All File Changes

v501_preview to v501_preview2 (2026-07-06 to 2026-07-13) v501

• docs/browserSlideDecks.md
  • lines changed 62, context: html, text, full: html, text
    6d4b6f98a4144956ad7029bd7c1874ffd90fdf2f Wed Jul 8 09:23:00 2026 -0700
    redoing slides as embedded html slide deck, refs #37292
• docs/makefile
  • lines changed 8, context: html, text, full: html, text
    6d4b6f98a4144956ad7029bd7c1874ffd90fdf2f Wed Jul 8 09:23:00 2026 -0700
    redoing slides as embedded html slide deck, refs #37292
• docs/slideDecks/tutorial1-basics/presentation/index.html
  • lines changed 846, context: html, text, full: html, text
    6d4b6f98a4144956ad7029bd7c1874ffd90fdf2f Wed Jul 8 09:23:00 2026 -0700
    redoing slides as embedded html slide deck, refs #37292
• docs/slideDecks/tutorial1-basics/tableOfContents/index.html
  • lines changed 125, context: html, text, full: html, text
    6d4b6f98a4144956ad7029bd7c1874ffd90fdf2f Wed Jul 8 09:23:00 2026 -0700
    redoing slides as embedded html slide deck, refs #37292
• docs/slideDecks/tutorial2-cancer/presentation/index.html
  • lines changed 335, context: html, text, full: html, text
    6d4b6f98a4144956ad7029bd7c1874ffd90fdf2f Wed Jul 8 09:23:00 2026 -0700
    redoing slides as embedded html slide deck, refs #37292
• docs/slideDecks/tutorial2-cancer/tableOfContents/index.html
  • lines changed 79, context: html, text, full: html, text
    6d4b6f98a4144956ad7029bd7c1874ffd90fdf2f Wed Jul 8 09:23:00 2026 -0700
    redoing slides as embedded html slide deck, refs #37292
• docs/slideDecks/tutorial3-clinical/presentation/index.html
  • lines changed 610, context: html, text, full: html, text
    6d4b6f98a4144956ad7029bd7c1874ffd90fdf2f Wed Jul 8 09:23:00 2026 -0700
    redoing slides as embedded html slide deck, refs #37292
• docs/slideDecks/tutorial3-clinical/tableOfContents/index.html
  • lines changed 102, context: html, text, full: html, text
    6d4b6f98a4144956ad7029bd7c1874ffd90fdf2f Wed Jul 8 09:23:00 2026 -0700
    redoing slides as embedded html slide deck, refs #37292
• docs/slideDecks/tutorial4-clinical-cases/presentation/index.html
  • lines changed 335, context: html, text, full: html, text
    6d4b6f98a4144956ad7029bd7c1874ffd90fdf2f Wed Jul 8 09:23:00 2026 -0700
    redoing slides as embedded html slide deck, refs #37292
• docs/slideDecks/tutorial4-clinical-cases/tableOfContents/index.html
  • lines changed 97, context: html, text, full: html, text
    6d4b6f98a4144956ad7029bd7c1874ffd90fdf2f Wed Jul 8 09:23:00 2026 -0700
    redoing slides as embedded html slide deck, refs #37292
• docs/slideDecks/tutorial5-teaching/presentation/index.html
  • lines changed 346, context: html, text, full: html, text
    6d4b6f98a4144956ad7029bd7c1874ffd90fdf2f Wed Jul 8 09:23:00 2026 -0700
    redoing slides as embedded html slide deck, refs #37292
• docs/slideDecks/tutorial5-teaching/tableOfContents/index.html
  • lines changed 92, context: html, text, full: html, text
    6d4b6f98a4144956ad7029bd7c1874ffd90fdf2f Wed Jul 8 09:23:00 2026 -0700
    redoing slides as embedded html slide deck, refs #37292
• src/hg/hgBlat/hgBlat.c
  • lines changed 4, context: html, text, full: html, text
    94041c12e043016875ebd340568bda0ccaf122f6 Wed Jul 8 13:53:22 2026 -0700
    Add db= to cross-CGI hgTracks/hgTrackUi/hgc links to prevent wrong-assembly errors. refs #37840 Completes the incomplete work from #26892: links from the browser to a different CGI omitted db=, so the target CGI fell back to the cart's db (often wrong), producing "Can't find <track> in track database <db>" errors and broken shared links. Adds the current-assembly db to link builders across hgTracks (chromGraphTrack, expRatioTracks, config ruler and per-track configure links, variation), hgVai, hgFileUi, hgGtexTrackSettings, hgBlat, hgGene, hgNear, the barChart/GTEx faceted UI (facetedBar, barChartUi, gtexUi), and the hgTrackUi group-configure link.
• src/hg/hgFileUi/hgFileUi.c
  • lines changed 3, context: html, text, full: html, text
    94041c12e043016875ebd340568bda0ccaf122f6 Wed Jul 8 13:53:22 2026 -0700
    Add db= to cross-CGI hgTracks/hgTrackUi/hgc links to prevent wrong-assembly errors. refs #37840 Completes the incomplete work from #26892: links from the browser to a different CGI omitted db=, so the target CGI fell back to the cart's db (often wrong), producing "Can't find <track> in track database <db>" errors and broken shared links. Adds the current-assembly db to link builders across hgTracks (chromGraphTrack, expRatioTracks, config ruler and per-track configure links, variation), hgVai, hgFileUi, hgGtexTrackSettings, hgBlat, hgGene, hgNear, the barChart/GTEx faceted UI (facetedBar, barChartUi, gtexUi), and the hgTrackUi group-configure link.
• src/hg/hgGene/pseudoGene.c
  • lines changed 1, context: html, text, full: html, text
    94041c12e043016875ebd340568bda0ccaf122f6 Wed Jul 8 13:53:22 2026 -0700
    Add db= to cross-CGI hgTracks/hgTrackUi/hgc links to prevent wrong-assembly errors. refs #37840 Completes the incomplete work from #26892: links from the browser to a different CGI omitted db=, so the target CGI fell back to the cart's db (often wrong), producing "Can't find <track> in track database <db>" errors and broken shared links. Adds the current-assembly db to link builders across hgTracks (chromGraphTrack, expRatioTracks, config ruler and per-track configure links, variation), hgVai, hgFileUi, hgGtexTrackSettings, hgBlat, hgGene, hgNear, the barChart/GTEx faceted UI (facetedBar, barChartUi, gtexUi), and the hgTrackUi group-configure link.
• src/hg/hgGene/sequence.c
  • lines changed 6, context: html, text, full: html, text
    94041c12e043016875ebd340568bda0ccaf122f6 Wed Jul 8 13:53:22 2026 -0700
    Add db= to cross-CGI hgTracks/hgTrackUi/hgc links to prevent wrong-assembly errors. refs #37840 Completes the incomplete work from #26892: links from the browser to a different CGI omitted db=, so the target CGI fell back to the cart's db (often wrong), producing "Can't find <track> in track database <db>" errors and broken shared links. Adds the current-assembly db to link builders across hgTracks (chromGraphTrack, expRatioTracks, config ruler and per-track configure links, variation), hgVai, hgFileUi, hgGtexTrackSettings, hgBlat, hgGene, hgNear, the barChart/GTEx faceted UI (facetedBar, barChartUi, gtexUi), and the hgTrackUi group-configure link.
• src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c
  • lines changed 2, context: html, text, full: html, text
    94041c12e043016875ebd340568bda0ccaf122f6 Wed Jul 8 13:53:22 2026 -0700
    Add db= to cross-CGI hgTracks/hgTrackUi/hgc links to prevent wrong-assembly errors. refs #37840 Completes the incomplete work from #26892: links from the browser to a different CGI omitted db=, so the target CGI fell back to the cart's db (often wrong), producing "Can't find <track> in track database <db>" errors and broken shared links. Adds the current-assembly db to link builders across hgTracks (chromGraphTrack, expRatioTracks, config ruler and per-track configure links, variation), hgVai, hgFileUi, hgGtexTrackSettings, hgBlat, hgGene, hgNear, the barChart/GTEx faceted UI (facetedBar, barChartUi, gtexUi), and the hgTrackUi group-configure link.
• src/hg/hgLogin/hgLogin.c
  • lines changed 9, context: html, text, full: html, text
    32d8c9cb1c107f4bee849bdbf0db07b6bfb2a94d Wed Jul 8 05:35:07 2026 -0700
    hgLogin: require new user names to be at least two characters, refs #10138 Single-character user names are now reserved ("l" is used internally for anonymous shared-session links), so signup() rejects them. The check is only in the account-creation path, so existing accounts -- including any single-character ones -- keep working for login and sessions.
• src/hg/hgMenubar/hgMenubar.c
  • lines changed 40, context: html, text, full: html, text
    c5a326f3cc42beca0b59c284a2819763548c166a Wed Jul 8 05:31:13 2026 -0700
    Add top-right "Share a link" and "Login" links to the menu bar, refs #10138 New js/topLinks.js drives two links at the top-right of the menu bar on all pages: - Login: links to the login page when logged out; when logged in it shows the username and opens an account dialog (My Sessions / My Custom Tracks / My Track Hubs, change password, sign out). - Share a link: on hgTracks, one click saves the current view as a session and shows a copyable short link, with an optional "Specify name" rename step; works logged-in or anonymously (reserved user "l"). On hgTrackUi and the hgc/hgGene item-details popup it instead shares the page URL with the hgsid stripped and the db argument kept. hgSession gains two JSON endpoints (hgS_doSaveSessionJson, hgS_doRenameSessionJson) that reuse saveCartAsSession() and addSessionLink(). The menu bar is patched in lib/web.c (CGI pages) and hgMenubar.c (static pages) via comment placeholders in globalNavBar.inc. On narrow/phone screens the links collapse into a menu icon with a dropdown so they no longer overlap the menu.
• src/hg/hgSession/hgSession.c
  • lines changed 145, context: html, text, full: html, text
    c5a326f3cc42beca0b59c284a2819763548c166a Wed Jul 8 05:31:13 2026 -0700
    Add top-right "Share a link" and "Login" links to the menu bar, refs #10138 New js/topLinks.js drives two links at the top-right of the menu bar on all pages: - Login: links to the login page when logged out; when logged in it shows the username and opens an account dialog (My Sessions / My Custom Tracks / My Track Hubs, change password, sign out). - Share a link: on hgTracks, one click saves the current view as a session and shows a copyable short link, with an optional "Specify name" rename step; works logged-in or anonymously (reserved user "l"). On hgTrackUi and the hgc/hgGene item-details popup it instead shares the page URL with the hgsid stripped and the db argument kept. hgSession gains two JSON endpoints (hgS_doSaveSessionJson, hgS_doRenameSessionJson) that reuse saveCartAsSession() and addSessionLink(). The menu bar is patched in lib/web.c (CGI pages) and hgMenubar.c (static pages) via comment placeholders in globalNavBar.inc. On narrow/phone screens the links collapse into a menu icon with a dropdown so they no longer overlap the menu.
