All File Changes

v501_base to v502_preview (2026-07-20 to 2026-07-27) v502

• confs/hgwdev.hg.conf
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    3c69c099c7c4bad6193da7aa60a417037d437d08 Sun Jul 26 01:11:19 2026 -0700
    Installing updated hg.conf files from UCSC servers
• docs/browserSlideDecks.md
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
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    b120644088d912f130ada387e34067b40616edc0 Mon Jul 27 08:19:30 2026 -0700
    minor fixes based on CR, refs #37874
• docs/makefile
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• docs/slideDecks/reveal.js/LICENSE
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/reveal.css
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/reveal.js
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.eot
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.ttf
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-italic.woff
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.eot
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.ttf
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-regular.woff
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.eot
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.ttf
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-semibold.woff
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.eot
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.ttf
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro-semibolditalic.woff
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/fonts/source-sans-pro/source-sans-pro.css
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/dist/theme/white.css
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/reveal.js/plugin/notes/notes.js
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/tutorial1-basics/presentation/index.html
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• docs/slideDecks/tutorial1-basics/tableOfContents/index.html
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/tutorial2-cancer/presentation/index.html
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• docs/slideDecks/tutorial3-clinical/presentation/index.html
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• docs/slideDecks/tutorial3-clinical/tableOfContents/index.html
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/tutorial4-clinical-cases/presentation/index.html
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• docs/slideDecks/tutorial4-clinical-cases/tableOfContents/index.html
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
• docs/slideDecks/tutorial5-teaching/presentation/index.html
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    603a734862321da4d9bde067c47a4a13175acc02 Thu Jul 23 09:24:22 2026 -0700
    Changes to slide decks based on CR; Adding reveal.js to source tree, rather than using CDN, refs #37874 #37904
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• docs/slideDecks/tutorial5-teaching/tableOfContents/index.html
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    b120644088d912f130ada387e34067b40616edc0 Mon Jul 27 08:19:30 2026 -0700
    minor fixes based on CR, refs #37874
• docs/staticPage.html
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    cc288ac4e30c8c67b1858013f2347f4a90edfe70 Wed Jul 22 15:53:34 2026 -0700
    Adding a special case so the final section 'on this page' is highlighted when you reach the bottom of the docs page, no Redmine.
• docs/tutorials/customTrackTutorial.md
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• docs/tutorials/gatewayTutorial.md
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• docs/tutorials/gb101.md
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    fc9499685c393b53e740badf03554c65e1a0db79 Wed Jul 22 10:14:35 2026 -0700
    Fix gb101 tutorial typo and expand the blue-bar menu list Correct the track visibility modes (dense, squish, pack, full) and add the Downloads and View menus to the Navigating the Menus section. refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• docs/tutorials/tableBrowserTutorial.md
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
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    5b102cc916d4ae19459bdfc625ea3b3596684e91 Thu Jul 23 17:00:13 2026 -0700
    Adding link to UCLA year4 spreadsheet on timeline
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    de28111b7531f8adeefb084962b2452ec09e7013 Fri Jul 24 11:25:33 2026 -0700
    Adding link to MiNND year4 spreadsheet on timeline
• src/hg/hgBlat/hgBlat.c
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    c683ecb63d721deb02fa8ab15bf66f70f1c3a326 Sat Jul 25 18:25:00 2026 -0700
    hgBlat/hgc: single-page BLAT results view with shareable alignment links Add a modern single-page BLAT results table (hgBlat.js) and a non-frameset alignment view (showSomeAlignmentModern in hgc, gated by the blatNewPage cart var). Share/reopen a result set from a durable bigPsl custom track pinned in the cart via a saved session (htcBlatAlign / loadBlatShareSessionIfAny). Factor the shared helpers into a new blatShare module (lib/blatShare.c, inc/blatShare.h).
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    6ae582f5103a8b27420c44a8f92f210969f65f4c Sat Jul 25 21:36:18 2026 -0700
    hgc BLAT alignment viewer: table-free page, share dialog, chromAlias, block-count fix refs #37893 Modern base-alignment page (showSomeAlignmentModern): - Switch page chrome to webStartGbNoBanner()/webEndGb() (menubar + <main>, no legacy nested section tables) and draw the gold title bar + grey Back/Share buttons in plain HTML instead of injecting them with JS. - Full-height "jump to" sidebar; its links are position:sticky so they stay visible while scrolling the long alignment. The per-block "Block N" links use the block count the renderer returns, not psl->blockCount. The DNA path (ffShAliPart) merges blocks separated by gaps <= 8 bases, so raw psl->blockCount over-counted and produced links to #N anchors that did not exist; the returned count matches the emitted anchors. - Show the genomic sequence's chromAlias names ("Genome sequence chr7 is also known as: ..."), de-duplicated. Friendly assembly label (organism + accession) for hub databases instead of the internal hub_NNN_ name. Durable "Share a link": - Opens the shared topLinks.js "Share a link" modal and hands it a durable hgc?g=htcBlatAlign link. The link carries only the hit selectors (c/o/i) plus u=l&s=; db and the browser window come from the saved session. htcBlatAlign rebuilds the one alignment from the session's durable bigPsl custom track (no BLAT re-run). - Restore the per-hit "Alignment" links on shared-session results tables (hgBlat.c). lib/cart.c: - cartWriteHeaderAndCont() is now idempotent (guards on cartDidContentType). hgc writes the CGI header early, so a later webStartGb* would otherwise write a second Set-Cookie/Content-Type into the page body.
• src/hg/hgLinkIn/handlerList.c
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    cc5381e539ecba5b07109b194acf1d76b0c8f641 Thu Jul 23 06:22:48 2026 -0700
    Guard hDbForTaxon() callers against curated hub (GenArk) db names. hDbForTaxon() can now return a GenArk-only assembly with no real SQL database, which would abort in sqlConnect()/"use <db>"/cross-db sqlTableExists(). Treat a hubConnectIsCurated() db as no usable native db in uniProtAccToDb(), bacProbeInfo(), and getKnownGeneUrl(). refs #37909
• src/hg/hgLogin/hgLogin.c
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    80bedbcf180ec262a2b7b9b941f2f80d71c1551b Fri Jul 24 11:34:48 2026 -0700
    add password reveal button to hgLogin form refs ##37921
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    47f71e9a0be0d7fd2bbca54c7e85c6b22d622fe4 Fri Jul 24 11:35:35 2026 -0700
    remove DBG printfs refs ##37921
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    bd6f21753bfc7843721e5722e3a9cb5e556914f9 Fri Jul 24 12:45:17 2026 -0700
    default on for the password reveal function refs #37921
• src/hg/hgLogin/hgLogin.h
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    80bedbcf180ec262a2b7b9b941f2f80d71c1551b Fri Jul 24 11:34:48 2026 -0700
    add password reveal button to hgLogin form refs ##37921
• src/hg/hgTrackUi/hgTrackUi.c
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    835f3f2b9a18f63af202b71477744469e647b328 Tue Jul 21 08:32:17 2026 -0700
    Moving track description link to a more visible place and fixing hub ID parsing. Old method (parsing trackHubs cart variable) was failing as the contents can now be hubId:chainId (for quickLift). New approach uses a library function. refs #36320
• src/hg/hgTracks/bedTrack.c
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    2961c25331a73eba4ddbca0b848b43e4a467fa75 Thu Jul 23 11:12:40 2026 -0700
    Trying this again. Let users use a rightclick option to change the color of single bed-like items, gated via hg.conf setting canColorItems, refs #37778
• src/hg/hgTracks/cds.c
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    118634b1bb159357168a349dbf600f545e096f56 Fri Jul 24 08:17:41 2026 -0700
    Revert "hgTracks: strand-direction arrows on the zoomed-in codon/CDS and UTR display" This reverts commit ded41ea1968e30e2c248f65d1c9fec9793cb82fc.
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    43f042236ce180b8e0712d43c8baabc4ad8df1cd Sat Jul 25 18:21:54 2026 -0700
    hgTracks: add compactPack mode and codon strand-direction arrows When zoomed to codon-coloring level, draw strand-direction chevrons across the exons (white over coding codons when too small to label, contrasting color over UTRs), and a per-codon arrow between amino-acid letters via drawScaledBoxWithText. Add a compactPack trackDb setting for shorter pack/squish rows and a small squish-mode codon font. Adds mgFontForCellHeight() to memgfx and enables compactPack on the JASPAR track.
• src/hg/hgTracks/cds.h
  • lines changed 10, context: html, text, full: html, text
    118634b1bb159357168a349dbf600f545e096f56 Fri Jul 24 08:17:41 2026 -0700
    Revert "hgTracks: strand-direction arrows on the zoomed-in codon/CDS and UTR display" This reverts commit ded41ea1968e30e2c248f65d1c9fec9793cb82fc.
  • lines changed 10, context: html, text, full: html, text
    43f042236ce180b8e0712d43c8baabc4ad8df1cd Sat Jul 25 18:21:54 2026 -0700
    hgTracks: add compactPack mode and codon strand-direction arrows When zoomed to codon-coloring level, draw strand-direction chevrons across the exons (white over coding codons when too small to label, contrasting color over UTRs), and a per-codon arrow between amino-acid letters via drawScaledBoxWithText. Add a compactPack trackDb setting for shorter pack/squish rows and a small squish-mode codon font. Adds mgFontForCellHeight() to memgfx and enables compactPack on the JASPAR track.
• src/hg/hgTracks/hgTracks.c
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    2961c25331a73eba4ddbca0b848b43e4a467fa75 Thu Jul 23 11:12:40 2026 -0700
    Trying this again. Let users use a rightclick option to change the color of single bed-like items, gated via hg.conf setting canColorItems, refs #37778
  • lines changed 7, context: html, text, full: html, text
    15ba3603d692aa12c02d7d2f5979091c25b05d5f Thu Jul 23 11:22:47 2026 -0700
    hgTracks quickLift: show quickLifted superTrack child on first target load, refs #37535 When Convert/QuickLift lands on the target with hideTracks=on, the visibility of a quickLifted superTrack's parent was resolved from cgiOptionalString (URL params only), so the source assembly's carried-over "mavedb show" cart var was neither honored nor migrated to the hub-decorated name (hub_<n>_mavedb). The superTrack stayed hidden on the first load, so its heatmap child (e.g. mavedb_maps) drew no row until a reload; top-level quickLifted tracks (e.g. mane) were unaffected. QuickLifted tracks are exempt from hideTracks, so read the parent superTrack's visibility from the cart (and migrate the undecorated name) even under hideTracks. Non-quickLift paths are unchanged. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/hgTracks/hgTracks.h
  • lines changed 9, context: html, text, full: html, text
    2961c25331a73eba4ddbca0b848b43e4a467fa75 Thu Jul 23 11:12:40 2026 -0700
    Trying this again. Let users use a rightclick option to change the color of single bed-like items, gated via hg.conf setting canColorItems, refs #37778
  • lines changed 1, context: html, text, full: html, text
    43f042236ce180b8e0712d43c8baabc4ad8df1cd Sat Jul 25 18:21:54 2026 -0700
    hgTracks: add compactPack mode and codon strand-direction arrows When zoomed to codon-coloring level, draw strand-direction chevrons across the exons (white over coding codons when too small to label, contrasting color over UTRs), and a per-codon arrow between amino-acid letters via drawScaledBoxWithText. Add a compactPack trackDb setting for shorter pack/squish rows and a small squish-mode codon font. Adds mgFontForCellHeight() to memgfx and enables compactPack on the JASPAR track.
• src/hg/hgTracks/quickLift.c
  • lines changed 6, context: html, text, full: html, text
    11049a7e4e1de1b3218ec8184cdf5e9df8658681 Mon Jul 20 10:05:02 2026 -0700
    quickLift: highlight the clicked difference on the hgc details page hgTracks/quickLift.c now encodes the specific difference in each mapbox item name as chainId.type.chromStart.chromEnd (the "identical" region boxes keep the bare chain id). hgc.c parses that item name back into a chain id plus the clicked region, bolds the matching row in the Deletions/Insertions/Doubles/ Mismatches tables, and prints a note telling the user which row they clicked. Also adds bigQuickLiftChain to the set of types that suppress the details-page header item.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 42, context: html, text, full: html, text
    48886c882e7198f01b7c6bcaffa9ef107a291538 Tue Jul 21 13:38:08 2026 -0700
    hgTracks: merge pixel-adjacent blocks when drawing direction barbs Chain tracks show direction chevrons only on their aligned blocks, not on the connector line between blocks. When zoomed out the blocks smash together and individually most are too narrow to hold a chevron, so a chain showed only a couple of chevrons and its orientation was nearly invisible. Accumulate blocks that touch in pixel space into a single span and draw the barbs across the whole span, so the chevrons run continuously across a run of smashed-together blocks. The gap under which blocks merge is the new hg.conf setting barbMergePixels (default 3); set it to 0 to disable merging and get the old per-block barbs. Only pixel-adjacent blocks merge, so genes with visible introns and everything else render unchanged, refs #37889
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    e506d31b6278bb1251d8b260f75c67fa38c99a27 Thu Jul 23 10:20:01 2026 -0700
    Making it possible for multiWig containers to be children of composites, refs #36320
  • lines changed 128, context: html, text, full: html, text
    2961c25331a73eba4ddbca0b848b43e4a467fa75 Thu Jul 23 11:12:40 2026 -0700
    Trying this again. Let users use a rightclick option to change the color of single bed-like items, gated via hg.conf setting canColorItems, refs #37778
  • lines changed 19, context: html, text, full: html, text
    118634b1bb159357168a349dbf600f545e096f56 Fri Jul 24 08:17:41 2026 -0700
    Revert "hgTracks: strand-direction arrows on the zoomed-in codon/CDS and UTR display" This reverts commit ded41ea1968e30e2c248f65d1c9fec9793cb82fc.
  • lines changed 72, context: html, text, full: html, text
    43f042236ce180b8e0712d43c8baabc4ad8df1cd Sat Jul 25 18:21:54 2026 -0700
    hgTracks: add compactPack mode and codon strand-direction arrows When zoomed to codon-coloring level, draw strand-direction chevrons across the exons (white over coding codons when too small to label, contrasting color over UTRs), and a per-codon arrow between amino-acid letters via drawScaledBoxWithText. Add a compactPack trackDb setting for shorter pack/squish rows and a small squish-mode codon font. Adds mgFontForCellHeight() to memgfx and enables compactPack on the JASPAR track.
