dataVersion file is the only freshness signal a user sees there. Add one to the dbVar (dbVarSv), panelApp, clinGen (clinGenComp) and decipher (decipherContainer) containers. Each otto build script writes a per-assembly 'Last updated <date>' file when it actually updates the data, and the container stanza points to it via dataVersion. clinGen's container date is written by its three displayed feeds (makeDosage, makeGeneValidity, makeClinGenCspec); decipher writes hg38 only (hg19 is frozen).
• src/hg/makeDb/trackDb/human/trackDb.dbVar.ra
  • lines changed 1, context: html, text, full: html, text
    f2ef97844c0973a30cbbc1afcdd01b4096143a69 Wed Jun 3 10:56:07 2026 -0700
    Add date-based dataVersion to composite/superTrack otto containers. refs #36455 Composite and superTrack container pages do not display 'Data last updated at UCSC' (printUpdateTime returns early for them), so a dataVersion file is the only freshness signal a user sees there. Add one to the dbVar (dbVarSv), panelApp, clinGen (clinGenComp) and decipher (decipherContainer) containers. Each otto build script writes a per-assembly 'Last updated <date>' file when it actually updates the data, and the container stanza points to it via dataVersion. clinGen's container date is written by its three displayed feeds (makeDosage, makeGeneValidity, makeClinGenCspec); decipher writes hg38 only (hg19 is frozen).
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    9169db807b49113b231d35f2beec4e04c2fb1756 Wed Jun 3 08:29:02 2026 -0700
    Add dataVersion to Orphanet and ClinGen dosage tracks to show upstream release. refs #36455 Orphanet: parse the JDBOR release version (e.g. 1.3.42 / 4.1.8 [2025-03-03]) from the downloaded XML and write it to a per-assembly version.txt that the orphadata track points to via dataVersion. ClinGen: write the ClinGen dosage 'results as of' date (e.g. 28 Apr,2026) from the curation list header to a version file shared by the clinGenHaplo and clinGenTriplo subtracks. The other ClinGen feeds publish no dataset-level date, so they are left unversioned. The version file is written per assembly only after that assembly's bigBed is installed, surfacing the source's own release, which can differ from our otto update timestamp.
• src/hg/makeDb/trackDb/human/varFreqs.html
  • lines changed 69, context: html, text, full: html, text
    68c5b3b5dfc4053ff78a6b1d236bd1ac90251cfa Mon Jun 1 14:40:45 2026 -0700
    varFreqs: description pages for the three combined tracks and "SNV" rename sweep. Add varFreqsDisease.html and varFreqsArray.html so the two new combined tracks have full Description/Display/Methods/Data Access/References. Add a Caveats section on varFreqsArray about chip-data quality vs sequencing. Update varFreqsAll.html and the supertrack varFreqs.html to reflect the three-combined-track family (cross-links between siblings, new "Combined Tracks" section, new table rows, and updated source/variant counts). Add a GoNL row to the supertrack table. Sweep 37 subtrack longLabels and four cross-referencing description pages (colorsDbSnv.html, mei.html, meiSwegen.html, phasedVars.html) from "Variant Frequencies:" to "SNV Frequencies:" to match the supertrack shortLabel. refs #36642
  • lines changed 25, context: html, text, full: html, text
    64a3f9e7813e823cf724ea188c3928a911578286 Thu Jun 4 00:32:22 2026 -0700
    varFreqs: replace All Databases Combined with two phenotype-split tracks Replace the single varFreqsAll combined track (and drop the varFreqsDisease track) with two matched tracks for visual case-vs-background comparison: varFreqsAffected - variants seen in the affected/case arms of disease cohorts (SFARI SPARK WES/WGS ASD probands, SCHEMA cases, GREGoR affected, GA4K); ~130,000 individuals varFreqsBackground - population reference cohorts + the unaffected/control arms of disease cohorts ("all other variants"); ~1.5 million individuals A variant seen in both groups appears in both tracks. Genotyping-array cohorts stay out of both (varFreqsArray unchanged). vcfToBigBed.py gains --split-affected to emit both tracks in one pass; it reads phenotype tags (affected/unaffected/unknown) from populations.tsv and is_disease/disease_role from databases.tsv, and derives the length-filter ranges from the observed data. TOPMed reclassified as a population cohort. SPARK WGS display name changed to SFARI SPARK WGS for consistency with the standalone subtracks. Fixed the trackDb mouseOver $-substitution prefix collision by wrapping fields in ${}. New description pages for both tracks. refs #36642
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    a729e1ee610d17d3dcb36a45437f1709e5699558 Fri Jun 5 02:18:09 2026 -0700
    varFreqs: fix collection page leftovers from the combined-track redesign Update the SNV Frequencies collection description page for the two-track (Affected / Background) layout: correct the combined-track count to three, rewrite the Methods paragraph that still described building the old single "All Databases" track (now describes the phenotype split via vcfToBigBed.py --split-affected), and set the Affected/Background sample-count cells in the dataset table to ~130k and ~1.5M. refs #36642
  • lines changed 1, context: html, text, full: html, text
    196b96d04435ca93e8a7366127a41afe6b791b98 Fri Jun 5 14:22:48 2026 -0700
    varFreqs.html: clarify SCHEMA cohort size in the supertrack Cohort cell - keep the 24k/97k Singh 2022 primary-meta-analysis headline, note that the SCHEMA browser VCF we use aggregates further cohorts up to ~73k/~182k. Per QA feedback. refs #36642
  • lines changed 104, context: html, text, full: html, text
    ef70dfff0e8710e8aa4bc369a939f838c75947fb Fri Jun 5 14:59:06 2026 -0700
    varFreqs: Phase-7 audit cleanup on the supertrack and combined-track description pages. Supertrack varFreqs.html: - Restore the consequence-filter "Other" bucket explanation that was lost when varFreqsAll.html was replaced by the Affected+Background pair (now documented once on the supertrack page, since all three combined tracks share the filter). - Add 6 primary citations that were already in standalone subtrack pages but not carried up: Bycroft (UK Biobank), Cao (ChinaMAP), Cong (WBBC), Genome of the Netherlands Consortium (GoNL), Malomane (Saudi), Yang (TPMI). - Reorder Ameur, Singh into correct alphabetical position. - Lowercase <A HREF= -> <a href= per house style. varFreqsArray.html: - Replace four stale hgTrackUi?g=varFreqsAll links with the appropriate sibling combined tracks (varFreqsAffected / varFreqsBackground) or the supertrack. - Match the consequence color table style to varFreqsAffected.html and varFreqsBackground.html (color swatch instead of named-color text). refs #36642
• src/hg/makeDb/trackDb/human/varFreqs.ra
  • lines changed 37, context: html, text, full: html, text
    68c5b3b5dfc4053ff78a6b1d236bd1ac90251cfa Mon Jun 1 14:40:45 2026 -0700
    varFreqs: description pages for the three combined tracks and "SNV" rename sweep. Add varFreqsDisease.html and varFreqsArray.html so the two new combined tracks have full Description/Display/Methods/Data Access/References. Add a Caveats section on varFreqsArray about chip-data quality vs sequencing. Update varFreqsAll.html and the supertrack varFreqs.html to reflect the three-combined-track family (cross-links between siblings, new "Combined Tracks" section, new table rows, and updated source/variant counts). Add a GoNL row to the supertrack table. Sweep 37 subtrack longLabels and four cross-referencing description pages (colorsDbSnv.html, mei.html, meiSwegen.html, phasedVars.html) from "Variant Frequencies:" to "SNV Frequencies:" to match the supertrack shortLabel. refs #36642