• src/hg/hgSession/hgSession.h
  • lines changed 7, context: html, text, full: html, text
    c5a326f3cc42beca0b59c284a2819763548c166a Wed Jul 8 05:31:13 2026 -0700
    Add top-right "Share a link" and "Login" links to the menu bar, refs #10138 New js/topLinks.js drives two links at the top-right of the menu bar on all pages: - Login: links to the login page when logged out; when logged in it shows the username and opens an account dialog (My Sessions / My Custom Tracks / My Track Hubs, change password, sign out). - Share a link: on hgTracks, one click saves the current view as a session and shows a copyable short link, with an optional "Specify name" rename step; works logged-in or anonymously (reserved user "l"). On hgTrackUi and the hgc/hgGene item-details popup it instead shares the page URL with the hgsid stripped and the db argument kept. hgSession gains two JSON endpoints (hgS_doSaveSessionJson, hgS_doRenameSessionJson) that reuse saveCartAsSession() and addSessionLink(). The menu bar is patched in lib/web.c (CGI pages) and hgMenubar.c (static pages) via comment placeholders in globalNavBar.inc. On narrow/phone screens the links collapse into a menu icon with a dropdown so they no longer overlap the menu.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    94041c12e043016875ebd340568bda0ccaf122f6 Wed Jul 8 13:53:22 2026 -0700
    Add db= to cross-CGI hgTracks/hgTrackUi/hgc links to prevent wrong-assembly errors. refs #37840 Completes the incomplete work from #26892: links from the browser to a different CGI omitted db=, so the target CGI fell back to the cart's db (often wrong), producing "Can't find <track> in track database <db>" errors and broken shared links. Adds the current-assembly db to link builders across hgTracks (chromGraphTrack, expRatioTracks, config ruler and per-track configure links, variation), hgVai, hgFileUi, hgGtexTrackSettings, hgBlat, hgGene, hgNear, the barChart/GTEx faceted UI (facetedBar, barChartUi, gtexUi), and the hgTrackUi group-configure link.
  • lines changed 14, context: html, text, full: html, text
    2d9d194b4bb0e2ec25ca1d45739fdd418632dbb8 Wed Jul 8 13:53:54 2026 -0700
    Add db= to same-CGI self-links in hgTrackUi and hgc. refs #37840 Extends #37840 to same-CGI links that omitted db= and relied on the cart db, which still broke as shared, bookmarked, or search-indexed URLs. In hgTrackUi adds db to the superTrack member list, container-configure, description, sibling-track, duplicate/unduplicate, and quickLift-remove links. In hgc adds the current assembly's db to the shared anchor helpers (hgcAnchorSomewhereExt, hgcAnchorPosition, hgcAnchorWindow, hgcAnchorTranslatedChain, hgcAnchorPseudoGene), covering all their callers, plus the getDna, htcExtSeq, refGene, stsMap, cutter, cgapSage, mgc, peakClusters, regMotif, and pubs links. The foreign-assembly variant hgcAnchorSomewhereDb and the db2=/qlSourceDb= params are left untouched.
• src/hg/hgTracks/cds.c
  • lines changed 9, context: html, text, full: html, text
    4aa77873cb618e254b2f90d091d7bdef844947c2 Wed Jul 8 04:28:42 2026 -0700
    Let assembly hubs assign genetic codes per sequence for amino acid display Adds a "codonTable" genomes.txt setting, e.g. "codonTable default=1 NC_017929.1=13", so an assembly hub can pick the NCBI translation table used to show amino acids for each sequence. New hGeneticCodeForChrom(db, chrom) in hdb.c resolves the code (per-db cached), falling back to the previous behavior: chrM/chrMT use the vertebrate mitochondrial code, everything else the standard code. Wired into the two browser display paths, which both go through cds.c's baseColorLookupCodon: the base position track three-frame translation and codon-colored annotation tracks such as gene predictions (also PSL/BAM). Also used for the hgc SNP amino acid details, and genePredTranslate gains a db parameter (genePredToProt gains an optional -db flag) so command-line translation can honor the same setting. Documented in assemblyHubHelp.html. refs #16550
• src/hg/hgTracks/chromGraphTrack.c
  • lines changed 2, context: html, text, full: html, text
    94041c12e043016875ebd340568bda0ccaf122f6 Wed Jul 8 13:53:22 2026 -0700
    Add db= to cross-CGI hgTracks/hgTrackUi/hgc links to prevent wrong-assembly errors. refs #37840 Completes the incomplete work from #26892: links from the browser to a different CGI omitted db=, so the target CGI fell back to the cart's db (often wrong), producing "Can't find <track> in track database <db>" errors and broken shared links. Adds the current-assembly db to link builders across hgTracks (chromGraphTrack, expRatioTracks, config ruler and per-track configure links, variation), hgVai, hgFileUi, hgGtexTrackSettings, hgBlat, hgGene, hgNear, the barChart/GTEx faceted UI (facetedBar, barChartUi, gtexUi), and the hgTrackUi group-configure link.
• src/hg/hgTracks/config.c
  • lines changed 4, context: html, text, full: html, text
    94041c12e043016875ebd340568bda0ccaf122f6 Wed Jul 8 13:53:22 2026 -0700
    Add db= to cross-CGI hgTracks/hgTrackUi/hgc links to prevent wrong-assembly errors. refs #37840 Completes the incomplete work from #26892: links from the browser to a different CGI omitted db=, so the target CGI fell back to the cart's db (often wrong), producing "Can't find <track> in track database <db>" errors and broken shared links. Adds the current-assembly db to link builders across hgTracks (chromGraphTrack, expRatioTracks, config ruler and per-track configure links, variation), hgVai, hgFileUi, hgGtexTrackSettings, hgBlat, hgGene, hgNear, the barChart/GTEx faceted UI (facetedBar, barChartUi, gtexUi), and the hgTrackUi group-configure link.
• src/hg/hgTracks/expRatioTracks.c
  • lines changed 3, context: html, text, full: html, text
    94041c12e043016875ebd340568bda0ccaf122f6 Wed Jul 8 13:53:22 2026 -0700
    Add db= to cross-CGI hgTracks/hgTrackUi/hgc links to prevent wrong-assembly errors. refs #37840 Completes the incomplete work from #26892: links from the browser to a different CGI omitted db=, so the target CGI fell back to the cart's db (often wrong), producing "Can't find <track> in track database <db>" errors and broken shared links. Adds the current-assembly db to link builders across hgTracks (chromGraphTrack, expRatioTracks, config ruler and per-track configure links, variation), hgVai, hgFileUi, hgGtexTrackSettings, hgBlat, hgGene, hgNear, the barChart/GTEx faceted UI (facetedBar, barChartUi, gtexUi), and the hgTrackUi group-configure link.
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    94041c12e043016875ebd340568bda0ccaf122f6 Wed Jul 8 13:53:22 2026 -0700
    Add db= to cross-CGI hgTracks/hgTrackUi/hgc links to prevent wrong-assembly errors. refs #37840 Completes the incomplete work from #26892: links from the browser to a different CGI omitted db=, so the target CGI fell back to the cart's db (often wrong), producing "Can't find <track> in track database <db>" errors and broken shared links. Adds the current-assembly db to link builders across hgTracks (chromGraphTrack, expRatioTracks, config ruler and per-track configure links, variation), hgVai, hgFileUi, hgGtexTrackSettings, hgBlat, hgGene, hgNear, the barChart/GTEx faceted UI (facetedBar, barChartUi, gtexUi), and the hgTrackUi group-configure link.
  • lines changed 8, context: html, text, full: html, text
    94f9b53d3db05371699a8fae11407acf0b30e02f Wed Jul 8 16:22:22 2026 -0700
    Fix three base-position ruler click issues: show "1 base" instead of "0 bases" at single-base zoom, make single clicks recenter symmetrically instead of drifting one base left, and stop a click on the ruler track's grey side-label strip from hijacking the config popup to do a zoom. refs #27113
• src/hg/hgTracks/simpleTracks.c
  • lines changed 4, context: html, text, full: html, text
    3126025a52d8ee7cd03a13869722f78f996063ad Fri Jul 10 04:52:16 2026 -0700
    Fix codon mouseover protein position: 1-based single p. and singular label The zoomed-in codon mouseover printed the protein position as a 0-based two-position range, e.g. the first codon read c.1-3 (p.0-1). A codon is a single amino acid, and p. should be 1-based to match the adjacent c. numbering, so it now reads c.1-3 (p.1). Also corrected the label from the plural Codons to Codon since each mouseover covers one codon. refs #37773
• src/hg/hgTracks/variation.c
  • lines changed 8, context: html, text, full: html, text
    94041c12e043016875ebd340568bda0ccaf122f6 Wed Jul 8 13:53:22 2026 -0700
    Add db= to cross-CGI hgTracks/hgTrackUi/hgc links to prevent wrong-assembly errors. refs #37840 Completes the incomplete work from #26892: links from the browser to a different CGI omitted db=, so the target CGI fell back to the cart's db (often wrong), producing "Can't find <track> in track database <db>" errors and broken shared links. Adds the current-assembly db to link builders across hgTracks (chromGraphTrack, expRatioTracks, config ruler and per-track configure links, variation), hgVai, hgFileUi, hgGtexTrackSettings, hgBlat, hgGene, hgNear, the barChart/GTEx faceted UI (facetedBar, barChartUi, gtexUi), and the hgTrackUi group-configure link.
• src/hg/hgVai/hgVai.c
  • lines changed 4, context: html, text, full: html, text
    94041c12e043016875ebd340568bda0ccaf122f6 Wed Jul 8 13:53:22 2026 -0700
    Add db= to cross-CGI hgTracks/hgTrackUi/hgc links to prevent wrong-assembly errors. refs #37840 Completes the incomplete work from #26892: links from the browser to a different CGI omitted db=, so the target CGI fell back to the cart's db (often wrong), producing "Can't find <track> in track database <db>" errors and broken shared links. Adds the current-assembly db to link builders across hgTracks (chromGraphTrack, expRatioTracks, config ruler and per-track configure links, variation), hgVai, hgFileUi, hgGtexTrackSettings, hgBlat, hgGene, hgNear, the barChart/GTEx faceted UI (facetedBar, barChartUi, gtexUi), and the hgTrackUi group-configure link.
• src/hg/hgc/bigRmskClick.c
  • lines changed 2, context: html, text, full: html, text
    2d9d194b4bb0e2ec25ca1d45739fdd418632dbb8 Wed Jul 8 13:53:54 2026 -0700
    Add db= to same-CGI self-links in hgTrackUi and hgc. refs #37840 Extends #37840 to same-CGI links that omitted db= and relied on the cart db, which still broke as shared, bookmarked, or search-indexed URLs. In hgTrackUi adds db to the superTrack member list, container-configure, description, sibling-track, duplicate/unduplicate, and quickLift-remove links. In hgc adds the current assembly's db to the shared anchor helpers (hgcAnchorSomewhereExt, hgcAnchorPosition, hgcAnchorWindow, hgcAnchorTranslatedChain, hgcAnchorPseudoGene), covering all their callers, plus the getDna, htcExtSeq, refGene, stsMap, cutter, cgapSage, mgc, peakClusters, regMotif, and pubs links. The foreign-assembly variant hgcAnchorSomewhereDb and the db2=/qlSourceDb= params are left untouched.
• src/hg/hgc/cgapSageClick.c
  • lines changed 4, context: html, text, full: html, text
    2d9d194b4bb0e2ec25ca1d45739fdd418632dbb8 Wed Jul 8 13:53:54 2026 -0700
    Add db= to same-CGI self-links in hgTrackUi and hgc. refs #37840 Extends #37840 to same-CGI links that omitted db= and relied on the cart db, which still broke as shared, bookmarked, or search-indexed URLs. In hgTrackUi adds db to the superTrack member list, container-configure, description, sibling-track, duplicate/unduplicate, and quickLift-remove links. In hgc adds the current assembly's db to the shared anchor helpers (hgcAnchorSomewhereExt, hgcAnchorPosition, hgcAnchorWindow, hgcAnchorTranslatedChain, hgcAnchorPseudoGene), covering all their callers, plus the getDna, htcExtSeq, refGene, stsMap, cutter, cgapSage, mgc, peakClusters, regMotif, and pubs links. The foreign-assembly variant hgcAnchorSomewhereDb and the db2=/qlSourceDb= params are left untouched.