• src/hg/hgTracks/vcfTrack.c
  • lines changed 44, context: html, text, full: html, text
    be36584718d57384b01657483422f51adf29f0bb Sat Jul 25 18:22:02 2026 -0700
    vcfTrack: add minimum alternate allele count (minAc) filter, refs #37927 When a VCF INFO column includes AC, offer a 'minimum allele count' filter in the track UI (e.g. 2 to hide singletons) and drop records whose largest alternate allele count is below the threshold.
• src/hg/hgc/hgc.c
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    11049a7e4e1de1b3218ec8184cdf5e9df8658681 Mon Jul 20 10:05:02 2026 -0700
    quickLift: highlight the clicked difference on the hgc details page hgTracks/quickLift.c now encodes the specific difference in each mapbox item name as chainId.type.chromStart.chromEnd (the "identical" region boxes keep the bare chain id). hgc.c parses that item name back into a chain id plus the clicked region, bolds the matching row in the Deletions/Insertions/Doubles/ Mismatches tables, and prints a note telling the user which row they clicked. Also adds bigQuickLiftChain to the set of types that suppress the details-page header item.
  • lines changed 256, context: html, text, full: html, text
    c683ecb63d721deb02fa8ab15bf66f70f1c3a326 Sat Jul 25 18:25:00 2026 -0700
    hgBlat/hgc: single-page BLAT results view with shareable alignment links Add a modern single-page BLAT results table (hgBlat.js) and a non-frameset alignment view (showSomeAlignmentModern in hgc, gated by the blatNewPage cart var). Share/reopen a result set from a durable bigPsl custom track pinned in the cart via a saved session (htcBlatAlign / loadBlatShareSessionIfAny). Factor the shared helpers into a new blatShare module (lib/blatShare.c, inc/blatShare.h).
  • lines changed 208, context: html, text, full: html, text
    6ae582f5103a8b27420c44a8f92f210969f65f4c Sat Jul 25 21:36:18 2026 -0700
    hgc BLAT alignment viewer: table-free page, share dialog, chromAlias, block-count fix refs #37893 Modern base-alignment page (showSomeAlignmentModern): - Switch page chrome to webStartGbNoBanner()/webEndGb() (menubar + <main>, no legacy nested section tables) and draw the gold title bar + grey Back/Share buttons in plain HTML instead of injecting them with JS. - Full-height "jump to" sidebar; its links are position:sticky so they stay visible while scrolling the long alignment. The per-block "Block N" links use the block count the renderer returns, not psl->blockCount. The DNA path (ffShAliPart) merges blocks separated by gaps <= 8 bases, so raw psl->blockCount over-counted and produced links to #N anchors that did not exist; the returned count matches the emitted anchors. - Show the genomic sequence's chromAlias names ("Genome sequence chr7 is also known as: ..."), de-duplicated. Friendly assembly label (organism + accession) for hub databases instead of the internal hub_NNN_ name. Durable "Share a link": - Opens the shared topLinks.js "Share a link" modal and hands it a durable hgc?g=htcBlatAlign link. The link carries only the hit selectors (c/o/i) plus u=l&s=; db and the browser window come from the saved session. htcBlatAlign rebuilds the one alignment from the session's durable bigPsl custom track (no BLAT re-run). - Restore the per-hit "Alignment" links on shared-session results tables (hgBlat.c). lib/cart.c: - cartWriteHeaderAndCont() is now idempotent (guards on cartDidContentType). hgc writes the CGI header early, so a later webStartGb* would otherwise write a second Set-Cookie/Content-Type into the page body.
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-italic.eot
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-italic.ttf
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-italic.woff
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-regular.eot
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-regular.ttf
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-regular.woff
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-semibold.eot
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-semibold.ttf
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-semibold.woff
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-semibolditalic.eot
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-semibolditalic.ttf
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro-semibolditalic.woff
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/fonts/source-sans-pro/source-sans-pro.css
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/trackDb/makefile
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    c92b7ac58ea534772ba25477955105271d72855c Tue Jul 21 16:14:38 2026 -0700
    Fix a couple trackDbLibary typos and bump makefile version number to match actual document version number, refs #37908
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
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    c92b7ac58ea534772ba25477955105271d72855c Tue Jul 21 16:14:38 2026 -0700
    Fix a couple trackDbLibary typos and bump makefile version number to match actual document version number, refs #37908
• src/hg/htdocs/goldenPath/newsarch.html
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    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
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    bbddaf74c88b5e590f0943b73dd5c0d40f42e42d Fri Jul 24 15:22:34 2026 -0700
    Update Long-read SVs announcement counts for cardSv/noyvertSv additions. refs #37888 Bump the container from 14 to 16 studies and roughly 2.3 to 2.6 million merged SV sites, and add NIH CARD (Americas) and Noyvert 888 (1000 Genomes) to the region summary table.
• src/hg/htdocs/images/assemblySelection.gif
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/images/defineRegions.gif
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/images/downloadData.gif
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/images/encode4Regulation.png
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    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
• src/hg/htdocs/images/encode4Release.png
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    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
• src/hg/htdocs/images/tableBrowserAnnotated.png
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/images/tableSelection.gif
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/images/trackSelection.gif
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/images/tutorialImages/gif/hgCustomStep1.gif
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/images/tutorialImages/gif/hgCustomStep4.gif
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/images/tutorialImages/hgCustomAnnotated_pt1.png
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    dd6958bf3e8dfeb13dad8906a5c471293c471152 Wed Jul 22 07:56:17 2026 -0700
    Update Gateway, Table Browser, and Custom Track tutorials for the new assembly search box Replaced the old Clade/Genome/Assembly drop-down wording and screenshots with the current genome search box, re-recorded the step GIFs, and expanded the guided walkthroughs (Table Browser filter/intersection and output fields, Custom Track track line, Gateway GenArk/recent-genomes and species tree). refs #37355 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/indexNews.html
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    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
• src/hg/htdocs/liftRequest.html
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    bf2ec86e676e6806bf3f531e11b14da6312afdb6 Tue Jul 21 15:48:29 2026 -0700
    eliminate the unnecessary HGStyle.css and fix the ending close page correctly refs #31811
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    e8eff86dfac3b23f35eeb4cb6a0ec23e6f4d9a8c Tue Jul 21 19:52:32 2026 -0700
    eliminate the redundant duplicate inclusion of utils.js refs #31811
• src/hg/htdocs/style/liftRequest.css
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    bf2ec86e676e6806bf3f531e11b14da6312afdb6 Tue Jul 21 15:48:29 2026 -0700
    eliminate the unnecessary HGStyle.css and fix the ending close page correctly refs #31811
• src/hg/htdocs/style/makefile
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/style/reveal-5.1.0.css
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/style/reveal-white-5.1.0.css
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/hubApi/apiUtils.c
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    e2c9cfc1bb6a71ba957b8f2b674491595a232353 Fri Jul 24 09:51:39 2026 -0700
    refactor the ottoRequest table access with relay requests from Euro/Asia nodes to the RR system refs #31811
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    a9b3f6390b742c276dd6df49e581d5a26b987168 Fri Jul 24 10:09:59 2026 -0700
    avoiding an existing situation with sqlUpdateRows() function refs #31811
• src/hg/hubApi/assemblyList.py
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    8cd2af3f5f15571eb78ae62c1a470e492aecf22d Fri Jul 24 14:13:13 2026 -0700
    temporary field count error in assembly_summary_refseq.txt ignore bad records refs #31811
• src/hg/hubApi/dataApi.h
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    e2c9cfc1bb6a71ba957b8f2b674491595a232353 Fri Jul 24 09:51:39 2026 -0700
    refactor the ottoRequest table access with relay requests from Euro/Asia nodes to the RR system refs #31811
• src/hg/hubApi/findGenome.c
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    e2c9cfc1bb6a71ba957b8f2b674491595a232353 Fri Jul 24 09:51:39 2026 -0700
    refactor the ottoRequest table access with relay requests from Euro/Asia nodes to the RR system refs #31811
• src/hg/hubApi/hubApi.c
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    e2c9cfc1bb6a71ba957b8f2b674491595a232353 Fri Jul 24 09:51:39 2026 -0700
    refactor the ottoRequest table access with relay requests from Euro/Asia nodes to the RR system refs #31811
• src/hg/hubApi/liftOver.c
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    755541f8af03c4956b3fe167dddc9f27d8ad9b62 Wed Jul 22 15:34:31 2026 -0700
    improve the login/logout function refs #31811
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    0441be0515c7b1988115a3161659563dc13cdbb6 Thu Jul 23 08:02:54 2026 -0700
    fixup the problem of using getenv() for the host name to correctly use gethostname() refs #31811
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    e4187a3e3f5f47339190d1daead5dfaa6644c0d8 Thu Jul 23 09:00:57 2026 -0700
    use hg.conf to determine .ucsc.edu domain - does not work with gethostname() refs #31811
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    a2f0dc37bc0088b880ce3efed8ba68352a849707 Thu Jul 23 11:40:46 2026 -0700
    turns out hgwbeta is NOT privateHost refs #31811
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    e2c9cfc1bb6a71ba957b8f2b674491595a232353 Fri Jul 24 09:51:39 2026 -0700
    refactor the ottoRequest table access with relay requests from Euro/Asia nodes to the RR system refs #31811
• src/hg/inc/blatShare.h
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    c683ecb63d721deb02fa8ab15bf66f70f1c3a326 Sat Jul 25 18:25:00 2026 -0700
    hgBlat/hgc: single-page BLAT results view with shareable alignment links Add a modern single-page BLAT results table (hgBlat.js) and a non-frameset alignment view (showSomeAlignmentModern in hgc, gated by the blatNewPage cart var). Share/reopen a result set from a durable bigPsl custom track pinned in the cart via a saved session (htcBlatAlign / loadBlatShareSessionIfAny). Factor the shared helpers into a new blatShare module (lib/blatShare.c, inc/blatShare.h).
• src/hg/inc/trackDb.h
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    e506d31b6278bb1251d8b260f75c67fa38c99a27 Thu Jul 23 10:20:01 2026 -0700
    Making it possible for multiWig containers to be children of composites, refs #36320
• src/hg/inc/vcfUi.h
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    be36584718d57384b01657483422f51adf29f0bb Sat Jul 25 18:22:02 2026 -0700
    vcfTrack: add minimum alternate allele count (minAc) filter, refs #37927 When a VCF INFO column includes AC, offer a 'minimum allele count' filter in the track UI (e.g. 2 to hide singletons) and drop records whose largest alternate allele count is below the threshold.
• src/hg/js/external/makefile
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/js/external/reveal-5.1.0.LICENSE
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/js/external/reveal-5.1.0.js
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/js/external/reveal-notes-5.1.0.js
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    9b8e3a4bcd84ad0ee122031ec21680730c02df2f Thu Jul 23 15:34:52 2026 -0700
    Move vendored reveal.js library out of docs/slideDecks into the source tree Per code review feedback on #37904, the reveal.js 5.1.0 files used by the training slide decks now live in their conventional homes rather than bundled under docs/slideDecks/reveal.js: - JS -> src/hg/js/external/ (reveal-5.1.0.js, reveal-notes-5.1.0.js), added to that makefile; MIT LICENSE kept alongside. - CSS -> src/hg/htdocs/style/ (reveal-5.1.0.css, reveal-white-5.1.0.css), added to that makefile. - Source Sans Pro fonts -> src/hg/htdocs/fonts/source-sans-pro/, matching the existing font-awesome pattern (auto-rsynced, no makefile edit). The white theme's @import and the five deck index.html files were updated to reference the assets by absolute /js, /style, and /fonts paths. refs #37904 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/js/hgBlat.js
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    c683ecb63d721deb02fa8ab15bf66f70f1c3a326 Sat Jul 25 18:25:00 2026 -0700
    hgBlat/hgc: single-page BLAT results view with shareable alignment links Add a modern single-page BLAT results table (hgBlat.js) and a non-frameset alignment view (showSomeAlignmentModern in hgc, gated by the blatNewPage cart var). Share/reopen a result set from a durable bigPsl custom track pinned in the cart via a saved session (htcBlatAlign / loadBlatShareSessionIfAny). Factor the shared helpers into a new blatShare module (lib/blatShare.c, inc/blatShare.h).
• src/hg/js/hgTracks.js
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    2961c25331a73eba4ddbca0b848b43e4a467fa75 Thu Jul 23 11:12:40 2026 -0700
    Trying this again. Let users use a rightclick option to change the color of single bed-like items, gated via hg.conf setting canColorItems, refs #37778
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    9e9ee32a4c8a76f7d674148f840476ba3efd4de9 Thu Jul 23 12:13:44 2026 -0700
    prevent faceted bar chart tracks from showing item details in popups as their hgc pages rely on forms that resubmit on every click of the facet, refs #37878
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    cbf4bf3cac2bf99f8dbe8645a74d6a4bc61559fa Thu Jul 23 12:56:07 2026 -0700
    Ensuring that multiwig children of composites can be configured via right-click in hgTracks, refs #36320
• src/hg/js/makefile
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    c683ecb63d721deb02fa8ab15bf66f70f1c3a326 Sat Jul 25 18:25:00 2026 -0700
    hgBlat/hgc: single-page BLAT results view with shareable alignment links Add a modern single-page BLAT results table (hgBlat.js) and a non-frameset alignment view (showSomeAlignmentModern in hgc, gated by the blatNewPage cart var). Share/reopen a result set from a durable bigPsl custom track pinned in the cart via a saved session (htcBlatAlign / loadBlatShareSessionIfAny). Factor the shared helpers into a new blatShare module (lib/blatShare.c, inc/blatShare.h).
• src/hg/lib/blatShare.c
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    c683ecb63d721deb02fa8ab15bf66f70f1c3a326 Sat Jul 25 18:25:00 2026 -0700
    hgBlat/hgc: single-page BLAT results view with shareable alignment links Add a modern single-page BLAT results table (hgBlat.js) and a non-frameset alignment view (showSomeAlignmentModern in hgc, gated by the blatNewPage cart var). Share/reopen a result set from a durable bigPsl custom track pinned in the cart via a saved session (htcBlatAlign / loadBlatShareSessionIfAny). Factor the shared helpers into a new blatShare module (lib/blatShare.c, inc/blatShare.h).