  • lines changed 445, context: html, text, full: html, text
    64a3f9e7813e823cf724ea188c3928a911578286 Thu Jun 4 00:32:22 2026 -0700
    varFreqs: replace All Databases Combined with two phenotype-split tracks Replace the single varFreqsAll combined track (and drop the varFreqsDisease track) with two matched tracks for visual case-vs-background comparison: varFreqsAffected - variants seen in the affected/case arms of disease cohorts (SFARI SPARK WES/WGS ASD probands, SCHEMA cases, GREGoR affected, GA4K); ~130,000 individuals varFreqsBackground - population reference cohorts + the unaffected/control arms of disease cohorts ("all other variants"); ~1.5 million individuals A variant seen in both groups appears in both tracks. Genotyping-array cohorts stay out of both (varFreqsArray unchanged). vcfToBigBed.py gains --split-affected to emit both tracks in one pass; it reads phenotype tags (affected/unaffected/unknown) from populations.tsv and is_disease/disease_role from databases.tsv, and derives the length-filter ranges from the observed data. TOPMed reclassified as a population cohort. SPARK WGS display name changed to SFARI SPARK WGS for consistency with the standalone subtracks. Fixed the trackDb mouseOver $-substitution prefix collision by wrapping fields in ${}. New description pages for both tracks. refs #36642
  • lines changed 2, context: html, text, full: html, text
    ee8f8d6e46a060af155da2687f756620f64c8626 Fri Jun 5 15:03:47 2026 -0700
    varFreqs: swap priorities so Population + Unaffected (varFreqsBackground) appears first in the listing, Affected/Case Individuals second. varFreqsBackground 0.11 -> 0.1; varFreqsAffected 0.1 -> 0.11. refs #36642
• src/hg/makeDb/trackDb/human/varFreqsAffected.html
  • lines changed 134, context: html, text, full: html, text
    64a3f9e7813e823cf724ea188c3928a911578286 Thu Jun 4 00:32:22 2026 -0700
    varFreqs: replace All Databases Combined with two phenotype-split tracks Replace the single varFreqsAll combined track (and drop the varFreqsDisease track) with two matched tracks for visual case-vs-background comparison: varFreqsAffected - variants seen in the affected/case arms of disease cohorts (SFARI SPARK WES/WGS ASD probands, SCHEMA cases, GREGoR affected, GA4K); ~130,000 individuals varFreqsBackground - population reference cohorts + the unaffected/control arms of disease cohorts ("all other variants"); ~1.5 million individuals A variant seen in both groups appears in both tracks. Genotyping-array cohorts stay out of both (varFreqsArray unchanged). vcfToBigBed.py gains --split-affected to emit both tracks in one pass; it reads phenotype tags (affected/unaffected/unknown) from populations.tsv and is_disease/disease_role from databases.tsv, and derives the length-filter ranges from the observed data. TOPMed reclassified as a population cohort. SPARK WGS display name changed to SFARI SPARK WGS for consistency with the standalone subtracks. Fixed the trackDb mouseOver $-substitution prefix collision by wrapping fields in ${}. New description pages for both tracks. refs #36642
• src/hg/makeDb/trackDb/human/varFreqsAll.html
  • lines changed 51, context: html, text, full: html, text
    68c5b3b5dfc4053ff78a6b1d236bd1ac90251cfa Mon Jun 1 14:40:45 2026 -0700
    varFreqs: description pages for the three combined tracks and "SNV" rename sweep. Add varFreqsDisease.html and varFreqsArray.html so the two new combined tracks have full Description/Display/Methods/Data Access/References. Add a Caveats section on varFreqsArray about chip-data quality vs sequencing. Update varFreqsAll.html and the supertrack varFreqs.html to reflect the three-combined-track family (cross-links between siblings, new "Combined Tracks" section, new table rows, and updated source/variant counts). Add a GoNL row to the supertrack table. Sweep 37 subtrack longLabels and four cross-referencing description pages (colorsDbSnv.html, mei.html, meiSwegen.html, phasedVars.html) from "Variant Frequencies:" to "SNV Frequencies:" to match the supertrack shortLabel. refs #36642
  • lines changed 244, context: html, text, full: html, text
    64a3f9e7813e823cf724ea188c3928a911578286 Thu Jun 4 00:32:22 2026 -0700
    varFreqs: replace All Databases Combined with two phenotype-split tracks Replace the single varFreqsAll combined track (and drop the varFreqsDisease track) with two matched tracks for visual case-vs-background comparison: varFreqsAffected - variants seen in the affected/case arms of disease cohorts (SFARI SPARK WES/WGS ASD probands, SCHEMA cases, GREGoR affected, GA4K); ~130,000 individuals varFreqsBackground - population reference cohorts + the unaffected/control arms of disease cohorts ("all other variants"); ~1.5 million individuals A variant seen in both groups appears in both tracks. Genotyping-array cohorts stay out of both (varFreqsArray unchanged). vcfToBigBed.py gains --split-affected to emit both tracks in one pass; it reads phenotype tags (affected/unaffected/unknown) from populations.tsv and is_disease/disease_role from databases.tsv, and derives the length-filter ranges from the observed data. TOPMed reclassified as a population cohort. SPARK WGS display name changed to SFARI SPARK WGS for consistency with the standalone subtracks. Fixed the trackDb mouseOver $-substitution prefix collision by wrapping fields in ${}. New description pages for both tracks. refs #36642
• src/hg/makeDb/trackDb/human/varFreqsArray.html
  • lines changed 181, context: html, text, full: html, text
    68c5b3b5dfc4053ff78a6b1d236bd1ac90251cfa Mon Jun 1 14:40:45 2026 -0700
    varFreqs: description pages for the three combined tracks and "SNV" rename sweep. Add varFreqsDisease.html and varFreqsArray.html so the two new combined tracks have full Description/Display/Methods/Data Access/References. Add a Caveats section on varFreqsArray about chip-data quality vs sequencing. Update varFreqsAll.html and the supertrack varFreqs.html to reflect the three-combined-track family (cross-links between siblings, new "Combined Tracks" section, new table rows, and updated source/variant counts). Add a GoNL row to the supertrack table. Sweep 37 subtrack longLabels and four cross-referencing description pages (colorsDbSnv.html, mei.html, meiSwegen.html, phasedVars.html) from "Variant Frequencies:" to "SNV Frequencies:" to match the supertrack shortLabel. refs #36642
  • lines changed 30, context: html, text, full: html, text
    ef70dfff0e8710e8aa4bc369a939f838c75947fb Fri Jun 5 14:59:06 2026 -0700
    varFreqs: Phase-7 audit cleanup on the supertrack and combined-track description pages. Supertrack varFreqs.html: - Restore the consequence-filter "Other" bucket explanation that was lost when varFreqsAll.html was replaced by the Affected+Background pair (now documented once on the supertrack page, since all three combined tracks share the filter). - Add 6 primary citations that were already in standalone subtrack pages but not carried up: Bycroft (UK Biobank), Cao (ChinaMAP), Cong (WBBC), Genome of the Netherlands Consortium (GoNL), Malomane (Saudi), Yang (TPMI). - Reorder Ameur, Singh into correct alphabetical position. - Lowercase <A HREF= -> <a href= per house style. varFreqsArray.html: - Replace four stale hgTrackUi?g=varFreqsAll links with the appropriate sibling combined tracks (varFreqsAffected / varFreqsBackground) or the supertrack. - Match the consequence color table style to varFreqsAffected.html and varFreqsBackground.html (color swatch instead of named-color text). refs #36642