• src/hg/hgc/facetedBar.c
  • lines changed 1, context: html, text, full: html, text
    94041c12e043016875ebd340568bda0ccaf122f6 Wed Jul 8 13:53:22 2026 -0700
    Add db= to cross-CGI hgTracks/hgTrackUi/hgc links to prevent wrong-assembly errors. refs #37840 Completes the incomplete work from #26892: links from the browser to a different CGI omitted db=, so the target CGI fell back to the cart's db (often wrong), producing "Can't find <track> in track database <db>" errors and broken shared links. Adds the current-assembly db to link builders across hgTracks (chromGraphTrack, expRatioTracks, config ruler and per-track configure links, variation), hgVai, hgFileUi, hgGtexTrackSettings, hgBlat, hgGene, hgNear, the barChart/GTEx faceted UI (facetedBar, barChartUi, gtexUi), and the hgTrackUi group-configure link.
• src/hg/hgc/hgc.c
  • lines changed 9, context: html, text, full: html, text
    4aa77873cb618e254b2f90d091d7bdef844947c2 Wed Jul 8 04:28:42 2026 -0700
    Let assembly hubs assign genetic codes per sequence for amino acid display Adds a "codonTable" genomes.txt setting, e.g. "codonTable default=1 NC_017929.1=13", so an assembly hub can pick the NCBI translation table used to show amino acids for each sequence. New hGeneticCodeForChrom(db, chrom) in hdb.c resolves the code (per-db cached), falling back to the previous behavior: chrM/chrMT use the vertebrate mitochondrial code, everything else the standard code. Wired into the two browser display paths, which both go through cds.c's baseColorLookupCodon: the base position track three-frame translation and codon-colored annotation tracks such as gene predictions (also PSL/BAM). Also used for the hgc SNP amino acid details, and genePredTranslate gains a db parameter (genePredToProt gains an optional -db flag) so command-line translation can honor the same setting. Documented in assemblyHubHelp.html. refs #16550
  • lines changed 35, context: html, text, full: html, text
    2d9d194b4bb0e2ec25ca1d45739fdd418632dbb8 Wed Jul 8 13:53:54 2026 -0700
    Add db= to same-CGI self-links in hgTrackUi and hgc. refs #37840 Extends #37840 to same-CGI links that omitted db= and relied on the cart db, which still broke as shared, bookmarked, or search-indexed URLs. In hgTrackUi adds db to the superTrack member list, container-configure, description, sibling-track, duplicate/unduplicate, and quickLift-remove links. In hgc adds the current assembly's db to the shared anchor helpers (hgcAnchorSomewhereExt, hgcAnchorPosition, hgcAnchorWindow, hgcAnchorTranslatedChain, hgcAnchorPseudoGene), covering all their callers, plus the getDna, htcExtSeq, refGene, stsMap, cutter, cgapSage, mgc, peakClusters, regMotif, and pubs links. The foreign-assembly variant hgcAnchorSomewhereDb and the db2=/qlSourceDb= params are left untouched.
• src/hg/hgc/mgcClick.c
  • lines changed 2, context: html, text, full: html, text
    2d9d194b4bb0e2ec25ca1d45739fdd418632dbb8 Wed Jul 8 13:53:54 2026 -0700
    Add db= to same-CGI self-links in hgTrackUi and hgc. refs #37840 Extends #37840 to same-CGI links that omitted db= and relied on the cart db, which still broke as shared, bookmarked, or search-indexed URLs. In hgTrackUi adds db to the superTrack member list, container-configure, description, sibling-track, duplicate/unduplicate, and quickLift-remove links. In hgc adds the current assembly's db to the shared anchor helpers (hgcAnchorSomewhereExt, hgcAnchorPosition, hgcAnchorWindow, hgcAnchorTranslatedChain, hgcAnchorPseudoGene), covering all their callers, plus the getDna, htcExtSeq, refGene, stsMap, cutter, cgapSage, mgc, peakClusters, regMotif, and pubs links. The foreign-assembly variant hgcAnchorSomewhereDb and the db2=/qlSourceDb= params are left untouched.
• src/hg/hgc/peakClusters.c
  • lines changed 2, context: html, text, full: html, text
    2d9d194b4bb0e2ec25ca1d45739fdd418632dbb8 Wed Jul 8 13:53:54 2026 -0700
    Add db= to same-CGI self-links in hgTrackUi and hgc. refs #37840 Extends #37840 to same-CGI links that omitted db= and relied on the cart db, which still broke as shared, bookmarked, or search-indexed URLs. In hgTrackUi adds db to the superTrack member list, container-configure, description, sibling-track, duplicate/unduplicate, and quickLift-remove links. In hgc adds the current assembly's db to the shared anchor helpers (hgcAnchorSomewhereExt, hgcAnchorPosition, hgcAnchorWindow, hgcAnchorTranslatedChain, hgcAnchorPseudoGene), covering all their callers, plus the getDna, htcExtSeq, refGene, stsMap, cutter, cgapSage, mgc, peakClusters, regMotif, and pubs links. The foreign-assembly variant hgcAnchorSomewhereDb and the db2=/qlSourceDb= params are left untouched.
• src/hg/hgc/pubs.c
  • lines changed 2, context: html, text, full: html, text
    2d9d194b4bb0e2ec25ca1d45739fdd418632dbb8 Wed Jul 8 13:53:54 2026 -0700
    Add db= to same-CGI self-links in hgTrackUi and hgc. refs #37840 Extends #37840 to same-CGI links that omitted db= and relied on the cart db, which still broke as shared, bookmarked, or search-indexed URLs. In hgTrackUi adds db to the superTrack member list, container-configure, description, sibling-track, duplicate/unduplicate, and quickLift-remove links. In hgc adds the current assembly's db to the shared anchor helpers (hgcAnchorSomewhereExt, hgcAnchorPosition, hgcAnchorWindow, hgcAnchorTranslatedChain, hgcAnchorPseudoGene), covering all their callers, plus the getDna, htcExtSeq, refGene, stsMap, cutter, cgapSage, mgc, peakClusters, regMotif, and pubs links. The foreign-assembly variant hgcAnchorSomewhereDb and the db2=/qlSourceDb= params are left untouched.
• src/hg/hgc/regMotif.c
  • lines changed 1, context: html, text, full: html, text
    2d9d194b4bb0e2ec25ca1d45739fdd418632dbb8 Wed Jul 8 13:53:54 2026 -0700
    Add db= to same-CGI self-links in hgTrackUi and hgc. refs #37840 Extends #37840 to same-CGI links that omitted db= and relied on the cart db, which still broke as shared, bookmarked, or search-indexed URLs. In hgTrackUi adds db to the superTrack member list, container-configure, description, sibling-track, duplicate/unduplicate, and quickLift-remove links. In hgc adds the current assembly's db to the shared anchor helpers (hgcAnchorSomewhereExt, hgcAnchorPosition, hgcAnchorWindow, hgcAnchorTranslatedChain, hgcAnchorPseudoGene), covering all their callers, plus the getDna, htcExtSeq, refGene, stsMap, cutter, cgapSage, mgc, peakClusters, regMotif, and pubs links. The foreign-assembly variant hgcAnchorSomewhereDb and the db2=/qlSourceDb= params are left untouched.
• src/hg/hgc/rmskJoinedClick.c
  • lines changed 2, context: html, text, full: html, text
    2d9d194b4bb0e2ec25ca1d45739fdd418632dbb8 Wed Jul 8 13:53:54 2026 -0700
    Add db= to same-CGI self-links in hgTrackUi and hgc. refs #37840 Extends #37840 to same-CGI links that omitted db= and relied on the cart db, which still broke as shared, bookmarked, or search-indexed URLs. In hgTrackUi adds db to the superTrack member list, container-configure, description, sibling-track, duplicate/unduplicate, and quickLift-remove links. In hgc adds the current assembly's db to the shared anchor helpers (hgcAnchorSomewhereExt, hgcAnchorPosition, hgcAnchorWindow, hgcAnchorTranslatedChain, hgcAnchorPseudoGene), covering all their callers, plus the getDna, htcExtSeq, refGene, stsMap, cutter, cgapSage, mgc, peakClusters, regMotif, and pubs links. The foreign-assembly variant hgcAnchorSomewhereDb and the db2=/qlSourceDb= params are left untouched.
• src/hg/htdocs/goldenPath/help/assemblyHubHelp.html
  • lines changed 38, context: html, text, full: html, text
    4aa77873cb618e254b2f90d091d7bdef844947c2 Wed Jul 8 04:28:42 2026 -0700
    Let assembly hubs assign genetic codes per sequence for amino acid display Adds a "codonTable" genomes.txt setting, e.g. "codonTable default=1 NC_017929.1=13", so an assembly hub can pick the NCBI translation table used to show amino acids for each sequence. New hGeneticCodeForChrom(db, chrom) in hdb.c resolves the code (per-db cached), falling back to the previous behavior: chrM/chrMT use the vertebrate mitochondrial code, everything else the standard code. Wired into the two browser display paths, which both go through cds.c's baseColorLookupCodon: the base position track three-frame translation and codon-colored annotation tracks such as gene predictions (also PSL/BAM). Also used for the hgc SNP amino acid details, and genePredTranslate gains a db parameter (genePredToProt gains an optional -db flag) so command-line translation can honor the same setting. Documented in assemblyHubHelp.html. refs #16550
• src/hg/htdocs/goldenPath/help/trackDb/changes.html
  • lines changed 21, context: html, text, full: html, text
    aac2d475d4e656e52e1b56fc7a1891d56b513220 Wed Jul 8 10:01:35 2026 -0700
    Log codonTable and chromAuthority genomes.txt settings in trackDb changes.html These are assembly hub genome-stanza (genomes.txt) settings, not track settings, so each row is flagged accordingly and links to assemblyHubHelp.html. refs #16550
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 63, context: html, text, full: html, text
    d58a6063a92330e5224c8139443f3571e85fb000 Tue Jul 7 15:08:55 2026 -0700
    Announcing the v500 CGI release, refs #37702
  • lines changed 14, context: html, text, full: html, text
    44a7bbc4c8aa983e1f075c25c240e6f479e99dc3 Wed Jul 8 09:24:27 2026 -0700
    gentle intro to v500 release message
  • lines changed 2, context: html, text, full: html, text
    fe0627da07b9f989bc642d824af381968163d9a8 Wed Jul 8 13:40:04 2026 -0700
    varFreqs: move ALFA to Global reference panels; add shared-sample bias caveat to description pages. refs #36642 Per Max's post-release feedback on the ticket: ALFA is not a European cohort, it is an NCBI aggregator of dbGaP studies from many sources. Moved from Europe to Global reference panels in the newsarch entry. Also adds a shared-sample bias caveat to the Pooled allele frequency section of both varFreqsAffected.html and varFreqsBackground.html. The background page cites the concrete overlaps (1000 Genomes in both gnomAD HGDP+1kG and HRC; HGDP/SGDP; AllOfUs/TOPMed; ALFA aggregating dbGaP studies used elsewhere). The affected page cites the SPARK WGS cohort being a subset of SPARK WES. Both explain that pooled AN is inflated and pooled AF is skewed toward the frequency in the shared subset, and point users to the per-cohort AC/AF/AN fields for unbiased single-cohort numbers.
  • lines changed 221, context: html, text, full: html, text
    3f7562cabb5334750a34f8c0ee1681528cb6c84b Wed Jul 8 17:14:41 2026 -0700
    News post for the ENCODE4 cCREs and ENCODE4 Regulation tracks (hg38 and mm10). refs #37845 Announces the full ENCODE4 cCREs and ENCODE4 Regulation release, and notes that these tracks are now the default regulation tracks on hg38 and mm10, replacing the ENCODE3 cCREs and Regulation tracks (which remain available for archival use). Also reiterates the hg38 cCREs data originally announced in January 2026 for completeness of this combined release.