• src/hg/lib/cart.c
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    6ae582f5103a8b27420c44a8f92f210969f65f4c Sat Jul 25 21:36:18 2026 -0700
    hgc BLAT alignment viewer: table-free page, share dialog, chromAlias, block-count fix refs #37893 Modern base-alignment page (showSomeAlignmentModern): - Switch page chrome to webStartGbNoBanner()/webEndGb() (menubar + <main>, no legacy nested section tables) and draw the gold title bar + grey Back/Share buttons in plain HTML instead of injecting them with JS. - Full-height "jump to" sidebar; its links are position:sticky so they stay visible while scrolling the long alignment. The per-block "Block N" links use the block count the renderer returns, not psl->blockCount. The DNA path (ffShAliPart) merges blocks separated by gaps <= 8 bases, so raw psl->blockCount over-counted and produced links to #N anchors that did not exist; the returned count matches the emitted anchors. - Show the genomic sequence's chromAlias names ("Genome sequence chr7 is also known as: ..."), de-duplicated. Friendly assembly label (organism + accession) for hub databases instead of the internal hub_NNN_ name. Durable "Share a link": - Opens the shared topLinks.js "Share a link" modal and hands it a durable hgc?g=htcBlatAlign link. The link carries only the hit selectors (c/o/i) plus u=l&s=; db and the browser window come from the saved session. htcBlatAlign rebuilds the one alignment from the session's durable bigPsl custom track (no BLAT re-run). - Restore the per-hit "Alignment" links on shared-session results tables (hgBlat.c). lib/cart.c: - cartWriteHeaderAndCont() is now idempotent (guards on cartDidContentType). hgc writes the CGI header early, so a later webStartGb* would otherwise write a second Set-Cookie/Content-Type into the page body.
• src/hg/lib/hdb.c
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    6369f96481cd1d01d031b76bbd894c24210573a7 Wed Jul 22 13:43:52 2026 -0700
    Allow GenArk (curated hub) assemblies to be an organism's default in hDbForTaxon. Also fix the loop's break so it checks all rows, not just the first. refs #37909
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    e506d31b6278bb1251d8b260f75c67fa38c99a27 Thu Jul 23 10:20:01 2026 -0700
    Making it possible for multiWig containers to be children of composites, refs #36320
• src/hg/lib/hui.c
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    329cebf37d4a04c2a490121e21d166cab69e8562 Sat Jul 25 18:22:02 2026 -0700
    hui: warn when a numeric filter setting has no matching filter.<field>, refs #37927 A numeric range filter is only discovered from a filter.<field> (or <field>Filter) setting. Emit a warning for orphaned filter settings that will otherwise be silently ignored.
• src/hg/lib/makefile
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    c683ecb63d721deb02fa8ab15bf66f70f1c3a326 Sat Jul 25 18:25:00 2026 -0700
    hgBlat/hgc: single-page BLAT results view with shareable alignment links Add a modern single-page BLAT results table (hgBlat.js) and a non-frameset alignment view (showSomeAlignmentModern in hgc, gated by the blatNewPage cart var). Share/reopen a result set from a durable bigPsl custom track pinned in the cart via a saved session (htcBlatAlign / loadBlatShareSessionIfAny). Factor the shared helpers into a new blatShare module (lib/blatShare.c, inc/blatShare.h).
• src/hg/lib/trackDbCustom.c
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    e506d31b6278bb1251d8b260f75c67fa38c99a27 Thu Jul 23 10:20:01 2026 -0700
    Making it possible for multiWig containers to be children of composites, refs #36320
• src/hg/lib/vcfUi.c
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    be36584718d57384b01657483422f51adf29f0bb Sat Jul 25 18:22:02 2026 -0700
    vcfTrack: add minimum alternate allele count (minAc) filter, refs #37927 When a VCF INFO column includes AC, offer a 'minimum allele count' filter in the track UI (e.g. 2 to hide singletons) and drop records whose largest alternate allele count is below the threshold.
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
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    5aae6c38efd34ca5c4a0c5332bf6b180dfabb295 Mon Jul 20 15:59:58 2026 -0700
    add the writing of alpha.hub.txt for *any* contrib track refs #34917
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    07f22d708cefc4bc9f6d4147bc011fbc5147c5e5 Fri Jul 24 14:24:28 2026 -0700
    always write the alpha.hub.txt file refs #31811
• src/hg/makeDb/doc/hg38/clinvarMapped.txt
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    c9446936b026a803d97e7f5128404a327829fe2e Sun Jul 19 00:01:22 2026 -0700
    ClinVar Mapped: add Pfam-domain mapping method Maps ClinVar coding variants through Pfam protein domains as a second method under the clinvarMapped container. Each Pfam family's profile HMM gives a shared coordinate, so a variant inside a domain is projected to the residue in the same HMM match-state column in every other MANE Select gene carrying that domain, then mapped back to that gene's genomic codon. This links genes that share a domain without being paralogs (e.g. the SCN sodium channels and the CACNA1 calcium channels via Ion_trans). Each variant is shown at its 25 most conserved equivalents. Uses Pfam-A 38.2. Adds two alpha subtracks (Pfam Domain Variants, Pfam Domains), the hmmsearch/hmmalign build scripts, autoSql, makeDoc and description page, refs #37883
• src/hg/makeDb/doc/hg38/lrSv.txt
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    cc6ef4c74d072de9c22e8bb88ab0e0983e6f2f47 Wed Jul 22 18:09:16 2026 -0700
    lrSv cardSv: switch CARD count fields from carrier counts to allele counts The NIH CARD provider republished the display bigBed with the count columns changed to diploid allele counts (alleleCount = nabecAlleleCount + hbccAlleleCount). Re-downloaded and rebuilt; renamed the schema fields to AC / nabecAc / hbccAc, updated filter ranges (0:702, 0:410, 0:292) and labels to allele counts, and reworded cardSv.html and the lrSv.html summary. Also noted there are no Alzheimer's cases in these cohorts. Re-ran the merge so lrSvAll carries CARD's allele counts. refs #36258
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    0656b0a9ad98986ef3944b6ceaf305ab08ca4e39 Fri Jul 24 01:10:13 2026 -0700
    noyvertSv: swap UK Biobank r2 filter for leave-one-out metrics, revise description Per author (Boris Noyvert) request, replace the r2Ukb (UK Biobank imputation r2) filter with r2Loo and concordanceLoo, the primary SV imputation quality measures for the multi-ancestry reference panel (r2Ukb mainly reflects European-ancestry performance). Both fields already exist in noyvert.bb, so this is a trackDb-only change. Also update the description page with the author's revised text, including a comparison with the 1KG ONT Vienna dataset. refs #37888
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    798b37017a4e1b95f3ccdf7c8b477dfb5446a324 Fri Jul 24 15:22:34 2026 -0700
    lrSv: QA fixes for cardSv/noyvertSv additions - BND filter, makedoc, link targets. refs #37888 Add BND to filterValues.svType on the longReadVariants supertrack and the merged lrSvAll track (and the lrSvMergeAll.py generator) so the breakend variants that noyvertSv contributes are filterable. Correct a stale makedoc comment that said CARD was not in the lrSvAll merge (it is). Add target="_blank" to the API and hgdownload links in cardSv.html and noyvertSv.html.
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    7bdcd030cdf434c72f3f6a492ee8f84372c752c7 Sat Jul 25 19:22:57 2026 -0700
    noyvertSv: note the Boehringer/Vienna relationship and call-level overlap The Noyvert panel is an independent reprocessing of the same ONT reads as the 1KG ONT Vienna track (Schloissnig et al. 2025). Add a description sentence with the deletion counts (~38k vs ~58k, ~12k shared at 50% reciprocal overlap) and the concordance both ways (about a third of this track's deletions and a fifth of Vienna's at 50%, a quarter and a sixth at 90%; ~a quarter of insertions match within 100 bp). Overlap analysis recorded in the makeDoc. refs #37888
• src/hg/makeDb/doc/hg38/popEve.txt
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    7485753cb34c1c3fd4a3f7b8894d993110db50ff Thu Jul 23 14:03:39 2026 -0700
    Rebuild popEVE heatmap with the full per-amino-acid matrix. refs #37791 The track was built from the genomic single-nucleotide VCF, so each column showed only the ~6 of 19 substitutions reachable by a single nucleotide change. The popEVE authors confirmed the per-transcript CSV download carries the complete matrix, so the converter now takes the all-19 scores from those CSVs while reusing the genomic codon coordinates, strand, and blocks derived from the VCF. Proteins absent from the (older) CSV release fall back to the sparse VCF scores. Color anchors recomputed over the full-matrix distribution, and the mouseover's raw EVE field is relabeled "EVE index" to distinguish it from the EVE track's 0-1 score. Updates the description page and makedoc to match.
• src/hg/makeDb/doc/hg38/singleCellSignalsPeaks.txt
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    38d5c1e91f3a867c589da441f549c9d46bc9b9f4 Mon Jul 20 14:05:31 2026 -0700
    Add singleCellSignalsPeaks track to hg38 Native faceted composite built from the per-cell-type signal (bigWig) and peak (bigBed/bigNarrowPeak) tracks of the UCSC Cell Browser single-cell ATAC datasets, re-parented under one track in the regulation group. 936 subtracks across 9 datasets. Data files live in /hive/data/genomes/hg38/bed/singleCellSignalsPeaks and are served via a /gbdb/hg38/bbi symlink; the .ra is regenerated from the Cell Browser hub build by makeDb/scripts/singleCellSignalsPeaks/makeSingleCellSignalsPeaksRa.py. refs #37820 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
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    685641f93eec33b44e4b83f887f2aa75db1a887c Tue Jul 21 07:16:33 2026 -0700
    NCBI name change freom GCA_010909765.1_sAmbRad1.pri to GCA_010909765.1_sAmbRad1 refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
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    685641f93eec33b44e4b83f887f2aa75db1a887c Tue Jul 21 07:16:33 2026 -0700
    NCBI name change freom GCA_010909765.1_sAmbRad1.pri to GCA_010909765.1_sAmbRad1 refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
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    75122c6bdd333cd0f84eaf989617de7de18b279e Fri Jul 24 14:29:44 2026 -0700
    NCBI name change GCA_010909765.1_sAmbRad1.pri becomes GCA_010909765.1_sAmbRad1 refs #34370
• src/hg/makeDb/doc/vgpAsmHub/vgp.userTracks.tsv
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    75122c6bdd333cd0f84eaf989617de7de18b279e Fri Jul 24 14:29:44 2026 -0700
    NCBI name change GCA_010909765.1_sAmbRad1.pri becomes GCA_010909765.1_sAmbRad1 refs #34370
• src/hg/makeDb/hgLoadMaf/hgLoadMafSummary.c
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    2db6bab8db05291ff90bbc867784be7f7c9177f6 Sat Jul 25 21:48:14 2026 -0700
    hgLoadMafSummary: robustly split MAF sequence names into assembly and chrom Handle a pipe separator, no-dot names, GenArk accession dbs (GCA_/GCF_, which carry an accession.version dot), and a dotted chrom, without aborting on an ordinary assembly.chrom name that sits next to dotted query names. Fixes a regression from ae63ce5 (refs #36592). refs #37928
• src/hg/makeDb/scripts/clinvarMapped/clinvarMappedPfam.as
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    c9446936b026a803d97e7f5128404a327829fe2e Sun Jul 19 00:01:22 2026 -0700
    ClinVar Mapped: add Pfam-domain mapping method Maps ClinVar coding variants through Pfam protein domains as a second method under the clinvarMapped container. Each Pfam family's profile HMM gives a shared coordinate, so a variant inside a domain is projected to the residue in the same HMM match-state column in every other MANE Select gene carrying that domain, then mapped back to that gene's genomic codon. This links genes that share a domain without being paralogs (e.g. the SCN sodium channels and the CACNA1 calcium channels via Ion_trans). Each variant is shown at its 25 most conserved equivalents. Uses Pfam-A 38.2. Adds two alpha subtracks (Pfam Domain Variants, Pfam Domains), the hmmsearch/hmmalign build scripts, autoSql, makeDoc and description page, refs #37883
• src/hg/makeDb/scripts/clinvarMapped/clinvarMappedPfamAlign.py
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    c9446936b026a803d97e7f5128404a327829fe2e Sun Jul 19 00:01:22 2026 -0700
    ClinVar Mapped: add Pfam-domain mapping method Maps ClinVar coding variants through Pfam protein domains as a second method under the clinvarMapped container. Each Pfam family's profile HMM gives a shared coordinate, so a variant inside a domain is projected to the residue in the same HMM match-state column in every other MANE Select gene carrying that domain, then mapped back to that gene's genomic codon. This links genes that share a domain without being paralogs (e.g. the SCN sodium channels and the CACNA1 calcium channels via Ion_trans). Each variant is shown at its 25 most conserved equivalents. Uses Pfam-A 38.2. Adds two alpha subtracks (Pfam Domain Variants, Pfam Domains), the hmmsearch/hmmalign build scripts, autoSql, makeDoc and description page, refs #37883
• src/hg/makeDb/scripts/clinvarMapped/clinvarMappedPfamAln.as
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    c9446936b026a803d97e7f5128404a327829fe2e Sun Jul 19 00:01:22 2026 -0700
    ClinVar Mapped: add Pfam-domain mapping method Maps ClinVar coding variants through Pfam protein domains as a second method under the clinvarMapped container. Each Pfam family's profile HMM gives a shared coordinate, so a variant inside a domain is projected to the residue in the same HMM match-state column in every other MANE Select gene carrying that domain, then mapped back to that gene's genomic codon. This links genes that share a domain without being paralogs (e.g. the SCN sodium channels and the CACNA1 calcium channels via Ion_trans). Each variant is shown at its 25 most conserved equivalents. Uses Pfam-A 38.2. Adds two alpha subtracks (Pfam Domain Variants, Pfam Domains), the hmmsearch/hmmalign build scripts, autoSql, makeDoc and description page, refs #37883
• src/hg/makeDb/scripts/clinvarMapped/clinvarMappedPfamAln.py
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    c9446936b026a803d97e7f5128404a327829fe2e Sun Jul 19 00:01:22 2026 -0700
    ClinVar Mapped: add Pfam-domain mapping method Maps ClinVar coding variants through Pfam protein domains as a second method under the clinvarMapped container. Each Pfam family's profile HMM gives a shared coordinate, so a variant inside a domain is projected to the residue in the same HMM match-state column in every other MANE Select gene carrying that domain, then mapped back to that gene's genomic codon. This links genes that share a domain without being paralogs (e.g. the SCN sodium channels and the CACNA1 calcium channels via Ion_trans). Each variant is shown at its 25 most conserved equivalents. Uses Pfam-A 38.2. Adds two alpha subtracks (Pfam Domain Variants, Pfam Domains), the hmmsearch/hmmalign build scripts, autoSql, makeDoc and description page, refs #37883
• src/hg/makeDb/scripts/clinvarMapped/clinvarMappedPfamProject.py
  • lines changed 198, context: html, text, full: html, text
    c9446936b026a803d97e7f5128404a327829fe2e Sun Jul 19 00:01:22 2026 -0700
    ClinVar Mapped: add Pfam-domain mapping method Maps ClinVar coding variants through Pfam protein domains as a second method under the clinvarMapped container. Each Pfam family's profile HMM gives a shared coordinate, so a variant inside a domain is projected to the residue in the same HMM match-state column in every other MANE Select gene carrying that domain, then mapped back to that gene's genomic codon. This links genes that share a domain without being paralogs (e.g. the SCN sodium channels and the CACNA1 calcium channels via Ion_trans). Each variant is shown at its 25 most conserved equivalents. Uses Pfam-A 38.2. Adds two alpha subtracks (Pfam Domain Variants, Pfam Domains), the hmmsearch/hmmalign build scripts, autoSql, makeDoc and description page, refs #37883
• src/hg/makeDb/scripts/lrSv/lrSvCard.as
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    cc6ef4c74d072de9c22e8bb88ab0e0983e6f2f47 Wed Jul 22 18:09:16 2026 -0700
    lrSv cardSv: switch CARD count fields from carrier counts to allele counts The NIH CARD provider republished the display bigBed with the count columns changed to diploid allele counts (alleleCount = nabecAlleleCount + hbccAlleleCount). Re-downloaded and rebuilt; renamed the schema fields to AC / nabecAc / hbccAc, updated filter ranges (0:702, 0:410, 0:292) and labels to allele counts, and reworded cardSv.html and the lrSv.html summary. Also noted there are no Alzheimer's cases in these cohorts. Re-ran the merge so lrSvAll carries CARD's allele counts. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvCardBbToBed.py
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    cc6ef4c74d072de9c22e8bb88ab0e0983e6f2f47 Wed Jul 22 18:09:16 2026 -0700
    lrSv cardSv: switch CARD count fields from carrier counts to allele counts The NIH CARD provider republished the display bigBed with the count columns changed to diploid allele counts (alleleCount = nabecAlleleCount + hbccAlleleCount). Re-downloaded and rebuilt; renamed the schema fields to AC / nabecAc / hbccAc, updated filter ranges (0:702, 0:410, 0:292) and labels to allele counts, and reworded cardSv.html and the lrSv.html summary. Also noted there are no Alzheimer's cases in these cohorts. Re-ran the merge so lrSvAll carries CARD's allele counts. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py
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    798b37017a4e1b95f3ccdf7c8b477dfb5446a324 Fri Jul 24 15:22:34 2026 -0700
    lrSv: QA fixes for cardSv/noyvertSv additions - BND filter, makedoc, link targets. refs #37888 Add BND to filterValues.svType on the longReadVariants supertrack and the merged lrSvAll track (and the lrSvMergeAll.py generator) so the breakend variants that noyvertSv contributes are filterable. Correct a stale makedoc comment that said CARD was not in the lrSvAll merge (it is). Add target="_blank" to the API and hgdownload links in cardSv.html and noyvertSv.html.