• src/hg/makeDb/trackDb/human/varFreqsBackground.html
  • lines changed 121, context: html, text, full: html, text
    64a3f9e7813e823cf724ea188c3928a911578286 Thu Jun 4 00:32:22 2026 -0700
    varFreqs: replace All Databases Combined with two phenotype-split tracks Replace the single varFreqsAll combined track (and drop the varFreqsDisease track) with two matched tracks for visual case-vs-background comparison: varFreqsAffected - variants seen in the affected/case arms of disease cohorts (SFARI SPARK WES/WGS ASD probands, SCHEMA cases, GREGoR affected, GA4K); ~130,000 individuals varFreqsBackground - population reference cohorts + the unaffected/control arms of disease cohorts ("all other variants"); ~1.5 million individuals A variant seen in both groups appears in both tracks. Genotyping-array cohorts stay out of both (varFreqsArray unchanged). vcfToBigBed.py gains --split-affected to emit both tracks in one pass; it reads phenotype tags (affected/unaffected/unknown) from populations.tsv and is_disease/disease_role from databases.tsv, and derives the length-filter ranges from the observed data. TOPMed reclassified as a population cohort. SPARK WGS display name changed to SFARI SPARK WGS for consistency with the standalone subtracks. Fixed the trackDb mouseOver $-substitution prefix collision by wrapping fields in ${}. New description pages for both tracks. refs #36642
• src/hg/makeDb/trackDb/human/varFreqsDisease.html
  • lines changed 198, context: html, text, full: html, text
    68c5b3b5dfc4053ff78a6b1d236bd1ac90251cfa Mon Jun 1 14:40:45 2026 -0700
    varFreqs: description pages for the three combined tracks and "SNV" rename sweep. Add varFreqsDisease.html and varFreqsArray.html so the two new combined tracks have full Description/Display/Methods/Data Access/References. Add a Caveats section on varFreqsArray about chip-data quality vs sequencing. Update varFreqsAll.html and the supertrack varFreqs.html to reflect the three-combined-track family (cross-links between siblings, new "Combined Tracks" section, new table rows, and updated source/variant counts). Add a GoNL row to the supertrack table. Sweep 37 subtrack longLabels and four cross-referencing description pages (colorsDbSnv.html, mei.html, meiSwegen.html, phasedVars.html) from "Variant Frequencies:" to "SNV Frequencies:" to match the supertrack shortLabel. refs #36642
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    753e4fdfc8b960c8a8775e2282b0f87c73a95449 Tue Jun 2 07:49:03 2026 -0700
    varFreqsDisease.html: list six disease cohorts separately to match the "six cohorts" count in the opening sentence and the six per-source AC/AF columns in the bigBed schema. SPARK WES and SFARI WGS are two distinct sample sets, not one combined cohort. Per QA feedback. refs #36642
  • lines changed 198, context: html, text, full: html, text
    64a3f9e7813e823cf724ea188c3928a911578286 Thu Jun 4 00:32:22 2026 -0700
    varFreqs: replace All Databases Combined with two phenotype-split tracks Replace the single varFreqsAll combined track (and drop the varFreqsDisease track) with two matched tracks for visual case-vs-background comparison: varFreqsAffected - variants seen in the affected/case arms of disease cohorts (SFARI SPARK WES/WGS ASD probands, SCHEMA cases, GREGoR affected, GA4K); ~130,000 individuals varFreqsBackground - population reference cohorts + the unaffected/control arms of disease cohorts ("all other variants"); ~1.5 million individuals A variant seen in both groups appears in both tracks. Genotyping-array cohorts stay out of both (varFreqsArray unchanged). vcfToBigBed.py gains --split-affected to emit both tracks in one pass; it reads phenotype tags (affected/unaffected/unknown) from populations.tsv and is_disease/disease_role from databases.tsv, and derives the length-filter ranges from the observed data. TOPMed reclassified as a population cohort. SPARK WGS display name changed to SFARI SPARK WGS for consistency with the standalone subtracks. Fixed the trackDb mouseOver $-substitution prefix collision by wrapping fields in ${}. New description pages for both tracks. refs #36642
• src/hg/makeDb/trackDb/mouse/mm10/encode3.atac.ra
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    e5116de1d75b89b28693d3df2a3531f7b6c4a6eb Fri Jun 5 11:49:58 2026 -0700
    Restored the standalone ENCODE Expression superTrack on mm10 per team discussion on #37001. Added ENCODE3 Regulation and ENCODE4 Regulation as related tracks on mm10. Added a Released TBD pennantIcon on the mm10 and mm39 superTracks. refs #37001
• src/hg/makeDb/trackDb/mouse/mm10/encode3.chromHmm.ra
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    e5116de1d75b89b28693d3df2a3531f7b6c4a6eb Fri Jun 5 11:49:58 2026 -0700
    Restored the standalone ENCODE Expression superTrack on mm10 per team discussion on #37001. Added ENCODE3 Regulation and ENCODE4 Regulation as related tracks on mm10. Added a Released TBD pennantIcon on the mm10 and mm39 superTracks. refs #37001
• src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.html
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    df99c448f8e0386bb718da0044b22752fc145713 Thu Jun 4 00:15:12 2026 -0700
    Updating ENCODE4 Regulation labels and description pages for hg38 and mm10. refs #34923 - Capitalized 363 hg38 Layered organ shortLabels and shortened the over-length TF rPeaks and Indiv. composite longLabels; updated the mm10 TF ChIP container longLabel. - TF rPeaks: added the missing SHOX2 to filterValues.factor (now 912), and updated "911 factors"/"2,502 experiments" to "912"/"2,509". - Supertrack pages: changed Layered bullets from "highlights" to "displays", reworded the histone and CTCF bullets, updated the default-organ note, and updated stale hg38 organ counts to 38/41/26/38/36. - Updated the TF ChIP facet name "Tf" -> "TF" on both description pages. - Makedoc: updated hg38 "911-factor" -> "912-factor" and mm10 RNA-seq Unstranded "26" -> "8".
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra
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    4509fab8ce258ede7421c8112edb67f956b96e35 Mon Jun 1 19:23:28 2026 -0700
    Updating ENCODE4 Regulation Indiv. subtrack labels. Removes leading "with " from 818 hg38 longLabels, capitalizes the first letter of 8,559 longLabels, and updates 8,497 shortLabels to end with "Peak" or "Signal". refs #34923
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    df99c448f8e0386bb718da0044b22752fc145713 Thu Jun 4 00:15:12 2026 -0700
    Updating ENCODE4 Regulation labels and description pages for hg38 and mm10. refs #34923 - Capitalized 363 hg38 Layered organ shortLabels and shortened the over-length TF rPeaks and Indiv. composite longLabels; updated the mm10 TF ChIP container longLabel. - TF rPeaks: added the missing SHOX2 to filterValues.factor (now 912), and updated "911 factors"/"2,502 experiments" to "912"/"2,509". - Supertrack pages: changed Layered bullets from "highlights" to "displays", reworded the histone and CTCF bullets, updated the default-organ note, and updated stale hg38 organ counts to 38/41/26/38/36. - Updated the TF ChIP facet name "Tf" -> "TF" on both description pages. - Makedoc: updated hg38 "911-factor" -> "912-factor" and mm10 RNA-seq Unstranded "26" -> "8".