• src/hg/htdocs/images/newsArchImages/UCSCReleaseDownloads.png
  • lines changed 0, context: html, text, full: html, text
    d58a6063a92330e5224c8139443f3571e85fb000 Tue Jul 7 15:08:55 2026 -0700
    Announcing the v500 CGI release, refs #37702
• src/hg/htdocs/images/newsArchImages/intronerator.png
  • lines changed 0, context: html, text, full: html, text
    d58a6063a92330e5224c8139443f3571e85fb000 Tue Jul 7 15:08:55 2026 -0700
    Announcing the v500 CGI release, refs #37702
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 5, context: html, text, full: html, text
    c5a326f3cc42beca0b59c284a2819763548c166a Wed Jul 8 05:31:13 2026 -0700
    Add top-right "Share a link" and "Login" links to the menu bar, refs #10138 New js/topLinks.js drives two links at the top-right of the menu bar on all pages: - Login: links to the login page when logged out; when logged in it shows the username and opens an account dialog (My Sessions / My Custom Tracks / My Track Hubs, change password, sign out). - Share a link: on hgTracks, one click saves the current view as a session and shows a copyable short link, with an optional "Specify name" rename step; works logged-in or anonymously (reserved user "l"). On hgTrackUi and the hgc/hgGene item-details popup it instead shares the page URL with the hgsid stripped and the db argument kept. hgSession gains two JSON endpoints (hgS_doSaveSessionJson, hgS_doRenameSessionJson) that reuse saveCartAsSession() and addSessionLink(). The menu bar is patched in lib/web.c (CGI pages) and hgMenubar.c (static pages) via comment placeholders in globalNavBar.inc. On narrow/phone screens the links collapse into a menu icon with a dropdown so they no longer overlap the menu.
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    d58a6063a92330e5224c8139443f3571e85fb000 Tue Jul 7 15:08:55 2026 -0700
    Announcing the v500 CGI release, refs #37702
• src/hg/htdocs/staff.html
  • lines changed 12, context: html, text, full: html, text
    ca90693eb49a0c410c41381695cbf88a73e77f41 Tue Jul 7 15:48:06 2026 -0700
    Adding Theo to the staff page. Moving Jorge to the project alumni section. Adding the 2026 student interns, no Redmine
  • lines changed 3, context: html, text, full: html, text
    e16cd87737e2f7574cb98af5f65c5c6cda1c59cd Tue Jul 7 15:54:54 2026 -0700
    Editing the spacing for the student interns so they are all aligned, no Redmine
• src/hg/htdocs/style/nice_menu.css
  • lines changed 65, context: html, text, full: html, text
    c5a326f3cc42beca0b59c284a2819763548c166a Wed Jul 8 05:31:13 2026 -0700
    Add top-right "Share a link" and "Login" links to the menu bar, refs #10138 New js/topLinks.js drives two links at the top-right of the menu bar on all pages: - Login: links to the login page when logged out; when logged in it shows the username and opens an account dialog (My Sessions / My Custom Tracks / My Track Hubs, change password, sign out). - Share a link: on hgTracks, one click saves the current view as a session and shows a copyable short link, with an optional "Specify name" rename step; works logged-in or anonymously (reserved user "l"). On hgTrackUi and the hgc/hgGene item-details popup it instead shares the page URL with the hgsid stripped and the db argument kept. hgSession gains two JSON endpoints (hgS_doSaveSessionJson, hgS_doRenameSessionJson) that reuse saveCartAsSession() and addSessionLink(). The menu bar is patched in lib/web.c (CGI pages) and hgMenubar.c (static pages) via comment placeholders in globalNavBar.inc. On narrow/phone screens the links collapse into a menu icon with a dropdown so they no longer overlap the menu.
• src/hg/hubApi/tests/expected/list27.gz
  • lines changed 0, context: html, text, full: html, text
    545f71a129ea31257152009988fb6fd9fa3f2af9 Fri Jul 10 10:43:38 2026 -0700
    Refresh list27 expected output to drop the clade field, which the genark table no longer carries. refs #36463
• src/hg/inc/genePred.h
  • lines changed 5, context: html, text, full: html, text
    4aa77873cb618e254b2f90d091d7bdef844947c2 Wed Jul 8 04:28:42 2026 -0700
    Let assembly hubs assign genetic codes per sequence for amino acid display Adds a "codonTable" genomes.txt setting, e.g. "codonTable default=1 NC_017929.1=13", so an assembly hub can pick the NCBI translation table used to show amino acids for each sequence. New hGeneticCodeForChrom(db, chrom) in hdb.c resolves the code (per-db cached), falling back to the previous behavior: chrM/chrMT use the vertebrate mitochondrial code, everything else the standard code. Wired into the two browser display paths, which both go through cds.c's baseColorLookupCodon: the base position track three-frame translation and codon-colored annotation tracks such as gene predictions (also PSL/BAM). Also used for the hgc SNP amino acid details, and genePredTranslate gains a db parameter (genePredToProt gains an optional -db flag) so command-line translation can honor the same setting. Documented in assemblyHubHelp.html. refs #16550
• src/hg/inc/hdb.h
  • lines changed 7, context: html, text, full: html, text
    4aa77873cb618e254b2f90d091d7bdef844947c2 Wed Jul 8 04:28:42 2026 -0700
    Let assembly hubs assign genetic codes per sequence for amino acid display Adds a "codonTable" genomes.txt setting, e.g. "codonTable default=1 NC_017929.1=13", so an assembly hub can pick the NCBI translation table used to show amino acids for each sequence. New hGeneticCodeForChrom(db, chrom) in hdb.c resolves the code (per-db cached), falling back to the previous behavior: chrM/chrMT use the vertebrate mitochondrial code, everything else the standard code. Wired into the two browser display paths, which both go through cds.c's baseColorLookupCodon: the base position track three-frame translation and codon-colored annotation tracks such as gene predictions (also PSL/BAM). Also used for the hgc SNP amino acid details, and genePredTranslate gains a db parameter (genePredToProt gains an optional -db flag) so command-line translation can honor the same setting. Documented in assemblyHubHelp.html. refs #16550
• src/hg/js/facetedComposite.js
  • lines changed 176, context: html, text, full: html, text
    dadb8aee84f0f7663c3cf0d82f1e44d3c8b7c888 Mon Jul 6 15:04:34 2026 -0700
    Some faceted composite tweaks - better support for color files (match ID instead of full string), better label support in general, reworded Selected to Active, refs #36320
• src/hg/js/hgTracks.js
  • lines changed 12, context: html, text, full: html, text
    c5a326f3cc42beca0b59c284a2819763548c166a Wed Jul 8 05:31:13 2026 -0700
    Add top-right "Share a link" and "Login" links to the menu bar, refs #10138 New js/topLinks.js drives two links at the top-right of the menu bar on all pages: - Login: links to the login page when logged out; when logged in it shows the username and opens an account dialog (My Sessions / My Custom Tracks / My Track Hubs, change password, sign out). - Share a link: on hgTracks, one click saves the current view as a session and shows a copyable short link, with an optional "Specify name" rename step; works logged-in or anonymously (reserved user "l"). On hgTrackUi and the hgc/hgGene item-details popup it instead shares the page URL with the hgsid stripped and the db argument kept. hgSession gains two JSON endpoints (hgS_doSaveSessionJson, hgS_doRenameSessionJson) that reuse saveCartAsSession() and addSessionLink(). The menu bar is patched in lib/web.c (CGI pages) and hgMenubar.c (static pages) via comment placeholders in globalNavBar.inc. On narrow/phone screens the links collapse into a menu icon with a dropdown so they no longer overlap the menu.
  • lines changed 16, context: html, text, full: html, text
    94f9b53d3db05371699a8fae11407acf0b30e02f Wed Jul 8 16:22:22 2026 -0700
    Fix three base-position ruler click issues: show "1 base" instead of "0 bases" at single-base zoom, make single clicks recenter symmetrically instead of drifting one base left, and stop a click on the ruler track's grey side-label strip from hijacking the config popup to do a zoom. refs #27113
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    c5a326f3cc42beca0b59c284a2819763548c166a Wed Jul 8 05:31:13 2026 -0700
    Add top-right "Share a link" and "Login" links to the menu bar, refs #10138 New js/topLinks.js drives two links at the top-right of the menu bar on all pages: - Login: links to the login page when logged out; when logged in it shows the username and opens an account dialog (My Sessions / My Custom Tracks / My Track Hubs, change password, sign out). - Share a link: on hgTracks, one click saves the current view as a session and shows a copyable short link, with an optional "Specify name" rename step; works logged-in or anonymously (reserved user "l"). On hgTrackUi and the hgc/hgGene item-details popup it instead shares the page URL with the hgsid stripped and the db argument kept. hgSession gains two JSON endpoints (hgS_doSaveSessionJson, hgS_doRenameSessionJson) that reuse saveCartAsSession() and addSessionLink(). The menu bar is patched in lib/web.c (CGI pages) and hgMenubar.c (static pages) via comment placeholders in globalNavBar.inc. On narrow/phone screens the links collapse into a menu icon with a dropdown so they no longer overlap the menu.
• src/hg/js/topLinks.js
  • lines changed 383, context: html, text, full: html, text
    c5a326f3cc42beca0b59c284a2819763548c166a Wed Jul 8 05:31:13 2026 -0700
    Add top-right "Share a link" and "Login" links to the menu bar, refs #10138 New js/topLinks.js drives two links at the top-right of the menu bar on all pages: - Login: links to the login page when logged out; when logged in it shows the username and opens an account dialog (My Sessions / My Custom Tracks / My Track Hubs, change password, sign out). - Share a link: on hgTracks, one click saves the current view as a session and shows a copyable short link, with an optional "Specify name" rename step; works logged-in or anonymously (reserved user "l"). On hgTrackUi and the hgc/hgGene item-details popup it instead shares the page URL with the hgsid stripped and the db argument kept. hgSession gains two JSON endpoints (hgS_doSaveSessionJson, hgS_doRenameSessionJson) that reuse saveCartAsSession() and addSessionLink(). The menu bar is patched in lib/web.c (CGI pages) and hgMenubar.c (static pages) via comment placeholders in globalNavBar.inc. On narrow/phone screens the links collapse into a menu icon with a dropdown so they no longer overlap the menu.
• src/hg/lib/barChartUi.c
  • lines changed 3, context: html, text, full: html, text
    94041c12e043016875ebd340568bda0ccaf122f6 Wed Jul 8 13:53:22 2026 -0700
    Add db= to cross-CGI hgTracks/hgTrackUi/hgc links to prevent wrong-assembly errors. refs #37840 Completes the incomplete work from #26892: links from the browser to a different CGI omitted db=, so the target CGI fell back to the cart's db (often wrong), producing "Can't find <track> in track database <db>" errors and broken shared links. Adds the current-assembly db to link builders across hgTracks (chromGraphTrack, expRatioTracks, config ruler and per-track configure links, variation), hgVai, hgFileUi, hgGtexTrackSettings, hgBlat, hgGene, hgNear, the barChart/GTEx faceted UI (facetedBar, barChartUi, gtexUi), and the hgTrackUi group-configure link.
• src/hg/lib/cart.c
  • lines changed 4, context: html, text, full: html, text
    c60812dd154dc99e8045db2d617ea969c26a28a2 Wed Jul 8 08:07:55 2026 -0700
    cart: treat an empty position value the same as unset, refs #37794 cartGetPosition only fell back to the assembly default position when the cart position was NULL or the literal string "default". A stale empty "position=" value (e.g. hgTracks?position=, or a position carried over from a different assembly via a db= link) is returned verbatim as "" by cartUsualString, so it slipped past that check and made hgTracks abort with "Please go back and enter a coordinate range...". Treat an empty string like unset so we fall back to the default position instead of crashing.