• src/hg/makeDb/scripts/mei/meiDeepmei1kgVcfToBed.py
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    cff06e342525a24806d958cf8af28e9f54f1503c Sat Jul 25 18:25:07 2026 -0700
    mei: change item name format to <class>-<svLen>:<carrierCount>
• src/hg/makeDb/scripts/mei/meiHgsvc3CsvToBed.py
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    cff06e342525a24806d958cf8af28e9f54f1503c Sat Jul 25 18:25:07 2026 -0700
    mei: change item name format to <class>-<svLen>:<carrierCount>
• src/hg/makeDb/scripts/popEve/vcfToPopEveHeatmap.py
  • lines changed 95, context: html, text, full: html, text
    7485753cb34c1c3fd4a3f7b8894d993110db50ff Thu Jul 23 14:03:39 2026 -0700
    Rebuild popEVE heatmap with the full per-amino-acid matrix. refs #37791 The track was built from the genomic single-nucleotide VCF, so each column showed only the ~6 of 19 substitutions reachable by a single nucleotide change. The popEVE authors confirmed the per-transcript CSV download carries the complete matrix, so the converter now takes the all-19 scores from those CSVs while reusing the genomic codon coordinates, strand, and blocks derived from the VCF. Proteins absent from the (older) CSV release fall back to the sparse VCF scores. Color anchors recomputed over the full-matrix distribution, and the mouseover's raw EVE field is relabeled "EVE index" to distinguish it from the EVE track's 0-1 score. Updates the description page and makedoc to match.
• src/hg/makeDb/scripts/singleCellSignalsPeaks/makeSingleCellSignalsPeaksRa.py
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    38d5c1e91f3a867c589da441f549c9d46bc9b9f4 Mon Jul 20 14:05:31 2026 -0700
    Add singleCellSignalsPeaks track to hg38 Native faceted composite built from the per-cell-type signal (bigWig) and peak (bigBed/bigNarrowPeak) tracks of the UCSC Cell Browser single-cell ATAC datasets, re-parented under one track in the regulation group. 936 subtracks across 9 datasets. Data files live in /hive/data/genomes/hg38/bed/singleCellSignalsPeaks and are served via a /gbdb/hg38/bbi symlink; the .ra is regenerated from the Cell Browser hub build by makeDb/scripts/singleCellSignalsPeaks/makeSingleCellSignalsPeaksRa.py. refs #37820 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/tp53/tp53ProvisionalClass.py
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    ff04ae9d89641156d7b93d03e1d6162c8e070355 Mon Jul 20 17:01:25 2026 -0700
    Fix TP53 Provisional Classification bigBed type declaration from 9+9 to 9+10. The AUTOSQL and emitted data have 10 extra fields, and the trackDb declares bigBed 9 + 10, but the bedToBigBed -type arg and the docstring said 9+9. Corrected both so the bigBed header extraFieldCount is right and the script is self-consistent. refs #37399
• src/hg/makeDb/scripts/varFreqs/hostseqHtToVcf.py
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    d5302bd1e0cf296545df9ad3e0d3ab57859a51eb Fri Jul 24 17:17:17 2026 -0700
    varFreqs: post-QA polish on new hostseq subtrack. refs #37882 Findings from the qa-track pass on the gnomAD-Canada HostSeq subtrack added in 99764ad55bb: - hostseq.html: fix non-ASCII byte in Alföldi (Alf&#246;ldi), swap hardcoded hg38 for $db in the hgdownload URL, extend the FILTER enumeration to include InbreedingCoeff;RF (34,540 sites), add nhomalt and grpmax to the Display Conventions details-page list, and add an "Effective sample size per ancestry group" subsection warning that AF_fin (~4 individuals) and AF_mid (~72) are too sparse to be reliable population estimates. Collapsed a stray double blank line between refs. - populations.tsv, hostseqHtToVcf.py: harmonize the "oth" group label to "Remaining individuals" per the gnomAD README. The existing VCF header still shows the old label; it picks up the new one on the next re-emit (not worth re-running the 104 GB Hail table just for this). - varFreqs.ra: hostseq priority 2 -> 33 to break the sort-order collision with allofus (also at priority 2).
• src/hg/makeDb/scripts/varFreqs/populations.tsv
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    d5302bd1e0cf296545df9ad3e0d3ab57859a51eb Fri Jul 24 17:17:17 2026 -0700
    varFreqs: post-QA polish on new hostseq subtrack. refs #37882 Findings from the qa-track pass on the gnomAD-Canada HostSeq subtrack added in 99764ad55bb: - hostseq.html: fix non-ASCII byte in Alföldi (Alf&#246;ldi), swap hardcoded hg38 for $db in the hgdownload URL, extend the FILTER enumeration to include InbreedingCoeff;RF (34,540 sites), add nhomalt and grpmax to the Display Conventions details-page list, and add an "Effective sample size per ancestry group" subsection warning that AF_fin (~4 individuals) and AF_mid (~72) are too sparse to be reliable population estimates. Collapsed a stray double blank line between refs. - populations.tsv, hostseqHtToVcf.py: harmonize the "oth" group label to "Remaining individuals" per the gnomAD README. The existing VCF header still shows the old label; it picks up the new one on the next re-emit (not worth re-running the 104 GB Hail table just for this). - varFreqs.ra: hostseq priority 2 -> 33 to break the sort-order collision with allofus (also at priority 2).
• src/hg/makeDb/trackDb/human/cardSv.html
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    cc6ef4c74d072de9c22e8bb88ab0e0983e6f2f47 Wed Jul 22 18:09:16 2026 -0700
    lrSv cardSv: switch CARD count fields from carrier counts to allele counts The NIH CARD provider republished the display bigBed with the count columns changed to diploid allele counts (alleleCount = nabecAlleleCount + hbccAlleleCount). Re-downloaded and rebuilt; renamed the schema fields to AC / nabecAc / hbccAc, updated filter ranges (0:702, 0:410, 0:292) and labels to allele counts, and reworded cardSv.html and the lrSv.html summary. Also noted there are no Alzheimer's cases in these cohorts. Re-ran the merge so lrSvAll carries CARD's allele counts. refs #36258
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    798b37017a4e1b95f3ccdf7c8b477dfb5446a324 Fri Jul 24 15:22:34 2026 -0700
    lrSv: QA fixes for cardSv/noyvertSv additions - BND filter, makedoc, link targets. refs #37888 Add BND to filterValues.svType on the longReadVariants supertrack and the merged lrSvAll track (and the lrSvMergeAll.py generator) so the breakend variants that noyvertSv contributes are filterable. Correct a stale makedoc comment that said CARD was not in the lrSvAll merge (it is). Add target="_blank" to the API and hgdownload links in cardSv.html and noyvertSv.html.
• src/hg/makeDb/trackDb/human/gustafsonSv.html
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    3870b9e5e1b3fc67b0638fa77f6644bf5f133c9f Mon Jul 20 10:52:55 2026 -0700
    lrSv: relabel lrSv1kLin and gustafsonSv, write lrSv1kLin description Per Eichler lab request: relabel lrSv1kLin to 'Structural Variants from 1218 1KG individuals (HiFi, ONT & assembly)' and write its description page (drawn from HPRC year 2, HGSVC3, Vienna 1KG-ONT and UW 1KG-ONT). Relabel gustafsonSv as the University of Washington 1KG-ONT effort. Track names unchanged; no data rebuilt, counts kept honest at the current 100-sample Gustafson data. refs #36258
• src/hg/makeDb/trackDb/human/hg19/knownGene.alpha.ra
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    d10aba5d8ac8abc3655c599b9e421538a8a7e32e Wed Jul 22 10:56:04 2026 -0700
    Releasing GENCODE V50 knownGene tracks for hg38, hg19 (V50lift37), and mm39 (VM39). Promote knownGene from the alpha-gated staging file to the released trackDb: bump shortLabel/longLabel, bigDataUrl, html, and searchTrix to the new version; collapse the include to a single untagged knownGene.ra; and remove the knownGene.alpha.ra files. refs #37395 #37393 #37391
• src/hg/makeDb/trackDb/human/hg19/knownGene.ra
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    d10aba5d8ac8abc3655c599b9e421538a8a7e32e Wed Jul 22 10:56:04 2026 -0700
    Releasing GENCODE V50 knownGene tracks for hg38, hg19 (V50lift37), and mm39 (VM39). Promote knownGene from the alpha-gated staging file to the released trackDb: bump shortLabel/longLabel, bigDataUrl, html, and searchTrix to the new version; collapse the include to a single untagged knownGene.ra; and remove the knownGene.alpha.ra files. refs #37395 #37393 #37391
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    d10aba5d8ac8abc3655c599b9e421538a8a7e32e Wed Jul 22 10:56:04 2026 -0700
    Releasing GENCODE V50 knownGene tracks for hg38, hg19 (V50lift37), and mm39 (VM39). Promote knownGene from the alpha-gated staging file to the released trackDb: bump shortLabel/longLabel, bigDataUrl, html, and searchTrix to the new version; collapse the include to a single untagged knownGene.ra; and remove the knownGene.alpha.ra files. refs #37395 #37393 #37391
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
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    e6b7a180acff63d77b0d6d4cfba98a2298a7889e Wed Jul 22 11:25:18 2026 -0700
    Adding GENCODE V50/VM39 release notes to the GENCODE Versions container description page. The per-version subtrack pages were updated for the new release but the wgEncodeGencodeSuper container page Release Notes still topped out at the previous version. Add the new version-to-Ensembl correspondence line (V50/V50lift37/VM39 -> Ensembl 116) for hg38, hg19, and mm39. refs #37396 #37394 #37392
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV49lift37.ra
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    028e5a86ab2f9731bceae8eb1676488c175871f3 Wed Jul 22 10:56:04 2026 -0700
    Hiding previous GENCODE versions track now that V50/VM39 is released. Set visibility hide on wgEncodeGencodeV49 (hg38), wgEncodeGencodeV49lift37 (hg19), and wgEncodeGencodeVM38 (mm39) so the new version is the default shown in the GENCODE Versions container. refs #37396 #37394 #37392
• src/hg/makeDb/trackDb/human/hg38/clinvarMapped.html
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    c9446936b026a803d97e7f5128404a327829fe2e Sun Jul 19 00:01:22 2026 -0700
    ClinVar Mapped: add Pfam-domain mapping method Maps ClinVar coding variants through Pfam protein domains as a second method under the clinvarMapped container. Each Pfam family's profile HMM gives a shared coordinate, so a variant inside a domain is projected to the residue in the same HMM match-state column in every other MANE Select gene carrying that domain, then mapped back to that gene's genomic codon. This links genes that share a domain without being paralogs (e.g. the SCN sodium channels and the CACNA1 calcium channels via Ion_trans). Each variant is shown at its 25 most conserved equivalents. Uses Pfam-A 38.2. Adds two alpha subtracks (Pfam Domain Variants, Pfam Domains), the hmmsearch/hmmalign build scripts, autoSql, makeDoc and description page, refs #37883
• src/hg/makeDb/trackDb/human/hg38/clinvarMapped.ra
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    c9446936b026a803d97e7f5128404a327829fe2e Sun Jul 19 00:01:22 2026 -0700
    ClinVar Mapped: add Pfam-domain mapping method Maps ClinVar coding variants through Pfam protein domains as a second method under the clinvarMapped container. Each Pfam family's profile HMM gives a shared coordinate, so a variant inside a domain is projected to the residue in the same HMM match-state column in every other MANE Select gene carrying that domain, then mapped back to that gene's genomic codon. This links genes that share a domain without being paralogs (e.g. the SCN sodium channels and the CACNA1 calcium channels via Ion_trans). Each variant is shown at its 25 most conserved equivalents. Uses Pfam-A 38.2. Adds two alpha subtracks (Pfam Domain Variants, Pfam Domains), the hmmsearch/hmmalign build scripts, autoSql, makeDoc and description page, refs #37883
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
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    d10aba5d8ac8abc3655c599b9e421538a8a7e32e Wed Jul 22 10:56:04 2026 -0700
    Releasing GENCODE V50 knownGene tracks for hg38, hg19 (V50lift37), and mm39 (VM39). Promote knownGene from the alpha-gated staging file to the released trackDb: bump shortLabel/longLabel, bigDataUrl, html, and searchTrix to the new version; collapse the include to a single untagged knownGene.ra; and remove the knownGene.alpha.ra files. refs #37395 #37393 #37391
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
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    d10aba5d8ac8abc3655c599b9e421538a8a7e32e Wed Jul 22 10:56:04 2026 -0700
    Releasing GENCODE V50 knownGene tracks for hg38, hg19 (V50lift37), and mm39 (VM39). Promote knownGene from the alpha-gated staging file to the released trackDb: bump shortLabel/longLabel, bigDataUrl, html, and searchTrix to the new version; collapse the include to a single untagged knownGene.ra; and remove the knownGene.alpha.ra files. refs #37395 #37393 #37391
• src/hg/makeDb/trackDb/human/hg38/nmd.html
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    b86eab362ce697c350764ffe438ccdba8829e0f3 Mon Jul 20 17:37:35 2026 -0700
    Fixing the NMDetective-A/B score-range text (0 to 1, not -1 to +1), updating the citation to Lindeboom et al. 2019, and changing viewLimits to -0.3:1.5 on all four NMDetective subtracks. refs #37843
• src/hg/makeDb/trackDb/human/hg38/nmd.ra
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    b86eab362ce697c350764ffe438ccdba8829e0f3 Mon Jul 20 17:37:35 2026 -0700
    Fixing the NMDetective-A/B score-range text (0 to 1, not -1 to +1), updating the citation to Lindeboom et al. 2019, and changing viewLimits to -0.3:1.5 on all four NMDetective subtracks. refs #37843
• src/hg/makeDb/trackDb/human/hg38/nmdDetective.html