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    8069aa69b6f4d04621a7bcae3b43cea2bb6623c5 Thu Jun 4 11:17:27 2026 -0700
    Updating the accession metadata column header to uppercase (Accession) in the six ENCODE4 Regulation faceted composites' primaryKey and subtrackUrls. refs #34923
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.ra
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    4509fab8ce258ede7421c8112edb67f956b96e35 Mon Jun 1 19:23:28 2026 -0700
    Updating ENCODE4 Regulation Indiv. subtrack labels. Removes leading "with " from 818 hg38 longLabels, capitalizes the first letter of 8,559 longLabels, and updates 8,497 shortLabels to end with "Peak" or "Signal". refs #34923
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    8069aa69b6f4d04621a7bcae3b43cea2bb6623c5 Thu Jun 4 11:17:27 2026 -0700
    Updating the accession metadata column header to uppercase (Accession) in the six ENCODE4 Regulation faceted composites' primaryKey and subtrackUrls. refs #34923
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.html
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    df99c448f8e0386bb718da0044b22752fc145713 Thu Jun 4 00:15:12 2026 -0700
    Updating ENCODE4 Regulation labels and description pages for hg38 and mm10. refs #34923 - Capitalized 363 hg38 Layered organ shortLabels and shortened the over-length TF rPeaks and Indiv. composite longLabels; updated the mm10 TF ChIP container longLabel. - TF rPeaks: added the missing SHOX2 to filterValues.factor (now 912), and updated "911 factors"/"2,502 experiments" to "912"/"2,509". - Supertrack pages: changed Layered bullets from "highlights" to "displays", reworded the histone and CTCF bullets, updated the default-organ note, and updated stale hg38 organ counts to 38/41/26/38/36. - Updated the TF ChIP facet name "Tf" -> "TF" on both description pages. - Makedoc: updated hg38 "911-factor" -> "912-factor" and mm10 RNA-seq Unstranded "26" -> "8".
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra
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    4509fab8ce258ede7421c8112edb67f956b96e35 Mon Jun 1 19:23:28 2026 -0700
    Updating ENCODE4 Regulation Indiv. subtrack labels. Removes leading "with " from 818 hg38 longLabels, capitalizes the first letter of 8,559 longLabels, and updates 8,497 shortLabels to end with "Peak" or "Signal". refs #34923
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    df99c448f8e0386bb718da0044b22752fc145713 Thu Jun 4 00:15:12 2026 -0700
    Updating ENCODE4 Regulation labels and description pages for hg38 and mm10. refs #34923 - Capitalized 363 hg38 Layered organ shortLabels and shortened the over-length TF rPeaks and Indiv. composite longLabels; updated the mm10 TF ChIP container longLabel. - TF rPeaks: added the missing SHOX2 to filterValues.factor (now 912), and updated "911 factors"/"2,502 experiments" to "912"/"2,509". - Supertrack pages: changed Layered bullets from "highlights" to "displays", reworded the histone and CTCF bullets, updated the default-organ note, and updated stale hg38 organ counts to 38/41/26/38/36. - Updated the TF ChIP facet name "Tf" -> "TF" on both description pages. - Makedoc: updated hg38 "911-factor" -> "912-factor" and mm10 RNA-seq Unstranded "26" -> "8".
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    8069aa69b6f4d04621a7bcae3b43cea2bb6623c5 Thu Jun 4 11:17:27 2026 -0700
    Updating the accession metadata column header to uppercase (Accession) in the six ENCODE4 Regulation faceted composites' primaryKey and subtrackUrls. refs #34923
• src/hg/makeDb/trackDb/mouse/mm10/mouseDevTimecourse.ra
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    e5116de1d75b89b28693d3df2a3531f7b6c4a6eb Fri Jun 5 11:49:58 2026 -0700
    Restored the standalone ENCODE Expression superTrack on mm10 per team discussion on #37001. Added ENCODE3 Regulation and ENCODE4 Regulation as related tracks on mm10. Added a Released TBD pennantIcon on the mm10 and mm39 superTracks. refs #37001
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.alpha.ra
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    e5116de1d75b89b28693d3df2a3531f7b6c4a6eb Fri Jun 5 11:49:58 2026 -0700
    Restored the standalone ENCODE Expression superTrack on mm10 per team discussion on #37001. Added ENCODE3 Regulation and ENCODE4 Regulation as related tracks on mm10. Added a Released TBD pennantIcon on the mm10 and mm39 superTracks. refs #37001
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.ra
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    e5116de1d75b89b28693d3df2a3531f7b6c4a6eb Fri Jun 5 11:49:58 2026 -0700
    Restored the standalone ENCODE Expression superTrack on mm10 per team discussion on #37001. Added ENCODE3 Regulation and ENCODE4 Regulation as related tracks on mm10. Added a Released TBD pennantIcon on the mm10 and mm39 superTracks. refs #37001
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    aba7745711570d17c8bcc1cc2236eeaaae1857f9 Thu Jun 4 00:27:41 2026 -0700
    Staging the ENCODE4 Regulation track for hg38 and mm10 on hgwbeta, refs #34923
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    e5116de1d75b89b28693d3df2a3531f7b6c4a6eb Fri Jun 5 11:49:58 2026 -0700
    Restored the standalone ENCODE Expression superTrack on mm10 per team discussion on #37001. Added ENCODE3 Regulation and ENCODE4 Regulation as related tracks on mm10. Added a Released TBD pennantIcon on the mm10 and mm39 superTracks. refs #37001
• src/hg/makeDb/trackDb/mouse/mm39/mouseDevTimecourse.ra
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    e5116de1d75b89b28693d3df2a3531f7b6c4a6eb Fri Jun 5 11:49:58 2026 -0700
    Restored the standalone ENCODE Expression superTrack on mm10 per team discussion on #37001. Added ENCODE3 Regulation and ENCODE4 Regulation as related tracks on mm10. Added a Released TBD pennantIcon on the mm10 and mm39 superTracks. refs #37001
• src/hg/makeDb/trackDb/relatedTracks.ra
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    dfe4ce8ecd6ca71b2bc90b98b4f4ac73fad0c9eb Wed Jun 3 06:47:31 2026 -0700
    EVE track QA fixes: longLabel sentence case, dataVersion, relatedTracks cross-links Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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    e5116de1d75b89b28693d3df2a3531f7b6c4a6eb Fri Jun 5 11:49:58 2026 -0700
    Restored the standalone ENCODE Expression superTrack on mm10 per team discussion on #37001. Added ENCODE3 Regulation and ENCODE4 Regulation as related tracks on mm10. Added a Released TBD pennantIcon on the mm10 and mm39 superTracks. refs #37001
• src/hg/makeDb/trackDb/tagTypes.tab
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    5dc1d6e658ab009f27314e192340275a6bb70237 Tue Jun 2 16:20:48 2026 -0700