• src/hg/lib/genePred.c
  • lines changed 13, context: html, text, full: html, text
    4aa77873cb618e254b2f90d091d7bdef844947c2 Wed Jul 8 04:28:42 2026 -0700
    Let assembly hubs assign genetic codes per sequence for amino acid display Adds a "codonTable" genomes.txt setting, e.g. "codonTable default=1 NC_017929.1=13", so an assembly hub can pick the NCBI translation table used to show amino acids for each sequence. New hGeneticCodeForChrom(db, chrom) in hdb.c resolves the code (per-db cached), falling back to the previous behavior: chrM/chrMT use the vertebrate mitochondrial code, everything else the standard code. Wired into the two browser display paths, which both go through cds.c's baseColorLookupCodon: the base position track three-frame translation and codon-colored annotation tracks such as gene predictions (also PSL/BAM). Also used for the hgc SNP amino acid details, and genePredTranslate gains a db parameter (genePredToProt gains an optional -db flag) so command-line translation can honor the same setting. Documented in assemblyHubHelp.html. refs #16550
• src/hg/lib/gtexUi.c
  • lines changed 4, context: html, text, full: html, text
    94041c12e043016875ebd340568bda0ccaf122f6 Wed Jul 8 13:53:22 2026 -0700
    Add db= to cross-CGI hgTracks/hgTrackUi/hgc links to prevent wrong-assembly errors. refs #37840 Completes the incomplete work from #26892: links from the browser to a different CGI omitted db=, so the target CGI fell back to the cart's db (often wrong), producing "Can't find <track> in track database <db>" errors and broken shared links. Adds the current-assembly db to link builders across hgTracks (chromGraphTrack, expRatioTracks, config ruler and per-track configure links, variation), hgVai, hgFileUi, hgGtexTrackSettings, hgBlat, hgGene, hgNear, the barChart/GTEx faceted UI (facetedBar, barChartUi, gtexUi), and the hgTrackUi group-configure link.
• src/hg/lib/hdb.c
  • lines changed 78, context: html, text, full: html, text
    4aa77873cb618e254b2f90d091d7bdef844947c2 Wed Jul 8 04:28:42 2026 -0700
    Let assembly hubs assign genetic codes per sequence for amino acid display Adds a "codonTable" genomes.txt setting, e.g. "codonTable default=1 NC_017929.1=13", so an assembly hub can pick the NCBI translation table used to show amino acids for each sequence. New hGeneticCodeForChrom(db, chrom) in hdb.c resolves the code (per-db cached), falling back to the previous behavior: chrM/chrMT use the vertebrate mitochondrial code, everything else the standard code. Wired into the two browser display paths, which both go through cds.c's baseColorLookupCodon: the base position track three-frame translation and codon-colored annotation tracks such as gene predictions (also PSL/BAM). Also used for the hgc SNP amino acid details, and genePredTranslate gains a db parameter (genePredToProt gains an optional -db flag) so command-line translation can honor the same setting. Documented in assemblyHubHelp.html. refs #16550
• src/hg/lib/web.c
  • lines changed 58, context: html, text, full: html, text
    c5a326f3cc42beca0b59c284a2819763548c166a Wed Jul 8 05:31:13 2026 -0700
    Add top-right "Share a link" and "Login" links to the menu bar, refs #10138 New js/topLinks.js drives two links at the top-right of the menu bar on all pages: - Login: links to the login page when logged out; when logged in it shows the username and opens an account dialog (My Sessions / My Custom Tracks / My Track Hubs, change password, sign out). - Share a link: on hgTracks, one click saves the current view as a session and shows a copyable short link, with an optional "Specify name" rename step; works logged-in or anonymously (reserved user "l"). On hgTrackUi and the hgc/hgGene item-details popup it instead shares the page URL with the hgsid stripped and the db argument kept. hgSession gains two JSON endpoints (hgS_doSaveSessionJson, hgS_doRenameSessionJson) that reuse saveCartAsSession() and addSessionLink(). The menu bar is patched in lib/web.c (CGI pages) and hgMenubar.c (static pages) via comment placeholders in globalNavBar.inc. On narrow/phone screens the links collapse into a menu icon with a dropdown so they no longer overlap the menu.
• src/hg/makeDb/doc/Cardiomyopathy.txt
  • lines changed 24, context: html, text, full: html, text
    0d12a0f167c83fb30ff8e001de6aff57c0982447 Wed Jul 8 15:55:13 2026 -0700
    Reframe the Cardiomyopathy VCEP provisional track to a Computable ACMG Criteria Summary. refs #37446 Per the CM VCEP chair, the cmpVCEPProvisionalClass track no longer computes an overall ACMG classification. It now lists, per variant, only the computable ACMG codes that are triggered, each with its underlying value: gnomAD FAF95 for BA1/BS1/PM2_supporting, REVEL score for PP3/BP4, the PM1 hotspot region, the EvRepo codon reference for PS1/PM5, the NMD-escape basis for PM4, and SpliceAI/phyloP for BP7. Display is a single neutral color; a SpliceAI score >= 0.20 is recorded as an informational splice flag rather than overriding a call. The GN002 combining logic is retained in the script as classify() but is retired and no longer called. Makedoc B.11 updated to match.
• src/hg/makeDb/doc/archaeaAsmHub/archaea.orderList.tsv
  • lines changed 30, context: html, text, full: html, text
    9d0d70b2fb8d6e8f311dcaed573e3459e5887684 Mon Jul 6 19:53:42 2026 -0700
    RefSeq update refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 116, context: html, text, full: html, text
    9d0d70b2fb8d6e8f311dcaed573e3459e5887684 Mon Jul 6 19:53:42 2026 -0700
    RefSeq update refs #29545
  • lines changed 1, context: html, text, full: html, text
    322e27a7a9f1f6c5ae481c03064f766fac84aa5b Mon Jul 6 20:01:21 2026 -0700
    remove a duplicate refs #29545
• src/hg/makeDb/doc/brcAsmHub/brc.orderList.tsv
  • lines changed 7, context: html, text, full: html, text
    b83df0a0f2b68a923783aa695840045bfeda6a42 Tue Jul 7 17:51:26 2026 -0700
    BRC update refs #34337
  • lines changed 4, context: html, text, full: html, text
    47d2766e01e7da1630d11af073e3e4ab5bf0bd5e Tue Jul 7 18:34:36 2026 -0700
    remove duplicates refs #34337
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    9d0d70b2fb8d6e8f311dcaed573e3459e5887684 Mon Jul 6 19:53:42 2026 -0700
    RefSeq update refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    9d0d70b2fb8d6e8f311dcaed573e3459e5887684 Mon Jul 6 19:53:42 2026 -0700
    RefSeq update refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    9d0d70b2fb8d6e8f311dcaed573e3459e5887684 Mon Jul 6 19:53:42 2026 -0700
    RefSeq update refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 14, context: html, text, full: html, text
    9d0d70b2fb8d6e8f311dcaed573e3459e5887684 Mon Jul 6 19:53:42 2026 -0700
    RefSeq update refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    9d0d70b2fb8d6e8f311dcaed573e3459e5887684 Mon Jul 6 19:53:42 2026 -0700
    RefSeq update refs #29545
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    9d0d70b2fb8d6e8f311dcaed573e3459e5887684 Mon Jul 6 19:53:42 2026 -0700
    RefSeq update refs #29545
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPProvisionalClass.py
  • lines changed 66, context: html, text, full: html, text
    0d12a0f167c83fb30ff8e001de6aff57c0982447 Wed Jul 8 15:55:13 2026 -0700
    Reframe the Cardiomyopathy VCEP provisional track to a Computable ACMG Criteria Summary. refs #37446 Per the CM VCEP chair, the cmpVCEPProvisionalClass track no longer computes an overall ACMG classification. It now lists, per variant, only the computable ACMG codes that are triggered, each with its underlying value: gnomAD FAF95 for BA1/BS1/PM2_supporting, REVEL score for PP3/BP4, the PM1 hotspot region, the EvRepo codon reference for PS1/PM5, the NMD-escape basis for PM4, and SpliceAI/phyloP for BP7. Display is a single neutral color; a SpliceAI score >= 0.20 is recorded as an informational splice flag rather than overriding a call. The GN002 combining logic is retained in the script as classify() but is retired and no longer called. Makedoc B.11 updated to match.
• src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py
  • lines changed 2, context: html, text, full: html, text
    e6bcec351aa8f5bc7218e8862e15c149aadb3479 Fri Jul 10 12:18:40 2026 -0700
    lrSv: complete the longReadVariants rename - reparent subtracks and update refs. refs #36258 Completes the previous rename commit (which carried only the colorsDbLegacy file moves). Renames "track lrSv" to "track longReadVariants" in lrSv.ra (adds "html lrSv" to keep the existing description page), reparents all subtracks plus the merged lrSvAll and its lrSvMergeAll.py generator, and updates the hs1 override, relatedTracks.ra, and the mei/meiHgsvc3/srSv/lrSvAll cross-links. Retitles the retired colorsDbLegacy track and reparents its subtracks. Only the internal track name changes; subtrack names, /gbdb/$D/lrSv/ data paths, and the lrSv.ra filename are unchanged.
  • lines changed 2, context: html, text, full: html, text
    b24afd50025b4dd947bc69e6ff266831c6d76629 Mon Jul 13 07:48:56 2026 -0700
    lrSv: fix rename fallout from CR - broken generator string, missed link, stale comment. refs #36258 Fix a literal newline that leaked into a Python string literal in lrSvMergeAll.py during the longReadVariants rename (the file no longer parsed). Update the missed g=lrSv cross-link in hg38/viennaVntr.html to g=longReadVariants. Correct the stale "lrSv.filter." cart-key prefix in the lrSv.ra comment to "longReadVariants.filter.".
• src/hg/makeDb/scripts/tp53/tp53ProvisionalClass.py
  • lines changed 5, context: html, text, full: html, text
    efac0c1abcc802cd0bbd039e99c23c27e3166f70 Tue Jul 7 12:38:35 2026 -0700
    Fix BP7 miscategorization in TP53 Provisional Classification track. BP7 is a computational code (synonymous/intronic, SpliceAI-based), not a clinical one; it was incorrectly grouped with PS1/PS2/PS4/PP1/PP4/BS4 as requiring clinical observations. Reworded the docstring and mouseover to note BP7 is out of scope for this missense-only track. refs #37399
  • lines changed 2, context: html, text, full: html, text
    454b361596ac3494472e4e5dc6950326321e17c0 Tue Jul 7 17:55:41 2026 -0700
    Fix wrong column indices in TP53 Provisional Classification build summary. The post-build console summary read flds[13]/[14] (PS3 and PP3 labels) for the AF and BS2 counts instead of flds[15]/[16] (af_code and bs2), so it mislabeled PS3/BS3 as AF codes and always reported 0 BS2 rows. Emitted bigBed data was unaffected. refs #37399
• src/hg/makeDb/trackDb/human/colorsDbLegacy.html
  • lines changed 0, context: html, text, full: html, text
    ddb9135e955950dae01d348c21691c715d32a043 Fri Jul 10 12:16:23 2026 -0700
    lrSv: rename supertrack to longReadVariants (reuse old track), retire old track as colorsDbLegacy. refs #36258 Rename the "track lrSv" long-read SV supertrack to "track longReadVariants" so it reuses the existing (low-usage) longReadVariants track name, letting old sessions map to the new supertrack without a cart rewrite. Only the internal track name changes: subtrack names, /gbdb/$D/lrSv/ data paths, and the lrSv.ra filename stay the same, with "html lrSv" keeping the existing description page. Reparent all subtracks, the merged lrSvAll (and its lrSvMergeAll.py generator), and the hs1 override; update relatedTracks.ra and the mei/meiHgsvc3/srSv/lrSvAll cross-links. The previous longReadVariants track (CoLoRSdb small variants + SVs) is retired to colorsDbLegacy (files renamed, subtracks reparented, labels marked legacy) and gated to alpha (include colorsDbLegacy.ra alpha) so it stays on dev only.