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    b86eab362ce697c350764ffe438ccdba8829e0f3 Mon Jul 20 17:37:35 2026 -0700
    Fixing the NMDetective-A/B score-range text (0 to 1, not -1 to +1), updating the citation to Lindeboom et al. 2019, and changing viewLimits to -0.3:1.5 on all four NMDetective subtracks. refs #37843
• src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.html
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    38d5c1e91f3a867c589da441f549c9d46bc9b9f4 Mon Jul 20 14:05:31 2026 -0700
    Add singleCellSignalsPeaks track to hg38 Native faceted composite built from the per-cell-type signal (bigWig) and peak (bigBed/bigNarrowPeak) tracks of the UCSC Cell Browser single-cell ATAC datasets, re-parented under one track in the regulation group. 936 subtracks across 9 datasets. Data files live in /hive/data/genomes/hg38/bed/singleCellSignalsPeaks and are served via a /gbdb/hg38/bbi symlink; the .ra is regenerated from the Cell Browser hub build by makeDb/scripts/singleCellSignalsPeaks/makeSingleCellSignalsPeaksRa.py. refs #37820 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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    037672a61d01d3109e8b20dff4d9142f3c8a8c66 Mon Jul 20 16:28:24 2026 -0700
    singleCellSignalsPeaks.html: reword two dataset descriptions Recast two dangling participial phrases ("...describing about 1.2 million elements", "...defining 359,022 elements") as plain clauses. refs #37820 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.ra
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    38d5c1e91f3a867c589da441f549c9d46bc9b9f4 Mon Jul 20 14:05:31 2026 -0700
    Add singleCellSignalsPeaks track to hg38 Native faceted composite built from the per-cell-type signal (bigWig) and peak (bigBed/bigNarrowPeak) tracks of the UCSC Cell Browser single-cell ATAC datasets, re-parented under one track in the regulation group. 936 subtracks across 9 datasets. Data files live in /hive/data/genomes/hg38/bed/singleCellSignalsPeaks and are served via a /gbdb/hg38/bbi symlink; the .ra is regenerated from the Cell Browser hub build by makeDb/scripts/singleCellSignalsPeaks/makeSingleCellSignalsPeaksRa.py. refs #37820 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    38d5c1e91f3a867c589da441f549c9d46bc9b9f4 Mon Jul 20 14:05:31 2026 -0700
    Add singleCellSignalsPeaks track to hg38 Native faceted composite built from the per-cell-type signal (bigWig) and peak (bigBed/bigNarrowPeak) tracks of the UCSC Cell Browser single-cell ATAC datasets, re-parented under one track in the regulation group. 936 subtracks across 9 datasets. Data files live in /hive/data/genomes/hg38/bed/singleCellSignalsPeaks and are served via a /gbdb/hg38/bbi symlink; the .ra is regenerated from the Cell Browser hub build by makeDb/scripts/singleCellSignalsPeaks/makeSingleCellSignalsPeaksRa.py. refs #37820 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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    d10aba5d8ac8abc3655c599b9e421538a8a7e32e Wed Jul 22 10:56:04 2026 -0700
    Releasing GENCODE V50 knownGene tracks for hg38, hg19 (V50lift37), and mm39 (VM39). Promote knownGene from the alpha-gated staging file to the released trackDb: bump shortLabel/longLabel, bigDataUrl, html, and searchTrix to the new version; collapse the include to a single untagged knownGene.ra; and remove the knownGene.alpha.ra files. refs #37395 #37393 #37391
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    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
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    e6b7a180acff63d77b0d6d4cfba98a2298a7889e Wed Jul 22 11:25:18 2026 -0700
    Adding GENCODE V50/VM39 release notes to the GENCODE Versions container description page. The per-version subtrack pages were updated for the new release but the wgEncodeGencodeSuper container page Release Notes still topped out at the previous version. Add the new version-to-Ensembl correspondence line (V50/V50lift37/VM39 -> Ensembl 116) for hg38, hg19, and mm39. refs #37396 #37394 #37392
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV49.ra
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    028e5a86ab2f9731bceae8eb1676488c175871f3 Wed Jul 22 10:56:04 2026 -0700
    Hiding previous GENCODE versions track now that V50/VM39 is released. Set visibility hide on wgEncodeGencodeV49 (hg38), wgEncodeGencodeV49lift37 (hg19), and wgEncodeGencodeVM38 (mm39) so the new version is the default shown in the GENCODE Versions container. refs #37396 #37394 #37392
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.alpha.ra
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    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra
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    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
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    42e67e7ac80677bec2f1d71e01dba92625f0078c Thu Jul 23 11:10:20 2026 -0700
    Hiding the default hg38 ENCODE3 Regulation supertrack now that ENCODE4 Regulation is on by default. refs #37845 refs #34923
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.ra
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    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
• src/hg/makeDb/trackDb/human/hostseq.html
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    d5302bd1e0cf296545df9ad3e0d3ab57859a51eb Fri Jul 24 17:17:17 2026 -0700
    varFreqs: post-QA polish on new hostseq subtrack. refs #37882 Findings from the qa-track pass on the gnomAD-Canada HostSeq subtrack added in 99764ad55bb: - hostseq.html: fix non-ASCII byte in Alföldi (Alf&#246;ldi), swap hardcoded hg38 for $db in the hgdownload URL, extend the FILTER enumeration to include InbreedingCoeff;RF (34,540 sites), add nhomalt and grpmax to the Display Conventions details-page list, and add an "Effective sample size per ancestry group" subsection warning that AF_fin (~4 individuals) and AF_mid (~72) are too sparse to be reliable population estimates. Collapsed a stray double blank line between refs. - populations.tsv, hostseqHtToVcf.py: harmonize the "oth" group label to "Remaining individuals" per the gnomAD README. The existing VCF header still shows the old label; it picks up the new one on the next re-emit (not worth re-running the 104 GB Hail table just for this). - varFreqs.ra: hostseq priority 2 -> 33 to break the sort-order collision with allofus (also at priority 2).
• src/hg/makeDb/trackDb/human/jaspar.ra
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    43f042236ce180b8e0712d43c8baabc4ad8df1cd Sat Jul 25 18:21:54 2026 -0700
    hgTracks: add compactPack mode and codon strand-direction arrows When zoomed to codon-coloring level, draw strand-direction chevrons across the exons (white over coding codons when too small to label, contrasting color over UTRs), and a per-codon arrow between amino-acid letters via drawScaledBoxWithText. Add a compactPack trackDb setting for shorter pack/squish rows and a small squish-mode codon font. Adds mgFontForCellHeight() to memgfx and enables compactPack on the JASPAR track.
• src/hg/makeDb/trackDb/human/lrSv.html
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    3870b9e5e1b3fc67b0638fa77f6644bf5f133c9f Mon Jul 20 10:52:55 2026 -0700
    lrSv: relabel lrSv1kLin and gustafsonSv, write lrSv1kLin description Per Eichler lab request: relabel lrSv1kLin to 'Structural Variants from 1218 1KG individuals (HiFi, ONT & assembly)' and write its description page (drawn from HPRC year 2, HGSVC3, Vienna 1KG-ONT and UW 1KG-ONT). Relabel gustafsonSv as the University of Washington 1KG-ONT effort. Track names unchanged; no data rebuilt, counts kept honest at the current 100-sample Gustafson data. refs #36258
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    cc6ef4c74d072de9c22e8bb88ab0e0983e6f2f47 Wed Jul 22 18:09:16 2026 -0700
    lrSv cardSv: switch CARD count fields from carrier counts to allele counts The NIH CARD provider republished the display bigBed with the count columns changed to diploid allele counts (alleleCount = nabecAlleleCount + hbccAlleleCount). Re-downloaded and rebuilt; renamed the schema fields to AC / nabecAc / hbccAc, updated filter ranges (0:702, 0:410, 0:292) and labels to allele counts, and reworded cardSv.html and the lrSv.html summary. Also noted there are no Alzheimer's cases in these cohorts. Re-ran the merge so lrSvAll carries CARD's allele counts. refs #36258
• src/hg/makeDb/trackDb/human/lrSv.ra
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    3870b9e5e1b3fc67b0638fa77f6644bf5f133c9f Mon Jul 20 10:52:55 2026 -0700
    lrSv: relabel lrSv1kLin and gustafsonSv, write lrSv1kLin description Per Eichler lab request: relabel lrSv1kLin to 'Structural Variants from 1218 1KG individuals (HiFi, ONT & assembly)' and write its description page (drawn from HPRC year 2, HGSVC3, Vienna 1KG-ONT and UW 1KG-ONT). Relabel gustafsonSv as the University of Washington 1KG-ONT effort. Track names unchanged; no data rebuilt, counts kept honest at the current 100-sample Gustafson data. refs #36258
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    23f68df8fb0481fd1bd4351f4adbf913f039f237 Mon Jul 20 11:49:57 2026 -0700
    lrSv1kLin: add per-population AF filter defaults and full Data Access section Add missing filter.afAfr/afAmr/afEas/afEur/afSas default ranges so the per-population allele-frequency filters render. Expand the description page's Data Access section to the standard form with bigBed download URLs for both the hg38 and hs1 native builds. refs #36258
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    cc6ef4c74d072de9c22e8bb88ab0e0983e6f2f47 Wed Jul 22 18:09:16 2026 -0700
    lrSv cardSv: switch CARD count fields from carrier counts to allele counts The NIH CARD provider republished the display bigBed with the count columns changed to diploid allele counts (alleleCount = nabecAlleleCount + hbccAlleleCount). Re-downloaded and rebuilt; renamed the schema fields to AC / nabecAc / hbccAc, updated filter ranges (0:702, 0:410, 0:292) and labels to allele counts, and reworded cardSv.html and the lrSv.html summary. Also noted there are no Alzheimer's cases in these cohorts. Re-ran the merge so lrSvAll carries CARD's allele counts. refs #36258
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    27c2565b448892d69bbb365459b8b5dfe682b505 Fri Jul 24 00:31:50 2026 -0700
    changing lrSv labels, email from Evan Eichler
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    5a84070bbe697b8ebee5ab44903a67d0a2e642b0 Fri Jul 24 01:06:00 2026 -0700
    label changes after email from boris.noyvert@boehringer-ingelheim.com
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    0656b0a9ad98986ef3944b6ceaf305ab08ca4e39 Fri Jul 24 01:10:13 2026 -0700
    noyvertSv: swap UK Biobank r2 filter for leave-one-out metrics, revise description Per author (Boris Noyvert) request, replace the r2Ukb (UK Biobank imputation r2) filter with r2Loo and concordanceLoo, the primary SV imputation quality measures for the multi-ancestry reference panel (r2Ukb mainly reflects European-ancestry performance). Both fields already exist in noyvert.bb, so this is a trackDb-only change. Also update the description page with the author's revised text, including a comparison with the 1KG ONT Vienna dataset. refs #37888
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    798b37017a4e1b95f3ccdf7c8b477dfb5446a324 Fri Jul 24 15:22:34 2026 -0700
    lrSv: QA fixes for cardSv/noyvertSv additions - BND filter, makedoc, link targets. refs #37888 Add BND to filterValues.svType on the longReadVariants supertrack and the merged lrSvAll track (and the lrSvMergeAll.py generator) so the breakend variants that noyvertSv contributes are filterable. Correct a stale makedoc comment that said CARD was not in the lrSvAll merge (it is). Add target="_blank" to the API and hgdownload links in cardSv.html and noyvertSv.html.
• src/hg/makeDb/trackDb/human/lrSv1kLin.html
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    3870b9e5e1b3fc67b0638fa77f6644bf5f133c9f Mon Jul 20 10:52:55 2026 -0700
    lrSv: relabel lrSv1kLin and gustafsonSv, write lrSv1kLin description Per Eichler lab request: relabel lrSv1kLin to 'Structural Variants from 1218 1KG individuals (HiFi, ONT & assembly)' and write its description page (drawn from HPRC year 2, HGSVC3, Vienna 1KG-ONT and UW 1KG-ONT). Relabel gustafsonSv as the University of Washington 1KG-ONT effort. Track names unchanged; no data rebuilt, counts kept honest at the current 100-sample Gustafson data. refs #36258
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    23f68df8fb0481fd1bd4351f4adbf913f039f237 Mon Jul 20 11:49:57 2026 -0700
    lrSv1kLin: add per-population AF filter defaults and full Data Access section Add missing filter.afAfr/afAmr/afEas/afEur/afSas default ranges so the per-population allele-frequency filters render. Expand the description page's Data Access section to the standard form with bigBed download URLs for both the hg38 and hs1 native builds. refs #36258
• src/hg/makeDb/trackDb/human/lrSvAll.ra
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    798b37017a4e1b95f3ccdf7c8b477dfb5446a324 Fri Jul 24 15:22:34 2026 -0700
    lrSv: QA fixes for cardSv/noyvertSv additions - BND filter, makedoc, link targets. refs #37888 Add BND to filterValues.svType on the longReadVariants supertrack and the merged lrSvAll track (and the lrSvMergeAll.py generator) so the breakend variants that noyvertSv contributes are filterable. Correct a stale makedoc comment that said CARD was not in the lrSvAll merge (it is). Add target="_blank" to the API and hgdownload links in cardSv.html and noyvertSv.html.