    Add colorFields trackDb setting for bigBed/bigGenePred color scheme switching Adds a new trackDb statement `colorFields` that renders a "Color by:" dropdown in the track controls page, letting users switch among multiple pre-computed color schemes stored as extra bigBed fields containing R,G,B strings. The `default="label"` key renames the standard itemRgb option in the dropdown. Other entries name extra bigBed fields whose R,G,B values override itemRgb when selected. When a non-default scheme is active, a "(Coloring by: label)" suffix appears in the track long label. Changes: - hui.c/hui.h: new colorFieldsCfgUi() rendered inside bedScoreCfgUi() for bigBed - bigBedTrack.c: colorFieldIdx lookup + per-item filterColor override + longLabel suffix - tagTypes.tab: register colorFields for bigBed and bigGenePred - trackDbLibrary.shtml, trackDbDoc.html, trackDbHub.v3.html, changes.html: documentation refs #26253 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/utils/automation/asmHubTrackDb.sh
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    c91de9787fcb7f202a9e294d4e9e8734938d5389 Wed Jun 3 10:52:32 2026 -0700
    do not add the toga V1 tracks when the TOGAv2 is available refs #35776
• src/hg/utils/makefile
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    9aaf0a4a28e67a6c5f6ce62346cbadcc20d2c6a5 Fri Jun 5 10:44:17 2026 -0700
    Wire up rtsUpdate install via the standard utils/ make. Adds a small makefile under src/hg/utils/rts/ that copies the rtsUpdate script to \${BINDIR} (~/bin/\${MACHTYPE}/) so it lands on the user's PATH, and adds rts to the DIRS list in src/hg/utils/makefile so the top-level make descends into it. After this, either `make` from src/hg/utils/rts/ or `make` from src/hg/utils/ installs rtsUpdate. refs #32768
• src/hg/utils/otto/clinGen/checkClinGen.sh
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    351ed2fc24a13b86cf2a1fc9695309e2c0da9de5 Wed Jun 3 09:33:28 2026 -0700
    Make otto fetch failures loud and clinGen silent on no-update. refs #37697 Several otto jobs used 'wget -q'/'curl -s' under 'set -e', so a broken download aborted with no output and cron (which mails on output, not exit code) sent nothing -- the mode by which mastermind failed silently for months. - mastermind, malacards: add an ERR trap that echoes a failure message; switch mastermind's 'curl -s' to 'curl -sf' so an HTTP error fails loudly instead of writing a challenge page into the release file. - geneReviews: add an ERR trap (kept silent on no-update via the wrapper's mail -E). - All three use 'set -eE' (errtrace) so the ERR trap also fires for failures inside functions/subshells, not just top-level commands. - clinGen: capture each sub-build's exit status instead of swallowing it under 'set +e', and report which sub-build failed. Also drop the routine 'No ... update' echoes and the unconditional 'ClinGen update done.' line, and switch the wrapper to 'mail -E', so clinGen is now silent on no-update and only emails on a real update or a failure.
• src/hg/utils/otto/clinGen/clinGenWrapper.sh
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    351ed2fc24a13b86cf2a1fc9695309e2c0da9de5 Wed Jun 3 09:33:28 2026 -0700
    Make otto fetch failures loud and clinGen silent on no-update. refs #37697 Several otto jobs used 'wget -q'/'curl -s' under 'set -e', so a broken download aborted with no output and cron (which mails on output, not exit code) sent nothing -- the mode by which mastermind failed silently for months. - mastermind, malacards: add an ERR trap that echoes a failure message; switch mastermind's 'curl -s' to 'curl -sf' so an HTTP error fails loudly instead of writing a challenge page into the release file. - geneReviews: add an ERR trap (kept silent on no-update via the wrapper's mail -E). - All three use 'set -eE' (errtrace) so the ERR trap also fires for failures inside functions/subshells, not just top-level commands. - clinGen: capture each sub-build's exit status instead of swallowing it under 'set +e', and report which sub-build failed. Also drop the routine 'No ... update' echoes and the unconditional 'ClinGen update done.' line, and switch the wrapper to 'mail -E', so clinGen is now silent on no-update and only emails on a real update or a failure.
• src/hg/utils/otto/clinGen/makeClinGenCspec.sh
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    f2ef97844c0973a30cbbc1afcdd01b4096143a69 Wed Jun 3 10:56:07 2026 -0700
    Add date-based dataVersion to composite/superTrack otto containers. refs #36455 Composite and superTrack container pages do not display 'Data last updated at UCSC' (printUpdateTime returns early for them), so a dataVersion file is the only freshness signal a user sees there. Add one to the dbVar (dbVarSv), panelApp, clinGen (clinGenComp) and decipher (decipherContainer) containers. Each otto build script writes a per-assembly 'Last updated <date>' file when it actually updates the data, and the container stanza points to it via dataVersion. clinGen's container date is written by its three displayed feeds (makeDosage, makeGeneValidity, makeClinGenCspec); decipher writes hg38 only (hg19 is frozen).
• src/hg/utils/otto/clinGen/makeCnv.sh
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    351ed2fc24a13b86cf2a1fc9695309e2c0da9de5 Wed Jun 3 09:33:28 2026 -0700
    Make otto fetch failures loud and clinGen silent on no-update. refs #37697 Several otto jobs used 'wget -q'/'curl -s' under 'set -e', so a broken download aborted with no output and cron (which mails on output, not exit code) sent nothing -- the mode by which mastermind failed silently for months. - mastermind, malacards: add an ERR trap that echoes a failure message; switch mastermind's 'curl -s' to 'curl -sf' so an HTTP error fails loudly instead of writing a challenge page into the release file. - geneReviews: add an ERR trap (kept silent on no-update via the wrapper's mail -E). - All three use 'set -eE' (errtrace) so the ERR trap also fires for failures inside functions/subshells, not just top-level commands. - clinGen: capture each sub-build's exit status instead of swallowing it under 'set +e', and report which sub-build failed. Also drop the routine 'No ... update' echoes and the unconditional 'ClinGen update done.' line, and switch the wrapper to 'mail -E', so clinGen is now silent on no-update and only emails on a real update or a failure.
• src/hg/utils/otto/clinGen/makeDosage.sh
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    9169db807b49113b231d35f2beec4e04c2fb1756 Wed Jun 3 08:29:02 2026 -0700
    Add dataVersion to Orphanet and ClinGen dosage tracks to show upstream release. refs #36455 Orphanet: parse the JDBOR release version (e.g. 1.3.42 / 4.1.8 [2025-03-03]) from the downloaded XML and write it to a per-assembly version.txt that the orphadata track points to via dataVersion. ClinGen: write the ClinGen dosage 'results as of' date (e.g. 28 Apr,2026) from the curation list header to a version file shared by the clinGenHaplo and clinGenTriplo subtracks. The other ClinGen feeds publish no dataset-level date, so they are left unversioned. The version file is written per assembly only after that assembly's bigBed is installed, surfacing the source's own release, which can differ from our otto update timestamp.