• src/hg/makeDb/trackDb/human/colorsDbLegacy.ra
  • lines changed 0, context: html, text, full: html, text
    ddb9135e955950dae01d348c21691c715d32a043 Fri Jul 10 12:16:23 2026 -0700
    lrSv: rename supertrack to longReadVariants (reuse old track), retire old track as colorsDbLegacy. refs #36258 Rename the "track lrSv" long-read SV supertrack to "track longReadVariants" so it reuses the existing (low-usage) longReadVariants track name, letting old sessions map to the new supertrack without a cart rewrite. Only the internal track name changes: subtrack names, /gbdb/$D/lrSv/ data paths, and the lrSv.ra filename stay the same, with "html lrSv" keeping the existing description page. Reparent all subtracks, the merged lrSvAll (and its lrSvMergeAll.py generator), and the hs1 override; update relatedTracks.ra and the mei/meiHgsvc3/srSv/lrSvAll cross-links. The previous longReadVariants track (CoLoRSdb small variants + SVs) is retired to colorsDbLegacy (files renamed, subtracks reparented, labels marked legacy) and gated to alpha (include colorsDbLegacy.ra alpha) so it stays on dev only.
  • lines changed 5, context: html, text, full: html, text
    e6bcec351aa8f5bc7218e8862e15c149aadb3479 Fri Jul 10 12:18:40 2026 -0700
    lrSv: complete the longReadVariants rename - reparent subtracks and update refs. refs #36258 Completes the previous rename commit (which carried only the colorsDbLegacy file moves). Renames "track lrSv" to "track longReadVariants" in lrSv.ra (adds "html lrSv" to keep the existing description page), reparents all subtracks plus the merged lrSvAll and its lrSvMergeAll.py generator, and updates the hs1 override, relatedTracks.ra, and the mei/meiHgsvc3/srSv/lrSvAll cross-links. Retitles the retired colorsDbLegacy track and reparents its subtracks. Only the internal track name changes; subtrack names, /gbdb/$D/lrSv/ data paths, and the lrSv.ra filename are unchanged.
• src/hg/makeDb/trackDb/human/hg38/encode.cCREs.override.ra
  • lines changed 1, context: html, text, full: html, text
    1a9cdfb7971489ab9f8291970006af01a1813fc6 Wed Jul 8 12:28:23 2026 -0700
    Squashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg38/mb2.ra
  • lines changed 1, context: html, text, full: html, text
    1a9cdfb7971489ab9f8291970006af01a1813fc6 Wed Jul 8 12:28:23 2026 -0700
    Squashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg38/recount3.ra
  • lines changed 1, context: html, text, full: html, text
    1a9cdfb7971489ab9f8291970006af01a1813fc6 Wed Jul 8 12:28:23 2026 -0700
    Squashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/human/hg38/viennaVntr.html
  • lines changed 1, context: html, text, full: html, text
    b24afd50025b4dd947bc69e6ff266831c6d76629 Mon Jul 13 07:48:56 2026 -0700
    lrSv: fix rename fallout from CR - broken generator string, missed link, stale comment. refs #36258 Fix a literal newline that leaked into a Python string literal in lrSvMergeAll.py during the longReadVariants rename (the file no longer parsed). Update the missed g=lrSv cross-link in hg38/viennaVntr.html to g=longReadVariants. Correct the stale "lrSv.filter." cart-key prefix in the lrSv.ra comment to "longReadVariants.filter.".
• src/hg/makeDb/trackDb/human/hs1/html/lrSv.html
  • lines changed 116, context: html, text, full: html, text
    b9a59376d126a820a58fc0d0f239adc9347cf7b0 Thu Jul 9 12:05:41 2026 -0700
    lrSv: promote off alpha, add hs1 override description page, hold unpublished subtracks. refs #36258 - Remove the alpha release gating from the lrSv include (human/trackDb.ra and hs1/trackDb.ra) so the supertrack can graduate past dev/alpha. - Add per-track "release alpha" to kwanhoSv and lrSv1kLin so the two preliminary/unpublished subtracks stay dev-only when the container is promoted (now valid, since the include no longer supplies a release override). - Add an hs1 description-page override (hs1/lrSv.ra -> html/lrSv) with a T2T-CHM13-specific page (hs1/html/lrSv.html): describes the 6 natively-built datasets with per-dataset blurbs and hs1 SV counts, and cross-links to the hg38 track. - hs1 override: default colorsDbSv to visibility pack so it is shown when the (off-by-default) supertrack is first enabled, since hs1 has no merged track. - hg38 lrSv.html: correct the HPRC v2.1 blurb count (596k -> 550k) to match the deduped data.
  • lines changed 1, context: html, text, full: html, text
    e6bcec351aa8f5bc7218e8862e15c149aadb3479 Fri Jul 10 12:18:40 2026 -0700
    lrSv: complete the longReadVariants rename - reparent subtracks and update refs. refs #36258 Completes the previous rename commit (which carried only the colorsDbLegacy file moves). Renames "track lrSv" to "track longReadVariants" in lrSv.ra (adds "html lrSv" to keep the existing description page), reparents all subtracks plus the merged lrSvAll and its lrSvMergeAll.py generator, and updates the hs1 override, relatedTracks.ra, and the mei/meiHgsvc3/srSv/lrSvAll cross-links. Retitles the retired colorsDbLegacy track and reparents its subtracks. Only the internal track name changes; subtrack names, /gbdb/$D/lrSv/ data paths, and the lrSv.ra filename are unchanged.
• src/hg/makeDb/trackDb/human/hs1/lrSv.ra
  • lines changed 5, context: html, text, full: html, text
    b9a59376d126a820a58fc0d0f239adc9347cf7b0 Thu Jul 9 12:05:41 2026 -0700
    lrSv: promote off alpha, add hs1 override description page, hold unpublished subtracks. refs #36258 - Remove the alpha release gating from the lrSv include (human/trackDb.ra and hs1/trackDb.ra) so the supertrack can graduate past dev/alpha. - Add per-track "release alpha" to kwanhoSv and lrSv1kLin so the two preliminary/unpublished subtracks stay dev-only when the container is promoted (now valid, since the include no longer supplies a release override). - Add an hs1 description-page override (hs1/lrSv.ra -> html/lrSv) with a T2T-CHM13-specific page (hs1/html/lrSv.html): describes the 6 natively-built datasets with per-dataset blurbs and hs1 SV counts, and cross-links to the hg38 track. - hs1 override: default colorsDbSv to visibility pack so it is shown when the (off-by-default) supertrack is first enabled, since hs1 has no merged track. - hg38 lrSv.html: correct the HPRC v2.1 blurb count (596k -> 550k) to match the deduped data.
  • lines changed 1, context: html, text, full: html, text
    e6bcec351aa8f5bc7218e8862e15c149aadb3479 Fri Jul 10 12:18:40 2026 -0700
    lrSv: complete the longReadVariants rename - reparent subtracks and update refs. refs #36258 Completes the previous rename commit (which carried only the colorsDbLegacy file moves). Renames "track lrSv" to "track longReadVariants" in lrSv.ra (adds "html lrSv" to keep the existing description page), reparents all subtracks plus the merged lrSvAll and its lrSvMergeAll.py generator, and updates the hs1 override, relatedTracks.ra, and the mei/meiHgsvc3/srSv/lrSvAll cross-links. Retitles the retired colorsDbLegacy track and reparents its subtracks. Only the internal track name changes; subtrack names, /gbdb/$D/lrSv/ data paths, and the lrSv.ra filename are unchanged.
• src/hg/makeDb/trackDb/human/hs1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    b9a59376d126a820a58fc0d0f239adc9347cf7b0 Thu Jul 9 12:05:41 2026 -0700
    lrSv: promote off alpha, add hs1 override description page, hold unpublished subtracks. refs #36258 - Remove the alpha release gating from the lrSv include (human/trackDb.ra and hs1/trackDb.ra) so the supertrack can graduate past dev/alpha. - Add per-track "release alpha" to kwanhoSv and lrSv1kLin so the two preliminary/unpublished subtracks stay dev-only when the container is promoted (now valid, since the include no longer supplies a release override). - Add an hs1 description-page override (hs1/lrSv.ra -> html/lrSv) with a T2T-CHM13-specific page (hs1/html/lrSv.html): describes the 6 natively-built datasets with per-dataset blurbs and hs1 SV counts, and cross-links to the hg38 track. - hs1 override: default colorsDbSv to visibility pack so it is shown when the (off-by-default) supertrack is first enabled, since hs1 has no merged track. - hg38 lrSv.html: correct the HPRC v2.1 blurb count (596k -> 550k) to match the deduped data.
• src/hg/makeDb/trackDb/human/lrSv.html
  • lines changed 1, context: html, text, full: html, text
    b9a59376d126a820a58fc0d0f239adc9347cf7b0 Thu Jul 9 12:05:41 2026 -0700
    lrSv: promote off alpha, add hs1 override description page, hold unpublished subtracks. refs #36258 - Remove the alpha release gating from the lrSv include (human/trackDb.ra and hs1/trackDb.ra) so the supertrack can graduate past dev/alpha. - Add per-track "release alpha" to kwanhoSv and lrSv1kLin so the two preliminary/unpublished subtracks stay dev-only when the container is promoted (now valid, since the include no longer supplies a release override). - Add an hs1 description-page override (hs1/lrSv.ra -> html/lrSv) with a T2T-CHM13-specific page (hs1/html/lrSv.html): describes the 6 natively-built datasets with per-dataset blurbs and hs1 SV counts, and cross-links to the hg38 track. - hs1 override: default colorsDbSv to visibility pack so it is shown when the (off-by-default) supertrack is first enabled, since hs1 has no merged track. - hg38 lrSv.html: correct the HPRC v2.1 blurb count (596k -> 550k) to match the deduped data.
• src/hg/makeDb/trackDb/human/lrSv.ra
  • lines changed 2, context: html, text, full: html, text
    b9a59376d126a820a58fc0d0f239adc9347cf7b0 Thu Jul 9 12:05:41 2026 -0700
    lrSv: promote off alpha, add hs1 override description page, hold unpublished subtracks. refs #36258 - Remove the alpha release gating from the lrSv include (human/trackDb.ra and hs1/trackDb.ra) so the supertrack can graduate past dev/alpha. - Add per-track "release alpha" to kwanhoSv and lrSv1kLin so the two preliminary/unpublished subtracks stay dev-only when the container is promoted (now valid, since the include no longer supplies a release override). - Add an hs1 description-page override (hs1/lrSv.ra -> html/lrSv) with a T2T-CHM13-specific page (hs1/html/lrSv.html): describes the 6 natively-built datasets with per-dataset blurbs and hs1 SV counts, and cross-links to the hg38 track. - hs1 override: default colorsDbSv to visibility pack so it is shown when the (off-by-default) supertrack is first enabled, since hs1 has no merged track. - hg38 lrSv.html: correct the HPRC v2.1 blurb count (596k -> 550k) to match the deduped data.
  • lines changed 19, context: html, text, full: html, text
    e6bcec351aa8f5bc7218e8862e15c149aadb3479 Fri Jul 10 12:18:40 2026 -0700
    lrSv: complete the longReadVariants rename - reparent subtracks and update refs. refs #36258 Completes the previous rename commit (which carried only the colorsDbLegacy file moves). Renames "track lrSv" to "track longReadVariants" in lrSv.ra (adds "html lrSv" to keep the existing description page), reparents all subtracks plus the merged lrSvAll and its lrSvMergeAll.py generator, and updates the hs1 override, relatedTracks.ra, and the mei/meiHgsvc3/srSv/lrSvAll cross-links. Retitles the retired colorsDbLegacy track and reparents its subtracks. Only the internal track name changes; subtrack names, /gbdb/$D/lrSv/ data paths, and the lrSv.ra filename are unchanged.