• src/hg/makeDb/trackDb/human/noyvertSv.html
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    0656b0a9ad98986ef3944b6ceaf305ab08ca4e39 Fri Jul 24 01:10:13 2026 -0700
    noyvertSv: swap UK Biobank r2 filter for leave-one-out metrics, revise description Per author (Boris Noyvert) request, replace the r2Ukb (UK Biobank imputation r2) filter with r2Loo and concordanceLoo, the primary SV imputation quality measures for the multi-ancestry reference panel (r2Ukb mainly reflects European-ancestry performance). Both fields already exist in noyvert.bb, so this is a trackDb-only change. Also update the description page with the author's revised text, including a comparison with the 1KG ONT Vienna dataset. refs #37888
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    798b37017a4e1b95f3ccdf7c8b477dfb5446a324 Fri Jul 24 15:22:34 2026 -0700
    lrSv: QA fixes for cardSv/noyvertSv additions - BND filter, makedoc, link targets. refs #37888 Add BND to filterValues.svType on the longReadVariants supertrack and the merged lrSvAll track (and the lrSvMergeAll.py generator) so the breakend variants that noyvertSv contributes are filterable. Correct a stale makedoc comment that said CARD was not in the lrSvAll merge (it is). Add target="_blank" to the API and hgdownload links in cardSv.html and noyvertSv.html.
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    d2dff1a21b65cf37a89f2701c326e1dabf1a1272 Sat Jul 25 18:25:07 2026 -0700
    noyvertSv: clarify that the dataset is an independent reprocessing of the 1KG ONT Vienna reads
  • lines changed 8, context: html, text, full: html, text
    7bdcd030cdf434c72f3f6a492ee8f84372c752c7 Sat Jul 25 19:22:57 2026 -0700
    noyvertSv: note the Boehringer/Vienna relationship and call-level overlap The Noyvert panel is an independent reprocessing of the same ONT reads as the 1KG ONT Vienna track (Schloissnig et al. 2025). Add a description sentence with the deletion counts (~38k vs ~58k, ~12k shared at 50% reciprocal overlap) and the concordance both ways (about a third of this track's deletions and a fifth of Vienna's at 50%, a quarter and a sixth at 90%; ~a quarter of insertions match within 100 bp). Overlap analysis recorded in the makeDoc. refs #37888
• src/hg/makeDb/trackDb/human/popEve.html
  • lines changed 15, context: html, text, full: html, text
    7485753cb34c1c3fd4a3f7b8894d993110db50ff Thu Jul 23 14:03:39 2026 -0700
    Rebuild popEVE heatmap with the full per-amino-acid matrix. refs #37791 The track was built from the genomic single-nucleotide VCF, so each column showed only the ~6 of 19 substitutions reachable by a single nucleotide change. The popEVE authors confirmed the per-transcript CSV download carries the complete matrix, so the converter now takes the all-19 scores from those CSVs while reusing the genomic codon coordinates, strand, and blocks derived from the VCF. Proteins absent from the (older) CSV release fall back to the sparse VCF scores. Color anchors recomputed over the full-matrix distribution, and the mouseover's raw EVE field is relabeled "EVE index" to distinguish it from the EVE track's 0-1 score. Updates the description page and makedoc to match.
  • lines changed 2, context: html, text, full: html, text
    9a56fd00c6ee9cba19d36d6fe4ae0222523cdcd8 Thu Jul 23 14:10:55 2026 -0700
    Update popEVE color-legend anchors to the dense-rebuild values. refs #37791 The description page's color table still showed the sparse build's saturation anchors (-5.74 / -2.29); the dense rebuild recomputed them to -6.04 / -2.41. Caught in visual QA.
• src/hg/makeDb/trackDb/human/sfariSparkExomes.html
  • lines changed 22, context: html, text, full: html, text
    8d5759442b9034d07823c7c57ad4c53f7fc2d6bc Sat Jul 25 18:25:07 2026 -0700
    sfariSparkExomes: update track description
• src/hg/makeDb/trackDb/human/varFreqs.ra
  • lines changed 1, context: html, text, full: html, text
    d5302bd1e0cf296545df9ad3e0d3ab57859a51eb Fri Jul 24 17:17:17 2026 -0700
    varFreqs: post-QA polish on new hostseq subtrack. refs #37882 Findings from the qa-track pass on the gnomAD-Canada HostSeq subtrack added in 99764ad55bb: - hostseq.html: fix non-ASCII byte in Alföldi (Alf&#246;ldi), swap hardcoded hg38 for $db in the hgdownload URL, extend the FILTER enumeration to include InbreedingCoeff;RF (34,540 sites), add nhomalt and grpmax to the Display Conventions details-page list, and add an "Effective sample size per ancestry group" subsection warning that AF_fin (~4 individuals) and AF_mid (~72) are too sparse to be reliable population estimates. Collapsed a stray double blank line between refs. - populations.tsv, hostseqHtToVcf.py: harmonize the "oth" group label to "Remaining individuals" per the gnomAD README. The existing VCF header still shows the old label; it picks up the new one on the next re-emit (not worth re-running the 104 GB Hail table just for this). - varFreqs.ra: hostseq priority 2 -> 33 to break the sort-order collision with allofus (also at priority 2).
• src/hg/makeDb/trackDb/mouse/mm10/encode.cCREs.override.ra
  • lines changed 2, context: html, text, full: html, text
    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/encode4.ccres.ra
  • lines changed 1, context: html, text, full: html, text
    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.ra
  • lines changed 2, context: html, text, full: html, text
    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.alpha.ra
  • lines changed 41, context: html, text, full: html, text
    d10aba5d8ac8abc3655c599b9e421538a8a7e32e Wed Jul 22 10:56:04 2026 -0700
    Releasing GENCODE V50 knownGene tracks for hg38, hg19 (V50lift37), and mm39 (VM39). Promote knownGene from the alpha-gated staging file to the released trackDb: bump shortLabel/longLabel, bigDataUrl, html, and searchTrix to the new version; collapse the include to a single untagged knownGene.ra; and remove the knownGene.alpha.ra files. refs #37395 #37393 #37391
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra
  • lines changed 6, context: html, text, full: html, text
    d10aba5d8ac8abc3655c599b9e421538a8a7e32e Wed Jul 22 10:56:04 2026 -0700
    Releasing GENCODE V50 knownGene tracks for hg38, hg19 (V50lift37), and mm39 (VM39). Promote knownGene from the alpha-gated staging file to the released trackDb: bump shortLabel/longLabel, bigDataUrl, html, and searchTrix to the new version; collapse the include to a single untagged knownGene.ra; and remove the knownGene.alpha.ra files. refs #37395 #37393 #37391
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    d10aba5d8ac8abc3655c599b9e421538a8a7e32e Wed Jul 22 10:56:04 2026 -0700
    Releasing GENCODE V50 knownGene tracks for hg38, hg19 (V50lift37), and mm39 (VM39). Promote knownGene from the alpha-gated staging file to the released trackDb: bump shortLabel/longLabel, bigDataUrl, html, and searchTrix to the new version; collapse the include to a single untagged knownGene.ra; and remove the knownGene.alpha.ra files. refs #37395 #37393 #37391
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    e6b7a180acff63d77b0d6d4cfba98a2298a7889e Wed Jul 22 11:25:18 2026 -0700
    Adding GENCODE V50/VM39 release notes to the GENCODE Versions container description page. The per-version subtrack pages were updated for the new release but the wgEncodeGencodeSuper container page Release Notes still topped out at the previous version. Add the new version-to-Ensembl correspondence line (V50/V50lift37/VM39 -> Ensembl 116) for hg38, hg19, and mm39. refs #37396 #37394 #37392
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM38.ra
  • lines changed 1, context: html, text, full: html, text
    028e5a86ab2f9731bceae8eb1676488c175871f3 Wed Jul 22 10:56:04 2026 -0700
    Hiding previous GENCODE versions track now that V50/VM39 is released. Set visibility hide on wgEncodeGencodeV49 (hg38), wgEncodeGencodeV49lift37 (hg19), and wgEncodeGencodeVM38 (mm39) so the new version is the default shown in the GENCODE Versions container. refs #37396 #37394 #37392
• src/hg/utils/cartMcp/README.md
  • lines changed 110, context: html, text, full: html, text
    5feabe525b8b0cd0840cc5eff607bc4c42b1ac1c Sat Jul 25 18:33:06 2026 -0700
    add an AI front end that composes sessions, to find out what a JSON cart buys refs #37838 Test of an MCP server that turns AI user questions into browser sessions, and will write the JSON cart each one would be.
• src/hg/utils/cartMcp/cartMcp.py
  • lines changed 997, context: html, text, full: html, text
    5feabe525b8b0cd0840cc5eff607bc4c42b1ac1c Sat Jul 25 18:33:06 2026 -0700
    add an AI front end that composes sessions, to find out what a JSON cart buys refs #37838 Test of an MCP server that turns AI user questions into browser sessions, and will write the JSON cart each one would be.
• src/hg/utils/cartTrackVarCatalog/cartTrackVarCatalog.py
  • lines changed 1702, context: html, text, full: html, text
    2904215904f1e62317b16bb372a6b176c1f800bd Sat Jul 25 09:58:54 2026 -0700
    add an inventory of track-scoped cart variables refs #37838 Before changing the cart format we need to know what is actually stored in it. cartTrackVarCatalog.py holds a curated catalog of the 340 track-scoped cart variables in the tree, arranged as the hierarchy a JSON cart would use: track name, then the variables common to any track, then a layer per track type, then the leaf groups shared across types. It emits either JSON or a browsable HTML page, and --check verifies that every leaf group a type refers to exists. harvestCartVars.py is the scanner that seeds it. It finds the two ways a track-scoped name gets built, cart*ClosestToHome() and safef("%s.%s"), resolves macro identifiers to their string values, and attributes each hit to the function that reads or writes it. Its output still needs curation by hand, since it cannot tell a cart variable from a table name or a filename suffix. No makefile: this is a documentation generator, so it is left out of the utils DIRS list, same as hg/utils/otto.
• src/hg/utils/cartTrackVarCatalog/harvestCartVars.py
  • lines changed 359, context: html, text, full: html, text
    2904215904f1e62317b16bb372a6b176c1f800bd Sat Jul 25 09:58:54 2026 -0700
    add an inventory of track-scoped cart variables refs #37838 Before changing the cart format we need to know what is actually stored in it. cartTrackVarCatalog.py holds a curated catalog of the 340 track-scoped cart variables in the tree, arranged as the hierarchy a JSON cart would use: track name, then the variables common to any track, then a layer per track type, then the leaf groups shared across types. It emits either JSON or a browsable HTML page, and --check verifies that every leaf group a type refers to exists. harvestCartVars.py is the scanner that seeds it. It finds the two ways a track-scoped name gets built, cart*ClosestToHome() and safef("%s.%s"), resolves macro identifiers to their string values, and attributes each hit to the function that reads or writes it. Its output still needs curation by hand, since it cannot tell a cart variable from a table name or a filename suffix. No makefile: this is a documentation generator, so it is left out of the utils DIRS list, same as hg/utils/otto.