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    351ed2fc24a13b86cf2a1fc9695309e2c0da9de5 Wed Jun 3 09:33:28 2026 -0700
    Make otto fetch failures loud and clinGen silent on no-update. refs #37697 Several otto jobs used 'wget -q'/'curl -s' under 'set -e', so a broken download aborted with no output and cron (which mails on output, not exit code) sent nothing -- the mode by which mastermind failed silently for months. - mastermind, malacards: add an ERR trap that echoes a failure message; switch mastermind's 'curl -s' to 'curl -sf' so an HTTP error fails loudly instead of writing a challenge page into the release file. - geneReviews: add an ERR trap (kept silent on no-update via the wrapper's mail -E). - All three use 'set -eE' (errtrace) so the ERR trap also fires for failures inside functions/subshells, not just top-level commands. - clinGen: capture each sub-build's exit status instead of swallowing it under 'set +e', and report which sub-build failed. Also drop the routine 'No ... update' echoes and the unconditional 'ClinGen update done.' line, and switch the wrapper to 'mail -E', so clinGen is now silent on no-update and only emails on a real update or a failure.
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    f2ef97844c0973a30cbbc1afcdd01b4096143a69 Wed Jun 3 10:56:07 2026 -0700
    Add date-based dataVersion to composite/superTrack otto containers. refs #36455 Composite and superTrack container pages do not display 'Data last updated at UCSC' (printUpdateTime returns early for them), so a dataVersion file is the only freshness signal a user sees there. Add one to the dbVar (dbVarSv), panelApp, clinGen (clinGenComp) and decipher (decipherContainer) containers. Each otto build script writes a per-assembly 'Last updated <date>' file when it actually updates the data, and the container stanza points to it via dataVersion. clinGen's container date is written by its three displayed feeds (makeDosage, makeGeneValidity, makeClinGenCspec); decipher writes hg38 only (hg19 is frozen).
• src/hg/utils/otto/clinGen/makeGeneValidity.sh
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    351ed2fc24a13b86cf2a1fc9695309e2c0da9de5 Wed Jun 3 09:33:28 2026 -0700
    Make otto fetch failures loud and clinGen silent on no-update. refs #37697 Several otto jobs used 'wget -q'/'curl -s' under 'set -e', so a broken download aborted with no output and cron (which mails on output, not exit code) sent nothing -- the mode by which mastermind failed silently for months. - mastermind, malacards: add an ERR trap that echoes a failure message; switch mastermind's 'curl -s' to 'curl -sf' so an HTTP error fails loudly instead of writing a challenge page into the release file. - geneReviews: add an ERR trap (kept silent on no-update via the wrapper's mail -E). - All three use 'set -eE' (errtrace) so the ERR trap also fires for failures inside functions/subshells, not just top-level commands. - clinGen: capture each sub-build's exit status instead of swallowing it under 'set +e', and report which sub-build failed. Also drop the routine 'No ... update' echoes and the unconditional 'ClinGen update done.' line, and switch the wrapper to 'mail -E', so clinGen is now silent on no-update and only emails on a real update or a failure.
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    f2ef97844c0973a30cbbc1afcdd01b4096143a69 Wed Jun 3 10:56:07 2026 -0700
    Add date-based dataVersion to composite/superTrack otto containers. refs #36455 Composite and superTrack container pages do not display 'Data last updated at UCSC' (printUpdateTime returns early for them), so a dataVersion file is the only freshness signal a user sees there. Add one to the dbVar (dbVarSv), panelApp, clinGen (clinGenComp) and decipher (decipherContainer) containers. Each otto build script writes a per-assembly 'Last updated <date>' file when it actually updates the data, and the container stanza points to it via dataVersion. clinGen's container date is written by its three displayed feeds (makeDosage, makeGeneValidity, makeClinGenCspec); decipher writes hg38 only (hg19 is frozen).
• src/hg/utils/otto/dbVar/checkDbVar.sh
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    f2ef97844c0973a30cbbc1afcdd01b4096143a69 Wed Jun 3 10:56:07 2026 -0700
    Add date-based dataVersion to composite/superTrack otto containers. refs #36455 Composite and superTrack container pages do not display 'Data last updated at UCSC' (printUpdateTime returns early for them), so a dataVersion file is the only freshness signal a user sees there. Add one to the dbVar (dbVarSv), panelApp, clinGen (clinGenComp) and decipher (decipherContainer) containers. Each otto build script writes a per-assembly 'Last updated <date>' file when it actually updates the data, and the container stanza points to it via dataVersion. clinGen's container date is written by its three displayed feeds (makeDosage, makeGeneValidity, makeClinGenCspec); decipher writes hg38 only (hg19 is frozen).
• src/hg/utils/otto/decipher/checkDecipher.sh
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    f2ef97844c0973a30cbbc1afcdd01b4096143a69 Wed Jun 3 10:56:07 2026 -0700
    Add date-based dataVersion to composite/superTrack otto containers. refs #36455 Composite and superTrack container pages do not display 'Data last updated at UCSC' (printUpdateTime returns early for them), so a dataVersion file is the only freshness signal a user sees there. Add one to the dbVar (dbVarSv), panelApp, clinGen (clinGenComp) and decipher (decipherContainer) containers. Each otto build script writes a per-assembly 'Last updated <date>' file when it actually updates the data, and the container stanza points to it via dataVersion. clinGen's container date is written by its three displayed feeds (makeDosage, makeGeneValidity, makeClinGenCspec); decipher writes hg38 only (hg19 is frozen).
• src/hg/utils/otto/geneReviews/checkGeneReviews.sh
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    351ed2fc24a13b86cf2a1fc9695309e2c0da9de5 Wed Jun 3 09:33:28 2026 -0700
    Make otto fetch failures loud and clinGen silent on no-update. refs #37697 Several otto jobs used 'wget -q'/'curl -s' under 'set -e', so a broken download aborted with no output and cron (which mails on output, not exit code) sent nothing -- the mode by which mastermind failed silently for months. - mastermind, malacards: add an ERR trap that echoes a failure message; switch mastermind's 'curl -s' to 'curl -sf' so an HTTP error fails loudly instead of writing a challenge page into the release file. - geneReviews: add an ERR trap (kept silent on no-update via the wrapper's mail -E). - All three use 'set -eE' (errtrace) so the ERR trap also fires for failures inside functions/subshells, not just top-level commands. - clinGen: capture each sub-build's exit status instead of swallowing it under 'set +e', and report which sub-build failed. Also drop the routine 'No ... update' echoes and the unconditional 'ClinGen update done.' line, and switch the wrapper to 'mail -E', so clinGen is now silent on no-update and only emails on a real update or a failure.
• src/hg/utils/otto/malacards/update.sh
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    351ed2fc24a13b86cf2a1fc9695309e2c0da9de5 Wed Jun 3 09:33:28 2026 -0700
    Make otto fetch failures loud and clinGen silent on no-update. refs #37697 Several otto jobs used 'wget -q'/'curl -s' under 'set -e', so a broken download aborted with no output and cron (which mails on output, not exit code) sent nothing -- the mode by which mastermind failed silently for months. - mastermind, malacards: add an ERR trap that echoes a failure message; switch mastermind's 'curl -s' to 'curl -sf' so an HTTP error fails loudly instead of writing a challenge page into the release file. - geneReviews: add an ERR trap (kept silent on no-update via the wrapper's mail -E). - All three use 'set -eE' (errtrace) so the ERR trap also fires for failures inside functions/subshells, not just top-level commands. - clinGen: capture each sub-build's exit status instead of swallowing it under 'set +e', and report which sub-build failed. Also drop the routine 'No ... update' echoes and the unconditional 'ClinGen update done.' line, and switch the wrapper to 'mail -E', so clinGen is now silent on no-update and only emails on a real update or a failure.