  • lines changed 1, context: html, text, full: html, text
    b24afd50025b4dd947bc69e6ff266831c6d76629 Mon Jul 13 07:48:56 2026 -0700
    lrSv: fix rename fallout from CR - broken generator string, missed link, stale comment. refs #36258 Fix a literal newline that leaked into a Python string literal in lrSvMergeAll.py during the longReadVariants rename (the file no longer parsed). Update the missed g=lrSv cross-link in hg38/viennaVntr.html to g=longReadVariants. Correct the stale "lrSv.filter." cart-key prefix in the lrSv.ra comment to "longReadVariants.filter.".
• src/hg/makeDb/trackDb/human/lrSvAll.html
  • lines changed 1, context: html, text, full: html, text
    e6bcec351aa8f5bc7218e8862e15c149aadb3479 Fri Jul 10 12:18:40 2026 -0700
    lrSv: complete the longReadVariants rename - reparent subtracks and update refs. refs #36258 Completes the previous rename commit (which carried only the colorsDbLegacy file moves). Renames "track lrSv" to "track longReadVariants" in lrSv.ra (adds "html lrSv" to keep the existing description page), reparents all subtracks plus the merged lrSvAll and its lrSvMergeAll.py generator, and updates the hs1 override, relatedTracks.ra, and the mei/meiHgsvc3/srSv/lrSvAll cross-links. Retitles the retired colorsDbLegacy track and reparents its subtracks. Only the internal track name changes; subtrack names, /gbdb/$D/lrSv/ data paths, and the lrSv.ra filename are unchanged.
• src/hg/makeDb/trackDb/human/lrSvAll.ra
  • lines changed 1, context: html, text, full: html, text
    e6bcec351aa8f5bc7218e8862e15c149aadb3479 Fri Jul 10 12:18:40 2026 -0700
    lrSv: complete the longReadVariants rename - reparent subtracks and update refs. refs #36258 Completes the previous rename commit (which carried only the colorsDbLegacy file moves). Renames "track lrSv" to "track longReadVariants" in lrSv.ra (adds "html lrSv" to keep the existing description page), reparents all subtracks plus the merged lrSvAll and its lrSvMergeAll.py generator, and updates the hs1 override, relatedTracks.ra, and the mei/meiHgsvc3/srSv/lrSvAll cross-links. Retitles the retired colorsDbLegacy track and reparents its subtracks. Only the internal track name changes; subtrack names, /gbdb/$D/lrSv/ data paths, and the lrSv.ra filename are unchanged.
• src/hg/makeDb/trackDb/human/mei.html
  • lines changed 1, context: html, text, full: html, text
    e6bcec351aa8f5bc7218e8862e15c149aadb3479 Fri Jul 10 12:18:40 2026 -0700
    lrSv: complete the longReadVariants rename - reparent subtracks and update refs. refs #36258 Completes the previous rename commit (which carried only the colorsDbLegacy file moves). Renames "track lrSv" to "track longReadVariants" in lrSv.ra (adds "html lrSv" to keep the existing description page), reparents all subtracks plus the merged lrSvAll and its lrSvMergeAll.py generator, and updates the hs1 override, relatedTracks.ra, and the mei/meiHgsvc3/srSv/lrSvAll cross-links. Retitles the retired colorsDbLegacy track and reparents its subtracks. Only the internal track name changes; subtrack names, /gbdb/$D/lrSv/ data paths, and the lrSv.ra filename are unchanged.
• src/hg/makeDb/trackDb/human/meiHgsvc3.html
  • lines changed 1, context: html, text, full: html, text
    e6bcec351aa8f5bc7218e8862e15c149aadb3479 Fri Jul 10 12:18:40 2026 -0700
    lrSv: complete the longReadVariants rename - reparent subtracks and update refs. refs #36258 Completes the previous rename commit (which carried only the colorsDbLegacy file moves). Renames "track lrSv" to "track longReadVariants" in lrSv.ra (adds "html lrSv" to keep the existing description page), reparents all subtracks plus the merged lrSvAll and its lrSvMergeAll.py generator, and updates the hs1 override, relatedTracks.ra, and the mei/meiHgsvc3/srSv/lrSvAll cross-links. Retitles the retired colorsDbLegacy track and reparents its subtracks. Only the internal track name changes; subtrack names, /gbdb/$D/lrSv/ data paths, and the lrSv.ra filename are unchanged.
• src/hg/makeDb/trackDb/human/phasedVars.ra
  • lines changed 1, context: html, text, full: html, text
    1a9cdfb7971489ab9f8291970006af01a1813fc6 Wed Jul 8 12:28:23 2026 -0700
    Squashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/human/srSv.html
  • lines changed 1, context: html, text, full: html, text
    e6bcec351aa8f5bc7218e8862e15c149aadb3479 Fri Jul 10 12:18:40 2026 -0700
    lrSv: complete the longReadVariants rename - reparent subtracks and update refs. refs #36258 Completes the previous rename commit (which carried only the colorsDbLegacy file moves). Renames "track lrSv" to "track longReadVariants" in lrSv.ra (adds "html lrSv" to keep the existing description page), reparents all subtracks plus the merged lrSvAll and its lrSvMergeAll.py generator, and updates the hs1 override, relatedTracks.ra, and the mei/meiHgsvc3/srSv/lrSvAll cross-links. Retitles the retired colorsDbLegacy track and reparents its subtracks. Only the internal track name changes; subtrack names, /gbdb/$D/lrSv/ data paths, and the lrSv.ra filename are unchanged.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    1a9cdfb7971489ab9f8291970006af01a1813fc6 Wed Jul 8 12:28:23 2026 -0700
    Squashing old pennantIcons, no RM
  • lines changed 1, context: html, text, full: html, text
    b9a59376d126a820a58fc0d0f239adc9347cf7b0 Thu Jul 9 12:05:41 2026 -0700
    lrSv: promote off alpha, add hs1 override description page, hold unpublished subtracks. refs #36258 - Remove the alpha release gating from the lrSv include (human/trackDb.ra and hs1/trackDb.ra) so the supertrack can graduate past dev/alpha. - Add per-track "release alpha" to kwanhoSv and lrSv1kLin so the two preliminary/unpublished subtracks stay dev-only when the container is promoted (now valid, since the include no longer supplies a release override). - Add an hs1 description-page override (hs1/lrSv.ra -> html/lrSv) with a T2T-CHM13-specific page (hs1/html/lrSv.html): describes the 6 natively-built datasets with per-dataset blurbs and hs1 SV counts, and cross-links to the hg38 track. - hs1 override: default colorsDbSv to visibility pack so it is shown when the (off-by-default) supertrack is first enabled, since hs1 has no merged track. - hg38 lrSv.html: correct the HPRC v2.1 blurb count (596k -> 550k) to match the deduped data.
  • lines changed 1, context: html, text, full: html, text
    e6bcec351aa8f5bc7218e8862e15c149aadb3479 Fri Jul 10 12:18:40 2026 -0700
    lrSv: complete the longReadVariants rename - reparent subtracks and update refs. refs #36258 Completes the previous rename commit (which carried only the colorsDbLegacy file moves). Renames "track lrSv" to "track longReadVariants" in lrSv.ra (adds "html lrSv" to keep the existing description page), reparents all subtracks plus the merged lrSvAll and its lrSvMergeAll.py generator, and updates the hs1 override, relatedTracks.ra, and the mei/meiHgsvc3/srSv/lrSvAll cross-links. Retitles the retired colorsDbLegacy track and reparents its subtracks. Only the internal track name changes; subtrack names, /gbdb/$D/lrSv/ data paths, and the lrSv.ra filename are unchanged.
• src/hg/makeDb/trackDb/human/varFreqsAffected.html
  • lines changed 9, context: html, text, full: html, text
    fe0627da07b9f989bc642d824af381968163d9a8 Wed Jul 8 13:40:04 2026 -0700
    varFreqs: move ALFA to Global reference panels; add shared-sample bias caveat to description pages. refs #36642 Per Max's post-release feedback on the ticket: ALFA is not a European cohort, it is an NCBI aggregator of dbGaP studies from many sources. Moved from Europe to Global reference panels in the newsarch entry. Also adds a shared-sample bias caveat to the Pooled allele frequency section of both varFreqsAffected.html and varFreqsBackground.html. The background page cites the concrete overlaps (1000 Genomes in both gnomAD HGDP+1kG and HRC; HGDP/SGDP; AllOfUs/TOPMed; ALFA aggregating dbGaP studies used elsewhere). The affected page cites the SPARK WGS cohort being a subset of SPARK WES. Both explain that pooled AN is inflated and pooled AF is skewed toward the frequency in the shared subset, and point users to the per-cohort AC/AF/AN fields for unbiased single-cohort numbers.
• src/hg/makeDb/trackDb/human/varFreqsBackground.html
  • lines changed 10, context: html, text, full: html, text
    fe0627da07b9f989bc642d824af381968163d9a8 Wed Jul 8 13:40:04 2026 -0700
    varFreqs: move ALFA to Global reference panels; add shared-sample bias caveat to description pages. refs #36642 Per Max's post-release feedback on the ticket: ALFA is not a European cohort, it is an NCBI aggregator of dbGaP studies from many sources. Moved from Europe to Global reference panels in the newsarch entry. Also adds a shared-sample bias caveat to the Pooled allele frequency section of both varFreqsAffected.html and varFreqsBackground.html. The background page cites the concrete overlaps (1000 Genomes in both gnomAD HGDP+1kG and HRC; HGDP/SGDP; AllOfUs/TOPMed; ALFA aggregating dbGaP studies used elsewhere). The affected page cites the SPARK WGS cohort being a subset of SPARK WES. Both explain that pooled AN is inflated and pooled AF is skewed toward the frequency in the shared subset, and point users to the per-cohort AC/AF/AN fields for unbiased single-cohort numbers.
• src/hg/makeDb/trackDb/jaspar.ra
  • lines changed 1, context: html, text, full: html, text
    1a9cdfb7971489ab9f8291970006af01a1813fc6 Wed Jul 8 12:28:23 2026 -0700
    Squashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/mouse/mm10/recount3.ra
  • lines changed 1, context: html, text, full: html, text
    1a9cdfb7971489ab9f8291970006af01a1813fc6 Wed Jul 8 12:28:23 2026 -0700
    Squashing old pennantIcons, no RM
• src/hg/makeDb/trackDb/relatedTracks.ra
  • lines changed 12, context: html, text, full: html, text
    e6bcec351aa8f5bc7218e8862e15c149aadb3479 Fri Jul 10 12:18:40 2026 -0700
    lrSv: complete the longReadVariants rename - reparent subtracks and update refs. refs #36258 Completes the previous rename commit (which carried only the colorsDbLegacy file moves). Renames "track lrSv" to "track longReadVariants" in lrSv.ra (adds "html lrSv" to keep the existing description page), reparents all subtracks plus the merged lrSvAll and its lrSvMergeAll.py generator, and updates the hs1 override, relatedTracks.ra, and the mei/meiHgsvc3/srSv/lrSvAll cross-links. Retitles the retired colorsDbLegacy track and reparents its subtracks. Only the internal track name changes; subtrack names, /gbdb/$D/lrSv/ data paths, and the lrSv.ra filename are unchanged.
• src/hg/near/hgNear/hgNear.c
  • lines changed 2, context: html, text, full: html, text
    94041c12e043016875ebd340568bda0ccaf122f6 Wed Jul 8 13:53:22 2026 -0700
    Add db= to cross-CGI hgTracks/hgTrackUi/hgc links to prevent wrong-assembly errors. refs #37840 Completes the incomplete work from #26892: links from the browser to a different CGI omitted db=, so the target CGI fell back to the cart's db (often wrong), producing "Can't find <track> in track database <db>" errors and broken shared links. Adds the current-assembly db to link builders across hgTracks (chromGraphTrack, expRatioTracks, config ruler and per-track configure links, variation), hgVai, hgFileUi, hgGtexTrackSettings, hgBlat, hgGene, hgNear, the barChart/GTEx faceted UI (facetedBar, barChartUi, gtexUi), and the hgTrackUi group-configure link.