• src/hg/utils/docent/README.md
  • lines changed 135, context: html, text, full: html, text
    4bd85aa14161039a40fd499bd8416ab51f099d81 Sat Jul 25 18:34:48 2026 -0700
    add Docent, a language for authoring Genome Browser tours refs #37892 A Docent script is an ordered list of high-level verbs (go, hide, track, mouseover, convert, drag, shot) that drives a real browser against a real server, and renders to a silent mp4 plus a named PNG still at every shot marker. One source, both outputs, so a published figure is a frame of the tour and the two cannot drift apart. The verbs encode browser mechanics rather than selectors. convert: knows the Hide-defaults checkbox reverts when the Assembly menu reloads, track: {clinvar: pack} knows that composite's clean parameter set, and mouseover: knows a lifted track's DOM id gains a per-run hub_<n>_ prefix. The author writes intent. The surface syntax is YAML so ordinary editors highlight it; the language is the verb vocabulary on top, not the serialization. Scripts are named <base>.docent.yaml. This was built inside the quickLift Current Protocols paper repo, where it still has its six working scripts, and only the general parts move here: the renderer, the language reference, and the make rules a project includes to get incremental rebuilds. Nothing in the build refers to the directory, the same way cartTrackVarCatalog does not, since these are node scripts and need playwright and js-yaml. target: defaults to genome-test rather than the sandbox it grew up on, and resolves any hgwdev-<user> name, so a script that forgets to say where it runs does not quietly hit somebody's machine. Next step is #37838. Today a step reaches the browser as CGI variables, which is why the verbs have to know each composite by heart; once the cart takes a structured blob a step can name the state it wants instead. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/utils/docent/docent.js
  • lines changed 758, context: html, text, full: html, text
    4bd85aa14161039a40fd499bd8416ab51f099d81 Sat Jul 25 18:34:48 2026 -0700
    add Docent, a language for authoring Genome Browser tours refs #37892 A Docent script is an ordered list of high-level verbs (go, hide, track, mouseover, convert, drag, shot) that drives a real browser against a real server, and renders to a silent mp4 plus a named PNG still at every shot marker. One source, both outputs, so a published figure is a frame of the tour and the two cannot drift apart. The verbs encode browser mechanics rather than selectors. convert: knows the Hide-defaults checkbox reverts when the Assembly menu reloads, track: {clinvar: pack} knows that composite's clean parameter set, and mouseover: knows a lifted track's DOM id gains a per-run hub_<n>_ prefix. The author writes intent. The surface syntax is YAML so ordinary editors highlight it; the language is the verb vocabulary on top, not the serialization. Scripts are named <base>.docent.yaml. This was built inside the quickLift Current Protocols paper repo, where it still has its six working scripts, and only the general parts move here: the renderer, the language reference, and the make rules a project includes to get incremental rebuilds. Nothing in the build refers to the directory, the same way cartTrackVarCatalog does not, since these are node scripts and need playwright and js-yaml. target: defaults to genome-test rather than the sandbox it grew up on, and resolves any hgwdev-<user> name, so a script that forgets to say where it runs does not quietly hit somebody's machine. Next step is #37838. Today a step reaches the browser as CGI variables, which is why the verbs have to know each composite by heart; once the cart takes a structured blob a step can name the state it wants instead. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/utils/docent/docent.mk
  • lines changed 49, context: html, text, full: html, text
    4bd85aa14161039a40fd499bd8416ab51f099d81 Sat Jul 25 18:34:48 2026 -0700
    add Docent, a language for authoring Genome Browser tours refs #37892 A Docent script is an ordered list of high-level verbs (go, hide, track, mouseover, convert, drag, shot) that drives a real browser against a real server, and renders to a silent mp4 plus a named PNG still at every shot marker. One source, both outputs, so a published figure is a frame of the tour and the two cannot drift apart. The verbs encode browser mechanics rather than selectors. convert: knows the Hide-defaults checkbox reverts when the Assembly menu reloads, track: {clinvar: pack} knows that composite's clean parameter set, and mouseover: knows a lifted track's DOM id gains a per-run hub_<n>_ prefix. The author writes intent. The surface syntax is YAML so ordinary editors highlight it; the language is the verb vocabulary on top, not the serialization. Scripts are named <base>.docent.yaml. This was built inside the quickLift Current Protocols paper repo, where it still has its six working scripts, and only the general parts move here: the renderer, the language reference, and the make rules a project includes to get incremental rebuilds. Nothing in the build refers to the directory, the same way cartTrackVarCatalog does not, since these are node scripts and need playwright and js-yaml. target: defaults to genome-test rather than the sandbox it grew up on, and resolves any hgwdev-<user> name, so a script that forgets to say where it runs does not quietly hit somebody's machine. Next step is #37838. Today a step reaches the browser as CGI variables, which is why the verbs have to know each composite by heart; once the cart takes a structured blob a step can name the state it wants instead. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
• src/hg/utils/hgConfCatalog/harvestHgConf.py
  • lines changed 796, context: html, text, full: html, text
    20bd278408f2907cf1965c7a8789dc887222b546 Sat Jul 25 13:43:30 2026 -0700
    add a registry of hg.conf variables with a sunset mechanism for release gates refs #37925 Third of the browser configuration inventories, after hg/utils/cartTrackVarCatalog (#37838) and hg/utils/urlCommandCatalog (#37923), and built as a sibling of both: a curated registry plus a mechanical harvester it is reconciled against. harvestHgConf.py scans for every cfgOption* read. The accessors do not all take the setting name in the same argument, so it parses the argument list rather than matching the first string literal: cfgOptionEnv's first argument is an environment variable, not an hg.conf name, and cfgOption2 builds prefix.suffix from a prefix that is usually a runtime profile name. That last case is why ex.hg.conf documents archivecentral.password while the source contains no such literal. hgConfCatalog.py is the registry, with --json, --html, --check and --reconcile. What hg.conf needs that the other two did not is a way to retire a variable, so --sunset reports which release gates should be gone. The 58 boolean flags are split into gates, added to ship a feature dark and meant to be deleted once it is public, and knobs, which a mirror may set forever. --reconcile fails if any flag in the tree is left unclassified. Only that split is hand-written. Both lifecycle dates are read out of git: one history walk records when each variable was first read and when each flag's default first became TRUE, mapped onto the CGI_VERSION in effect at the time from the history of versionInfo.h. hgConfAges.json caches that walk, which otherwise costs two minutes. The audit found 18 shipped gates past a removal deadline, 9 more that have sat at a FALSE default without ever shipping (hgSession.shortLink since v374), and a documentation bug: ex.hg.conf tells mirrors to set userDbTableName but the code reads userDbName, so anyone who follows it is silently ignored. No makefile: this is a documentation generator, so it is left out of the utils DIRS list, same as hg/utils/otto and the two sibling catalogs. Nothing reads the registry yet and no CGI behavior changes.
  • lines changed 807, context: html, text, full: html, text
    561b79881323e97a48ceff25068d3890e23e03c3 Sat Jul 25 13:57:32 2026 -0700
    add a registry of hg.conf variables with a sunset mechanism for release gates refs #37925 Third of the browser configuration inventories, after hg/utils/cartTrackVarCatalog (#37838) and hg/utils/urlCommandCatalog (#37923), and built as a sibling of both: a curated registry plus a mechanical harvester it is reconciled against. harvestHgConf.py scans for every cfgOption* read. The accessors do not all take the setting name in the same argument, so it parses the argument list rather than matching the first string literal: cfgOptionEnv's first argument is an environment variable, not an hg.conf name, and cfgOption2 builds prefix.suffix from a prefix that is usually a runtime profile name. That last case is why ex.hg.conf documents archivecentral.password while the source contains no such literal. hgConfCatalog.py is the registry, with --json, --html, --check and --reconcile. What hg.conf needs that the other two did not is a way to retire a variable, so --sunset reports which release gates should be gone. The 58 boolean flags are split into gates, added to ship a feature dark and meant to be deleted once it is public, and knobs, which a mirror may set forever. --reconcile fails if any flag in the tree is left unclassified. Only that split is hand-written. Both lifecycle dates are read out of git: one history walk records when each variable was first read and when each flag's default first became TRUE, mapped onto the CGI_VERSION in effect at the time from the history of versionInfo.h. hgConfAges.json caches that walk, which otherwise costs two minutes. The audit found 18 shipped gates past a removal deadline, 9 more that have sat at a FALSE default without ever shipping (hgSession.shortLink since v374), and a documentation bug: ex.hg.conf tells mirrors to set userDbTableName but the code reads userDbName, so anyone who follows it is silently ignored. No makefile: this is a documentation generator, so it is left out of the utils DIRS list, same as hg/utils/otto and the two sibling catalogs. Nothing reads the registry yet and no CGI behavior changes.
  • lines changed 284, context: html, text, full: html, text
    d2cc543ed2c0fc032bc0cf8527ecff098b075aef Sun Jul 26 17:24:31 2026 -0700
    record the ticket that introduced each hg.conf variable refs #37925 Each setting now carries the Redmine ticket cited by the commit that added its read, or for a flag the commit that turned its default on. --sunset prints it per gate, --html links it, and harvestHgConf.py --tickets groups the settings by whether git can attribute them at all. Nothing looser is used: a commit that merely edits a line is not a commit about the setting on it. A second history walk dates the names that reach cfgOption through a macro, so hgConfAges.json is rebuilt and a refresh now costs about four minutes. No CGI behaviour changes.
• src/hg/utils/hgConfCatalog/hgConfAges.json
  • lines changed 3157, context: html, text, full: html, text
    20bd278408f2907cf1965c7a8789dc887222b546 Sat Jul 25 13:43:30 2026 -0700
    add a registry of hg.conf variables with a sunset mechanism for release gates refs #37925 Third of the browser configuration inventories, after hg/utils/cartTrackVarCatalog (#37838) and hg/utils/urlCommandCatalog (#37923), and built as a sibling of both: a curated registry plus a mechanical harvester it is reconciled against. harvestHgConf.py scans for every cfgOption* read. The accessors do not all take the setting name in the same argument, so it parses the argument list rather than matching the first string literal: cfgOptionEnv's first argument is an environment variable, not an hg.conf name, and cfgOption2 builds prefix.suffix from a prefix that is usually a runtime profile name. That last case is why ex.hg.conf documents archivecentral.password while the source contains no such literal. hgConfCatalog.py is the registry, with --json, --html, --check and --reconcile. What hg.conf needs that the other two did not is a way to retire a variable, so --sunset reports which release gates should be gone. The 58 boolean flags are split into gates, added to ship a feature dark and meant to be deleted once it is public, and knobs, which a mirror may set forever. --reconcile fails if any flag in the tree is left unclassified. Only that split is hand-written. Both lifecycle dates are read out of git: one history walk records when each variable was first read and when each flag's default first became TRUE, mapped onto the CGI_VERSION in effect at the time from the history of versionInfo.h. hgConfAges.json caches that walk, which otherwise costs two minutes. The audit found 18 shipped gates past a removal deadline, 9 more that have sat at a FALSE default without ever shipping (hgSession.shortLink since v374), and a documentation bug: ex.hg.conf tells mirrors to set userDbTableName but the code reads userDbName, so anyone who follows it is silently ignored. No makefile: this is a documentation generator, so it is left out of the utils DIRS list, same as hg/utils/otto and the two sibling catalogs. Nothing reads the registry yet and no CGI behavior changes.
  • lines changed 3157, context: html, text, full: html, text
    561b79881323e97a48ceff25068d3890e23e03c3 Sat Jul 25 13:57:32 2026 -0700
    add a registry of hg.conf variables with a sunset mechanism for release gates refs #37925 Third of the browser configuration inventories, after hg/utils/cartTrackVarCatalog (#37838) and hg/utils/urlCommandCatalog (#37923), and built as a sibling of both: a curated registry plus a mechanical harvester it is reconciled against. harvestHgConf.py scans for every cfgOption* read. The accessors do not all take the setting name in the same argument, so it parses the argument list rather than matching the first string literal: cfgOptionEnv's first argument is an environment variable, not an hg.conf name, and cfgOption2 builds prefix.suffix from a prefix that is usually a runtime profile name. That last case is why ex.hg.conf documents archivecentral.password while the source contains no such literal. hgConfCatalog.py is the registry, with --json, --html, --check and --reconcile. What hg.conf needs that the other two did not is a way to retire a variable, so --sunset reports which release gates should be gone. The 58 boolean flags are split into gates, added to ship a feature dark and meant to be deleted once it is public, and knobs, which a mirror may set forever. --reconcile fails if any flag in the tree is left unclassified. Only that split is hand-written. Both lifecycle dates are read out of git: one history walk records when each variable was first read and when each flag's default first became TRUE, mapped onto the CGI_VERSION in effect at the time from the history of versionInfo.h. hgConfAges.json caches that walk, which otherwise costs two minutes. The audit found 18 shipped gates past a removal deadline, 9 more that have sat at a FALSE default without ever shipping (hgSession.shortLink since v374), and a documentation bug: ex.hg.conf tells mirrors to set userDbTableName but the code reads userDbName, so anyone who follows it is silently ignored. No makefile: this is a documentation generator, so it is left out of the utils DIRS list, same as hg/utils/otto and the two sibling catalogs. Nothing reads the registry yet and no CGI behavior changes.
  • lines changed 2711, context: html, text, full: html, text
    d2cc543ed2c0fc032bc0cf8527ecff098b075aef Sun Jul 26 17:24:31 2026 -0700
    record the ticket that introduced each hg.conf variable refs #37925 Each setting now carries the Redmine ticket cited by the commit that added its read, or for a flag the commit that turned its default on. --sunset prints it per gate, --html links it, and harvestHgConf.py --tickets groups the settings by whether git can attribute them at all. Nothing looser is used: a commit that merely edits a line is not a commit about the setting on it. A second history walk dates the names that reach cfgOption through a macro, so hgConfAges.json is rebuilt and a refresh now costs about four minutes. No CGI behaviour changes.
• src/hg/utils/hgConfCatalog/hgConfCatalog.py
  • lines changed 1780, context: html, text, full: html, text
    20bd278408f2907cf1965c7a8789dc887222b546 Sat Jul 25 13:43:30 2026 -0700
    add a registry of hg.conf variables with a sunset mechanism for release gates refs #37925 Third of the browser configuration inventories, after hg/utils/cartTrackVarCatalog (#37838) and hg/utils/urlCommandCatalog (#37923), and built as a sibling of both: a curated registry plus a mechanical harvester it is reconciled against. harvestHgConf.py scans for every cfgOption* read. The accessors do not all take the setting name in the same argument, so it parses the argument list rather than matching the first string literal: cfgOptionEnv's first argument is an environment variable, not an hg.conf name, and cfgOption2 builds prefix.suffix from a prefix that is usually a runtime profile name. That last case is why ex.hg.conf documents archivecentral.password while the source contains no such literal. hgConfCatalog.py is the registry, with --json, --html, --check and --reconcile. What hg.conf needs that the other two did not is a way to retire a variable, so --sunset reports which release gates should be gone. The 58 boolean flags are split into gates, added to ship a feature dark and meant to be deleted once it is public, and knobs, which a mirror may set forever. --reconcile fails if any flag in the tree is left unclassified. Only that split is hand-written. Both lifecycle dates are read out of git: one history walk records when each variable was first read and when each flag's default first became TRUE, mapped onto the CGI_VERSION in effect at the time from the history of versionInfo.h. hgConfAges.json caches that walk, which otherwise costs two minutes. The audit found 18 shipped gates past a removal deadline, 9 more that have sat at a FALSE default without ever shipping (hgSession.shortLink since v374), and a documentation bug: ex.hg.conf tells mirrors to set userDbTableName but the code reads userDbName, so anyone who follows it is silently ignored. No makefile: this is a documentation generator, so it is left out of the utils DIRS list, same as hg/utils/otto and the two sibling catalogs. Nothing reads the registry yet and no CGI behavior changes.
  • lines changed 1800, context: html, text, full: html, text
    561b79881323e97a48ceff25068d3890e23e03c3 Sat Jul 25 13:57:32 2026 -0700
    add a registry of hg.conf variables with a sunset mechanism for release gates refs #37925 Third of the browser configuration inventories, after hg/utils/cartTrackVarCatalog (#37838) and hg/utils/urlCommandCatalog (#37923), and built as a sibling of both: a curated registry plus a mechanical harvester it is reconciled against. harvestHgConf.py scans for every cfgOption* read. The accessors do not all take the setting name in the same argument, so it parses the argument list rather than matching the first string literal: cfgOptionEnv's first argument is an environment variable, not an hg.conf name, and cfgOption2 builds prefix.suffix from a prefix that is usually a runtime profile name. That last case is why ex.hg.conf documents archivecentral.password while the source contains no such literal. hgConfCatalog.py is the registry, with --json, --html, --check and --reconcile. What hg.conf needs that the other two did not is a way to retire a variable, so --sunset reports which release gates should be gone. The 58 boolean flags are split into gates, added to ship a feature dark and meant to be deleted once it is public, and knobs, which a mirror may set forever. --reconcile fails if any flag in the tree is left unclassified. Only that split is hand-written. Both lifecycle dates are read out of git: one history walk records when each variable was first read and when each flag's default first became TRUE, mapped onto the CGI_VERSION in effect at the time from the history of versionInfo.h. hgConfAges.json caches that walk, which otherwise costs two minutes. The audit found 18 shipped gates past a removal deadline, 9 more that have sat at a FALSE default without ever shipping (hgSession.shortLink since v374), and a documentation bug: ex.hg.conf tells mirrors to set userDbTableName but the code reads userDbName, so anyone who follows it is silently ignored. No makefile: this is a documentation generator, so it is left out of the utils DIRS list, same as hg/utils/otto and the two sibling catalogs. Nothing reads the registry yet and no CGI behavior changes.