• src/hg/utils/otto/mastermind/buildMastermind.sh
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    351ed2fc24a13b86cf2a1fc9695309e2c0da9de5 Wed Jun 3 09:33:28 2026 -0700
    Make otto fetch failures loud and clinGen silent on no-update. refs #37697 Several otto jobs used 'wget -q'/'curl -s' under 'set -e', so a broken download aborted with no output and cron (which mails on output, not exit code) sent nothing -- the mode by which mastermind failed silently for months. - mastermind, malacards: add an ERR trap that echoes a failure message; switch mastermind's 'curl -s' to 'curl -sf' so an HTTP error fails loudly instead of writing a challenge page into the release file. - geneReviews: add an ERR trap (kept silent on no-update via the wrapper's mail -E). - All three use 'set -eE' (errtrace) so the ERR trap also fires for failures inside functions/subshells, not just top-level commands. - clinGen: capture each sub-build's exit status instead of swallowing it under 'set +e', and report which sub-build failed. Also drop the routine 'No ... update' echoes and the unconditional 'ClinGen update done.' line, and switch the wrapper to 'mail -E', so clinGen is now silent on no-update and only emails on a real update or a failure.
• src/hg/utils/otto/orphanet/checkOrphanet.sh
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    9169db807b49113b231d35f2beec4e04c2fb1756 Wed Jun 3 08:29:02 2026 -0700
    Add dataVersion to Orphanet and ClinGen dosage tracks to show upstream release. refs #36455 Orphanet: parse the JDBOR release version (e.g. 1.3.42 / 4.1.8 [2025-03-03]) from the downloaded XML and write it to a per-assembly version.txt that the orphadata track points to via dataVersion. ClinGen: write the ClinGen dosage 'results as of' date (e.g. 28 Apr,2026) from the curation list header to a version file shared by the clinGenHaplo and clinGenTriplo subtracks. The other ClinGen feeds publish no dataset-level date, so they are left unversioned. The version file is written per assembly only after that assembly's bigBed is installed, surfacing the source's own release, which can differ from our otto update timestamp.
• src/hg/utils/otto/otto.crontab
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    d57e386b7f6f2da8649984c0add4fd31810e78af Tue Jun 2 14:08:33 2026 -0700
    Add weekly otto notifier for new NCBI RefSeq historical releases. refs #35766 Silent check script (cron emails otto-group only when NCBI publishes a GRCh38 RefSeq historical release newer than lastHandledRelease.txt). Includes retry on the NCBI fetch to avoid false positives from sporadic FTP failures. Added a weekly Wednesday crontab entry next to the mitoMap check.
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    357abbbd5acaa1b3da8df40d9c1f3e0c564f47f2 Tue Jun 2 16:11:56 2026 -0700
    Retiring LRG which is no longer updated, refs #37694
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    c32c258125a52b45b4f4f7c80d5f7657dd81ce46 Wed Jun 3 08:43:22 2026 -0700
    Removing charlie as the only recipient to the civic otto, and moving up the otto to be with the other standard ones, no RM.
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    f8c800e00b3f3e2468f73055df267c5a4f6f06e8 Thu Jun 4 11:12:01 2026 -0700
    Turning off mastermind as they are no longer providing data updates (plus it has been failing for a while). Refs #37697
• src/hg/utils/otto/panelApp/doPanelApp.py
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    f2ef97844c0973a30cbbc1afcdd01b4096143a69 Wed Jun 3 10:56:07 2026 -0700
    Add date-based dataVersion to composite/superTrack otto containers. refs #36455 Composite and superTrack container pages do not display 'Data last updated at UCSC' (printUpdateTime returns early for them), so a dataVersion file is the only freshness signal a user sees there. Add one to the dbVar (dbVarSv), panelApp, clinGen (clinGenComp) and decipher (decipherContainer) containers. Each otto build script writes a per-assembly 'Last updated <date>' file when it actually updates the data, and the container stanza points to it via dataVersion. clinGen's container date is written by its three displayed feeds (makeDosage, makeGeneValidity, makeClinGenCspec); decipher writes hg38 only (hg19 is frozen).
• src/hg/utils/otto/refSeqHistorical/checkRefSeqHistoricalUpdate.sh
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    d57e386b7f6f2da8649984c0add4fd31810e78af Tue Jun 2 14:08:33 2026 -0700
    Add weekly otto notifier for new NCBI RefSeq historical releases. refs #35766 Silent check script (cron emails otto-group only when NCBI publishes a GRCh38 RefSeq historical release newer than lastHandledRelease.txt). Includes retry on the NCBI fetch to avoid false positives from sporadic FTP failures. Added a weekly Wednesday crontab entry next to the mitoMap check.
• src/hg/utils/otto/refSeqHistorical/lastHandledRelease.txt
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    d57e386b7f6f2da8649984c0add4fd31810e78af Tue Jun 2 14:08:33 2026 -0700
    Add weekly otto notifier for new NCBI RefSeq historical releases. refs #35766 Silent check script (cron emails otto-group only when NCBI publishes a GRCh38 RefSeq historical release newer than lastHandledRelease.txt). Includes retry on the NCBI fetch to avoid false positives from sporadic FTP failures. Added a weekly Wednesday crontab entry next to the mitoMap check.
• src/hg/utils/otto/userRequests/devAndRR.sh
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    305a444f30710dc5de4595a349fca62c4ba34503 Wed Jun 3 12:21:14 2026 -0700
    do NOT need to check the one on hgwdev, this would duplicate things refs #31811
• src/hg/utils/otto/userRequests/kegAlignLastz.sh
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    957b916c9cb686a1e2f21c8702db24369623cb85 Tue Jun 2 12:33:46 2026 -0700
    correct primate score matrix for lastz input refs #31811
• src/hg/utils/otto/userRequests/ottoLib.py
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    30701e4c2c2ad71f0d597ad9629da75c6a35dfba Wed Jun 3 14:31:24 2026 -0700
    fix the legacy construction procedure refs #31811
• src/hg/utils/otto/userRequests/ottoRequestPush.py
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    481b82eaafcf77f9b82bce0159ff84e9284c3325 Tue Jun 2 10:36:03 2026 -0700
    correctly capturing any stderr or stdout and only send it to cron stderr in case of error refs #31811
• src/hg/utils/rts/hg19/SNVs%20Clinical
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    ef826dbcf8ee0961e27c38050deee74c9870ac05 Tue Jun 2 12:43:26 2026 -0700
    Seed htdocs/data/recTrackSets/ for the upcoming file-based RTS loader: one example RTS per assembly (hg19/SNVs%20Clinical, hg38/Non_Coding_SNVs_hg38), plus copies of the recTrackSets.hg19.tab and recTrackSets.hg38.tab manifests at the top of the new directory. Per-session file format is the same one-key=value-per-line scrubbed cart produced by rtsUpdate. Also refreshes utils/rts/hg19/SNVs%20Clinical via rtsUpdate fetch (676 -> 660 vars after scrub) so both locations agree during the transition. refs #32768
• src/hg/utils/rts/makefile
  • lines changed 16, context: html, text, full: html, text
    9aaf0a4a28e67a6c5f6ce62346cbadcc20d2c6a5 Fri Jun 5 10:44:17 2026 -0700
    Wire up rtsUpdate install via the standard utils/ make. Adds a small makefile under src/hg/utils/rts/ that copies the rtsUpdate script to \${BINDIR} (~/bin/\${MACHTYPE}/) so it lands on the user's PATH, and adds rts to the DIRS list in src/hg/utils/makefile so the top-level make descends into it. After this, either `make` from src/hg/utils/rts/ or `make` from src/hg/utils/ installs rtsUpdate. refs #32768
• src/hg/utils/rts/rtsUpdate
  • lines changed 284, context: html, text, full: html, text
    973632e4fe10505fb0fd7c8da17f4b851ab5ac22 Fri Jun 5 10:00:30 2026 -0700
    Refactor rtsUpdate for the file-based RTS loader landed in 0df5f6317fd. The tool now writes to ~/kent/src/hg/htdocs/data/recTrackSets/<db>/<session>, where Chris's loader reads it; all DB writes are gone (push subcommand removed, dev UPDATE in fetch removed, /tmp backup logic removed, --i-confirm-rr removed). diff subcommand removed (git diff plus a sandbox click covers it). .tab validation tightened: --allow-new removed; target session must already appear in recTrackSets.<db>.tab. File writes are now atomic via temp+rename. verboten.lst expanded from 6 to 86 patterns covering: view-locking coords/position variants, session-load UI state (hgS_, hgsid, rtsLoad, hgPS_DataTableState, redirect, ...), user display preferences, hgHubConnect form fields (hubSearchTerms, hubDbFilter, ...), curator-local custom-track paths (ctfile_), and the full hgTracks excludeVars[] sweep for defense-in-depth. refs #32768
  • lines changed 4, context: html, text, full: html, text
    58e070461663f4d71ce17eb93b17225b20071371 Fri Jun 5 10:12:34 2026 -0700
    Expand verboten.lst with 18 more patterns surfaced during Phase C1 dry-run of the remaining 12 RTS sessions: leaked state from other CGIs (hgg_, hglft_, hgta_, hgHub_do_search), additional hgTracks UI state (hgt_, hgt_configGroupTarget, hgt_doJsCommand, hgt_mdbVal/Var, rulerBaseZoom, hgTracksConfigPage), debris (European, source, sessionTable_length), per-db reverse-complement toggle (complement_<db>), gateway-style position-search input (search), Track Search dialog state (ts*), and single-letter hgc track selector (g). Also drop pairs with empty or whitespace-tainted keys in scrub() to defend against future cart-string corruption (caught a stray ' hgsid=...' from a manually-edited 2021 cart row in BRCA1_BRCA2_ENIGMA_hg19). Re-fetch the 2 already-seeded files so the whole corpus uses the final scrub list. refs #32768
  • lines changed 6, context: html, text, full: html, text
    3ce53ed0c6c8847d87987d04c3f1846ee879d623 Fri Jun 5 13:37:31 2026 -0700
    Point rtsUpdate at the new authoritative .tab manifest location under htdocs/data/recTrackSets/. Chris moved the loader's .tab lookup there in 3b6659d987c so both the manifest and the per-session contents now live under one tree; rtsUpdate's find_db_for_session() needs to follow. Drops the now-unused INC_DIR constant, updates the comment, and points the "session not in manifest" error message at the new location. refs #32768
• src/hg/utils/rts/verboten.lst
  • lines changed 107, context: html, text, full: html, text
    973632e4fe10505fb0fd7c8da17f4b851ab5ac22 Fri Jun 5 10:00:30 2026 -0700
    Refactor rtsUpdate for the file-based RTS loader landed in 0df5f6317fd. The tool now writes to ~/kent/src/hg/htdocs/data/recTrackSets/<db>/<session>, where Chris's loader reads it; all DB writes are gone (push subcommand removed, dev UPDATE in fetch removed, /tmp backup logic removed, --i-confirm-rr removed). diff subcommand removed (git diff plus a sandbox click covers it). .tab validation tightened: --allow-new removed; target session must already appear in recTrackSets.<db>.tab. File writes are now atomic via temp+rename. verboten.lst expanded from 6 to 86 patterns covering: view-locking coords/position variants, session-load UI state (hgS_, hgsid, rtsLoad, hgPS_DataTableState, redirect, ...), user display preferences, hgHubConnect form fields (hubSearchTerms, hubDbFilter, ...), curator-local custom-track paths (ctfile_), and the full hgTracks excludeVars[] sweep for defense-in-depth. refs #32768
  • lines changed 34, context: html, text, full: html, text
    58e070461663f4d71ce17eb93b17225b20071371 Fri Jun 5 10:12:34 2026 -0700
    Expand verboten.lst with 18 more patterns surfaced during Phase C1 dry-run of the remaining 12 RTS sessions: leaked state from other CGIs (hgg_, hglft_, hgta_, hgHub_do_search), additional hgTracks UI state (hgt_, hgt_configGroupTarget, hgt_doJsCommand, hgt_mdbVal/Var, rulerBaseZoom, hgTracksConfigPage), debris (European, source, sessionTable_length), per-db reverse-complement toggle (complement_<db>), gateway-style position-search input (search), Track Search dialog state (ts*), and single-letter hgc track selector (g). Also drop pairs with empty or whitespace-tainted keys in scrub() to defend against future cart-string corruption (caught a stray ' hgsid=...' from a manually-edited 2021 cart row in BRCA1_BRCA2_ENIGMA_hg19). Re-fetch the 2 already-seeded files so the whole corpus uses the final scrub list. refs #32768
• src/inc/sqlList.h
  • lines changed 5, context: html, text, full: html, text
    4cffc3eb6f43e109452b5b52d1f760cf1ea6a981 Sun Jun 7 21:47:37 2026 -0700
    Adjusting sessionDb and userDb IDs to be 64-bit in the code, since the database is now ready for it and we're crossing the threshold. refs #33554
• src/lib/freeType.c
  • lines changed 151, context: html, text, full: html, text
    874066eeba199bb09909de98bb8ba2d75b1b019c Tue Jun 2 18:10:38 2026 -0700
    Cache FreeType glyph advances and rendered bitmaps for faster label drawing Drawing many long labels was dominated by FreeType reinterpreting each glyph outline (FT_Load_Char) on every call, both to measure widths and to render; profiling showed ~3/4 of the glyph loads were width measurement alone. Cache the advance and the rendered GRAY coverage bitmap per (pixel size, character). The cache hangs off face->generic.data (freed via face->generic.finalizer), so it is private to each FT_Face and needs no locking once the draw is multi-threaded with a per-thread face. Caching covers single-byte chars on the default identity-transform text path (ftText); ftTextInBox (transformed/scaled text) and Unicode fall back to a direct FT_Load_Char. Output is pixel-identical to before (verified AE=0/MAE=0 for both bitmap and FreeType fonts); roughly halves the FreeType render time on label-heavy views. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
• src/lib/sqlList.c
  • lines changed 12, context: html, text, full: html, text
    4cffc3eb6f43e109452b5b52d1f760cf1ea6a981 Sun Jun 7 21:47:37 2026 -0700
    Adjusting sessionDb and userDb IDs to be 64-bit in the code, since the database is now ready for it and we're crossing the threshold. refs #33554

• lines changed: 33118
• files changed: 272