  • lines changed 80, context: html, text, full: html, text
    d2cc543ed2c0fc032bc0cf8527ecff098b075aef Sun Jul 26 17:24:31 2026 -0700
    record the ticket that introduced each hg.conf variable refs #37925 Each setting now carries the Redmine ticket cited by the commit that added its read, or for a flag the commit that turned its default on. --sunset prints it per gate, --html links it, and harvestHgConf.py --tickets groups the settings by whether git can attribute them at all. Nothing looser is used: a commit that merely edits a line is not a commit about the setting on it. A second history walk dates the names that reach cfgOption through a macro, so hgConfAges.json is rebuilt and a refresh now costs about four minutes. No CGI behaviour changes.
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 10, context: html, text, full: html, text
    e506d31b6278bb1251d8b260f75c67fa38c99a27 Thu Jul 23 10:20:01 2026 -0700
    Making it possible for multiWig containers to be children of composites, refs #36320
• src/hg/utils/otto/genArk/updateHgcentral.sh
  • lines changed 8, context: html, text, full: html, text
    2bbb002f33905f1299a571c386ce94312e141ce7 Sat Jul 25 09:49:33 2026 -0700
    can gzip the list archive and eliminate the obsolete load of the table from olden times only do the new update refs #31811
  • lines changed 3, context: html, text, full: html, text
    f6c4dccbcda02c911b3e832fd9668b3b3f5dee4f Sat Jul 25 09:56:02 2026 -0700
    an informational printout refs #31811
• src/hg/utils/otto/otto.crontab
  • lines changed 3, context: html, text, full: html, text
    6d209db5907f28b72b8ec4937a80a77d2af3fecd Fri Jul 24 12:24:01 2026 -0700
    Updating otto crontab to match the live version, no Redmine
  • lines changed 5, context: html, text, full: html, text
    57bd4d13fdfcbf7c479087eb6151a4cf2f956cbb Mon Jul 27 09:17:50 2026 -0700
    otto cron: keep cbAnnotServer gunicorn alive, refs #37492
• src/hg/utils/sessionCartAudit/sessionCartAudit.py
  • lines changed 985, context: html, text, full: html, text
    20bd278408f2907cf1965c7a8789dc887222b546 Sat Jul 25 13:43:30 2026 -0700
    add a registry of hg.conf variables with a sunset mechanism for release gates refs #37925 Third of the browser configuration inventories, after hg/utils/cartTrackVarCatalog (#37838) and hg/utils/urlCommandCatalog (#37923), and built as a sibling of both: a curated registry plus a mechanical harvester it is reconciled against. harvestHgConf.py scans for every cfgOption* read. The accessors do not all take the setting name in the same argument, so it parses the argument list rather than matching the first string literal: cfgOptionEnv's first argument is an environment variable, not an hg.conf name, and cfgOption2 builds prefix.suffix from a prefix that is usually a runtime profile name. That last case is why ex.hg.conf documents archivecentral.password while the source contains no such literal. hgConfCatalog.py is the registry, with --json, --html, --check and --reconcile. What hg.conf needs that the other two did not is a way to retire a variable, so --sunset reports which release gates should be gone. The 58 boolean flags are split into gates, added to ship a feature dark and meant to be deleted once it is public, and knobs, which a mirror may set forever. --reconcile fails if any flag in the tree is left unclassified. Only that split is hand-written. Both lifecycle dates are read out of git: one history walk records when each variable was first read and when each flag's default first became TRUE, mapped onto the CGI_VERSION in effect at the time from the history of versionInfo.h. hgConfAges.json caches that walk, which otherwise costs two minutes. The audit found 18 shipped gates past a removal deadline, 9 more that have sat at a FALSE default without ever shipping (hgSession.shortLink since v374), and a documentation bug: ex.hg.conf tells mirrors to set userDbTableName but the code reads userDbName, so anyone who follows it is silently ignored. No makefile: this is a documentation generator, so it is left out of the utils DIRS list, same as hg/utils/otto and the two sibling catalogs. Nothing reads the registry yet and no CGI behavior changes.
  • lines changed 985, context: html, text, full: html, text
    1d306bb249823fe856c3b91e12c14951a0481efa Sat Jul 25 14:00:10 2026 -0700
    audit the cart catalogs against the named sessions refs #37838 refs #37923 Third sibling of cartTrackVarCatalog and urlCommandCatalog. Those two were built by reading the source; this one reads the other direction, pulling every named session out of namedSessionDb and asking which of the names in it neither catalog can account for. A source-derived catalog can only be as complete as the greps that built it. It cannot see a variable that only JavaScript writes, it cannot see a name assembled at run time from a track name plus a field name, and it cannot say which of the leaks it predicted are really sitting in somebody's saved session. Matching is right-anchored on the longest known suffix, never left-anchored at the first separator, because real track and species names contain dots, spaces and slashes. The catalog's bare wildcards are scored separately: they match any token, so counting them as hits absorbs every unrecognised name and the audit comes back clean having proved nothing. The prose findings are curated but every number in them is recomputed from the corpus, so the write-up cannot drift from the data.
• src/hg/utils/urlCommandCatalog/harvestUrlCommands.py
  • lines changed 383, context: html, text, full: html, text
    782f3aa9b28b73d50a12eb7ed7cdcfb43652892f Sat Jul 25 10:21:11 2026 -0700
    add a URL parameter catalog and harvester for the browser CGIs refs #37923 Two scripts under hg/utils/urlCommandCatalog, built as a sibling of hg/utils/cartTrackVarCatalog (refs #37838) and following the same curated-catalog plus mechanical-harvester shape. harvestUrlCommands.py scans the tree for the three ways a CGI accepts a URL parameter: membership in char *excludeVars[], a direct cgiOptionalString() read that bypasses the cart, and a cart read followed by cartRemove(). urlCommandCatalog.py is the curated registry, with --json, --html and --check. Its --reconcile mode imports the harvester and audits every persistence claim against what the tree actually does, so the catalog cannot quietly rot the way the hand-written help page did. The audit turned up 41 parameters that read as one-shot commands but are written into the user's session anyway, because cartExclude() is the only thing that keeps a CGI variable out of the saved cart and nothing excludes or removes them. Nothing reads the catalog yet and no CGI behavior changes. The public help page is untouched; the generated page is dev-URL only for now.
• src/hg/utils/urlCommandCatalog/urlCommandCatalog.py
  • lines changed 1478, context: html, text, full: html, text
    782f3aa9b28b73d50a12eb7ed7cdcfb43652892f Sat Jul 25 10:21:11 2026 -0700
    add a URL parameter catalog and harvester for the browser CGIs refs #37923 Two scripts under hg/utils/urlCommandCatalog, built as a sibling of hg/utils/cartTrackVarCatalog (refs #37838) and following the same curated-catalog plus mechanical-harvester shape. harvestUrlCommands.py scans the tree for the three ways a CGI accepts a URL parameter: membership in char *excludeVars[], a direct cgiOptionalString() read that bypasses the cart, and a cart read followed by cartRemove(). urlCommandCatalog.py is the curated registry, with --json, --html and --check. Its --reconcile mode imports the harvester and audits every persistence claim against what the tree actually does, so the catalog cannot quietly rot the way the hand-written help page did. The audit turned up 41 parameters that read as one-shot commands but are written into the user's session anyway, because cartExclude() is the only thing that keeps a CGI variable out of the saved cart and nothing excludes or removes them. Nothing reads the catalog yet and no CGI behavior changes. The public help page is untouched; the generated page is dev-URL only for now.
• src/hg/visiGene/hgVisiGene/printCaption.c
  • lines changed 7, context: html, text, full: html, text
    cc5381e539ecba5b07109b194acf1d76b0c8f641 Thu Jul 23 06:22:48 2026 -0700
    Guard hDbForTaxon() callers against curated hub (GenArk) db names. hDbForTaxon() can now return a GenArk-only assembly with no real SQL database, which would abort in sqlConnect()/"use <db>"/cross-db sqlTableExists(). Treat a hubConnectIsCurated() db as no usable native db in uniProtAccToDb(), bacProbeInfo(), and getKnownGeneUrl(). refs #37909
• src/hg/visiGene/hgVisiGene/probePage.c
  • lines changed 7, context: html, text, full: html, text
    cc5381e539ecba5b07109b194acf1d76b0c8f641 Thu Jul 23 06:22:48 2026 -0700
    Guard hDbForTaxon() callers against curated hub (GenArk) db names. hDbForTaxon() can now return a GenArk-only assembly with no real SQL database, which would abort in sqlConnect()/"use <db>"/cross-db sqlTableExists(). Treat a hubConnectIsCurated() db as no usable native db in uniProtAccToDb(), bacProbeInfo(), and getKnownGeneUrl(). refs #37909
• src/inc/memgfx.h
  • lines changed 6, context: html, text, full: html, text
    43f042236ce180b8e0712d43c8baabc4ad8df1cd Sat Jul 25 18:21:54 2026 -0700
    hgTracks: add compactPack mode and codon strand-direction arrows When zoomed to codon-coloring level, draw strand-direction chevrons across the exons (white over coding codons when too small to label, contrasting color over UTRs), and a per-codon arrow between amino-acid letters via drawScaledBoxWithText. Add a compactPack trackDb setting for shorter pack/squish rows and a small squish-mode codon font. Adds mgFontForCellHeight() to memgfx and enables compactPack on the JASPAR track.
• src/lib/memgfx.c
  • lines changed 16, context: html, text, full: html, text
    43f042236ce180b8e0712d43c8baabc4ad8df1cd Sat Jul 25 18:21:54 2026 -0700
    hgTracks: add compactPack mode and codon strand-direction arrows When zoomed to codon-coloring level, draw strand-direction chevrons across the exons (white over coding codons when too small to label, contrasting color over UTRs), and a per-codon arrow between amino-acid letters via drawScaledBoxWithText. Add a compactPack trackDb setting for shorter pack/squish rows and a small squish-mode codon font. Adds mgFontForCellHeight() to memgfx and enables compactPack on the JASPAR track.
• src/product/ex.hg.conf
  • lines changed 6, context: html, text, full: html, text
    48886c882e7198f01b7c6bcaffa9ef107a291538 Tue Jul 21 13:38:08 2026 -0700
    hgTracks: merge pixel-adjacent blocks when drawing direction barbs Chain tracks show direction chevrons only on their aligned blocks, not on the connector line between blocks. When zoomed out the blocks smash together and individually most are too narrow to hold a chevron, so a chain showed only a couple of chevrons and its orientation was nearly invisible. Accumulate blocks that touch in pixel space into a single span and draw the barbs across the whole span, so the chevrons run continuously across a run of smashed-together blocks. The gap under which blocks merge is the new hg.conf setting barbMergePixels (default 3); set it to 0 to disable merging and get the old per-block barbs. Only pixel-adjacent blocks merge, so genes with visible introns and everything else render unchanged, refs #37889
  • lines changed 4, context: html, text, full: html, text
    2961c25331a73eba4ddbca0b848b43e4a467fa75 Thu Jul 23 11:12:40 2026 -0700
    Trying this again. Let users use a rightclick option to change the color of single bed-like items, gated via hg.conf setting canColorItems, refs #37778
• src/submodules/submoduleSetup
  • lines changed 9, context: html, text, full: html, text
    504f030995a07120830b60b40619840c21fe72f9 Fri Jul 24 10:58:20 2026 -0700
    submoduleSetup: sync submodules to pinned commit on every build Run 'git submodule update --init --recursive' unconditionally when in a git work tree, rather than only when the submodule was uninitialized. This means a moved submodule pointer (e.g. after a pull) is checked out on every build, and --recursive keeps the nested htscodecs submodule in sync too. git is silent when already in sync. The non-git-work-tree (source release) branch is unchanged. No RM.
• src/utils/genark/genark
  • lines changed 301, context: html, text, full: html, text
    4c4c0b323e2b979d9b0b3dbe1b6fd66abd920584 Sat Jul 25 19:35:32 2026 -0700
    Add genark tool for managing GenArk assembly hubs New subcommand-based utility in src/utils/genark: - addContrib <name>: install a contributed track collection into the GenArk assembly hubs (symlink the .bb/.bw data files and doc pages into each assembly's contrib/<name>/ dir, write a per-assembly trackDb with hub-root relative paths, and wire that block into the assembly's useOneFile hub.txt; --remove uninstalls). - checkContrib <name>: run hubCheck across the assemblies carrying the collection and separate contrib-specific problems from the assemblies' own pre-existing hub warnings. refs #35415
• src/utils/genark/makefile
  • lines changed 18, context: html, text, full: html, text
    4c4c0b323e2b979d9b0b3dbe1b6fd66abd920584 Sat Jul 25 19:35:32 2026 -0700
    Add genark tool for managing GenArk assembly hubs New subcommand-based utility in src/utils/genark: - addContrib <name>: install a contributed track collection into the GenArk assembly hubs (symlink the .bb/.bw data files and doc pages into each assembly's contrib/<name>/ dir, write a per-assembly trackDb with hub-root relative paths, and wire that block into the assembly's useOneFile hub.txt; --remove uninstalls). - checkContrib <name>: run hubCheck across the assemblies carrying the collection and separate contrib-specific problems from the assemblies' own pre-existing hub warnings. refs #35415
• src/utils/qa/runCheckHgFindSpec
  • lines changed 7, context: html, text, full: html, text
    7753691572e05914d2d184bd295c9076cc9da463 Tue Jul 21 18:49:22 2026 -0700
    Skip active dbDb entries with no local database in runCheckHgFindSpec. refs #37836 The new GenArk hub assemblies added for #37836 are pure hub pointers (nibPath "hub:...") with no companion local MySQL database, unlike earlier additions such as rn8/hs1/mpxvRivers. The loop ran "hgsql $db" on every active dbDb name, which failed with "Unknown database" for these entries and tripped the QA cron with stderr noise. Guard the loop on the set of databases that actually exist so hub-only entries are skipped cleanly; the set of databases actually checked is unchanged.
• src/utils/redmineCli
  • lines changed 17, context: html, text, full: html, text
    7aab0f04919c3e598426fb33d914051d57cbfa29 Sat Jul 25 09:53:29 2026 -0700
    redmineCli: let update edit the ticket description refs #37281 Adds --description and --description-file to the update subcommand, which previously could not touch the description at all: that needed a raw API PUT. Mirrors how create handles the same two flags, with one difference. An empty --description clears the field rather than being an error, so the check is "is not None" instead of a truthiness test. The From Claude attribution is idempotent, so rewriting a description Claude already wrote does not stack a second header on it.

• lines changed: 37945
• files changed: 258