• src/hg/utils/genePredToProt/genePredToProt.c
  • lines changed 7, context: html, text, full: html, text
    4aa77873cb618e254b2f90d091d7bdef844947c2 Wed Jul 8 04:28:42 2026 -0700
    Let assembly hubs assign genetic codes per sequence for amino acid display Adds a "codonTable" genomes.txt setting, e.g. "codonTable default=1 NC_017929.1=13", so an assembly hub can pick the NCBI translation table used to show amino acids for each sequence. New hGeneticCodeForChrom(db, chrom) in hdb.c resolves the code (per-db cached), falling back to the previous behavior: chrM/chrMT use the vertebrate mitochondrial code, everything else the standard code. Wired into the two browser display paths, which both go through cds.c's baseColorLookupCodon: the base position track three-frame translation and codon-colored annotation tracks such as gene predictions (also PSL/BAM). Also used for the hgc SNP amino acid details, and genePredTranslate gains a db parameter (genePredToProt gains an optional -db flag) so command-line translation can honor the same setting. Documented in assemblyHubHelp.html. refs #16550
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 3, context: html, text, full: html, text
    6f2d5abe744c581bfa84f324ae161c92ca0a4dbb Wed Jul 8 12:12:27 2026 -0700
    Sort ClinVar HGVS expression list so output order is stable regardless of NCBI's row order in hgvs4variation.txt.gz. This stops the doUpdate maxDiff sanity check from tripping when NCBI reshuffles rows (a cosmetic reorder that made ~96% of lines differ while the data was unchanged). No RM.
• src/inc/dnautil.h
  • lines changed 38, context: html, text, full: html, text
    a1489c0fc1c99793e499e3915bc346b581664ad4 Wed Jul 8 02:37:20 2026 -0700
    Add support for all NCBI alternative genetic codes to dnautil Adds struct geneticCode plus the full set of NCBI translation tables (from gc.prt) so DNA can be translated with any genetic code, not just the Standard and Vertebrate Mitochondrial codes that were hardcoded. New API: geneticCodeForId/geneticCodeForName, lookupCodonInCode, isStopCodonInCode, dnaTranslateSomeInCode (explicit-handle, reentrant), and setDefaultGeneticCode for the process-global default. lookupCodon and friends are unchanged in behavior, still defaulting to the Standard code. The genetic code data lives in the auto-generated lib/geneticCodeTable.h, produced by oneShot/dnaGeneticCodes/dnaGeneticCodes.py from NCBI's gc.prt. Added a unit test under lib/tests. refs #16550
• src/lib/dnautil.c
  • lines changed 207, context: html, text, full: html, text
    a1489c0fc1c99793e499e3915bc346b581664ad4 Wed Jul 8 02:37:20 2026 -0700
    Add support for all NCBI alternative genetic codes to dnautil Adds struct geneticCode plus the full set of NCBI translation tables (from gc.prt) so DNA can be translated with any genetic code, not just the Standard and Vertebrate Mitochondrial codes that were hardcoded. New API: geneticCodeForId/geneticCodeForName, lookupCodonInCode, isStopCodonInCode, dnaTranslateSomeInCode (explicit-handle, reentrant), and setDefaultGeneticCode for the process-global default. lookupCodon and friends are unchanged in behavior, still defaulting to the Standard code. The genetic code data lives in the auto-generated lib/geneticCodeTable.h, produced by oneShot/dnaGeneticCodes/dnaGeneticCodes.py from NCBI's gc.prt. Added a unit test under lib/tests. refs #16550
• src/lib/geneticCodeTable.h
  • lines changed 92, context: html, text, full: html, text
    a1489c0fc1c99793e499e3915bc346b581664ad4 Wed Jul 8 02:37:20 2026 -0700
    Add support for all NCBI alternative genetic codes to dnautil Adds struct geneticCode plus the full set of NCBI translation tables (from gc.prt) so DNA can be translated with any genetic code, not just the Standard and Vertebrate Mitochondrial codes that were hardcoded. New API: geneticCodeForId/geneticCodeForName, lookupCodonInCode, isStopCodonInCode, dnaTranslateSomeInCode (explicit-handle, reentrant), and setDefaultGeneticCode for the process-global default. lookupCodon and friends are unchanged in behavior, still defaulting to the Standard code. The genetic code data lives in the auto-generated lib/geneticCodeTable.h, produced by oneShot/dnaGeneticCodes/dnaGeneticCodes.py from NCBI's gc.prt. Added a unit test under lib/tests. refs #16550
• src/lib/tests/dnaCodonTest.c
  • lines changed 54, context: html, text, full: html, text
    a1489c0fc1c99793e499e3915bc346b581664ad4 Wed Jul 8 02:37:20 2026 -0700
    Add support for all NCBI alternative genetic codes to dnautil Adds struct geneticCode plus the full set of NCBI translation tables (from gc.prt) so DNA can be translated with any genetic code, not just the Standard and Vertebrate Mitochondrial codes that were hardcoded. New API: geneticCodeForId/geneticCodeForName, lookupCodonInCode, isStopCodonInCode, dnaTranslateSomeInCode (explicit-handle, reentrant), and setDefaultGeneticCode for the process-global default. lookupCodon and friends are unchanged in behavior, still defaulting to the Standard code. The genetic code data lives in the auto-generated lib/geneticCodeTable.h, produced by oneShot/dnaGeneticCodes/dnaGeneticCodes.py from NCBI's gc.prt. Added a unit test under lib/tests. refs #16550
• src/lib/tests/expected/dnaCodonTest
  • lines changed 10, context: html, text, full: html, text
    a1489c0fc1c99793e499e3915bc346b581664ad4 Wed Jul 8 02:37:20 2026 -0700
    Add support for all NCBI alternative genetic codes to dnautil Adds struct geneticCode plus the full set of NCBI translation tables (from gc.prt) so DNA can be translated with any genetic code, not just the Standard and Vertebrate Mitochondrial codes that were hardcoded. New API: geneticCodeForId/geneticCodeForName, lookupCodonInCode, isStopCodonInCode, dnaTranslateSomeInCode (explicit-handle, reentrant), and setDefaultGeneticCode for the process-global default. lookupCodon and friends are unchanged in behavior, still defaulting to the Standard code. The genetic code data lives in the auto-generated lib/geneticCodeTable.h, produced by oneShot/dnaGeneticCodes/dnaGeneticCodes.py from NCBI's gc.prt. Added a unit test under lib/tests. refs #16550
• src/lib/tests/makefile
  • lines changed 9, context: html, text, full: html, text
    a1489c0fc1c99793e499e3915bc346b581664ad4 Wed Jul 8 02:37:20 2026 -0700
    Add support for all NCBI alternative genetic codes to dnautil Adds struct geneticCode plus the full set of NCBI translation tables (from gc.prt) so DNA can be translated with any genetic code, not just the Standard and Vertebrate Mitochondrial codes that were hardcoded. New API: geneticCodeForId/geneticCodeForName, lookupCodonInCode, isStopCodonInCode, dnaTranslateSomeInCode (explicit-handle, reentrant), and setDefaultGeneticCode for the process-global default. lookupCodon and friends are unchanged in behavior, still defaulting to the Standard code. The genetic code data lives in the auto-generated lib/geneticCodeTable.h, produced by oneShot/dnaGeneticCodes/dnaGeneticCodes.py from NCBI's gc.prt. Added a unit test under lib/tests. refs #16550
• src/oneShot/dnaGeneticCodes/dnaGeneticCodes.py
  • lines changed 80, context: html, text, full: html, text
    a1489c0fc1c99793e499e3915bc346b581664ad4 Wed Jul 8 02:37:20 2026 -0700
    Add support for all NCBI alternative genetic codes to dnautil Adds struct geneticCode plus the full set of NCBI translation tables (from gc.prt) so DNA can be translated with any genetic code, not just the Standard and Vertebrate Mitochondrial codes that were hardcoded. New API: geneticCodeForId/geneticCodeForName, lookupCodonInCode, isStopCodonInCode, dnaTranslateSomeInCode (explicit-handle, reentrant), and setDefaultGeneticCode for the process-global default. lookupCodon and friends are unchanged in behavior, still defaulting to the Standard code. The genetic code data lives in the auto-generated lib/geneticCodeTable.h, produced by oneShot/dnaGeneticCodes/dnaGeneticCodes.py from NCBI's gc.prt. Added a unit test under lib/tests. refs #16550
• src/utils/codeReviewAi.py
  • lines changed 132, context: html, text, full: html, text
    dc668958e7f016ce98df5c4b16dbab1598634950 Thu Jul 9 12:53:40 2026 -0700
    Add failure alerting to codeReviewAi.py daily mode and make output dir userless. refs #36890 Detect Claude CLI hard failures (auth/401 errors, empty output, or output that fails validation) instead of silently saving a broken review and marking it APPROVED. On failure the review is never emailed to the author; instead a single consolidated alert is emailed to browserqa-group@ucsc.edu and the script exits non-zero so the cron's failure guard fires. This addresses the daily reviews having failed silently since a token expiry. Replace the hardcoded /hive/users/lrnassar/codeReview output path with one derived from the current user (getpass.getuser()), and create it if missing so ticket/commit modes work for any account.
  • lines changed 32, context: html, text, full: html, text
    040099e4e758f5186ef775e0c5e749519018c38d Fri Jul 10 10:32:50 2026 -0700
    Make codeReviewAi.py Claude CLI auth resilient for cron. refs #36890 Add ensure_claude_auth(), which sources a long-lived setup-token from the CLAUDE_CODE_OAUTH_TOKEN env var or, failing that, from claude.oauthToken in ~/.hg.conf, exporting it so the CLI can authenticate in unattended cron runs that do not source a login shell. If no token is configured it falls back to the local ~/.claude/.credentials.json login. The active method is logged, and any residual auth failure is still caught and alerted. This fixes the daily reviews silently failing after the local subscription login expired.
  • lines changed 1, context: html, text, full: html, text
    37fc010656b75043d6ad0d4b91a9c672d915e327 Mon Jul 13 08:08:08 2026 -0700
    Fix codeReviewAi.py --daily exiting non-zero when there are no commits. refs #36890 The no-commits early return fell through to sys.exit(0 if ok else 1) as None, which is falsy, so a normal no-op run (e.g. a weekend with no commits) exited 1 and tripped the cron's failure guard. Return True from that path so an empty review window is treated as success.
• src/utils/pngToLolly/README.md
  • lines changed 95, context: html, text, full: html, text
    828e18dedab727a70100512daa1c13ecb3a243a2 Wed Jul 8 09:09:16 2026 -0700
    moved pngToLolly out of the kent tree
• src/utils/pngToLolly/makefile
  • lines changed 3, context: html, text, full: html, text
    828e18dedab727a70100512daa1c13ecb3a243a2 Wed Jul 8 09:09:16 2026 -0700
    moved pngToLolly out of the kent tree
• src/utils/pngToLolly/pngToLolly.c
  • lines changed 545, context: html, text, full: html, text
    828e18dedab727a70100512daa1c13ecb3a243a2 Wed Jul 8 09:09:16 2026 -0700
    moved pngToLolly out of the kent tree
• src/utils/qa/weeklybld/autoBuild.sh
  • lines changed 9, context: html, text, full: html, text
    88f4f3286f2b21c8fb65b3502adbbc2e7eaf60f1 Fri Jul 10 06:14:13 2026 -0700
    Automate GitHub source-archive upload with submodules, refs #37741 makeZip.csh now also builds jksrc.vNN.tar.gz next to the zip (both from the recurse-submodules clone, so both include the htslib submodule). doZip.csh hardlinks these to kent.src.zip / kent.src.tar.gz and uploads them to the GitHub release (creating it if needed). This works around git-archive omitting submodule contents, which is why GitHub's own auto-generated source archives are not buildable. autoBuild.sh now runs release-markdown before the zip step so the release doZip creates carries the real notes.
• src/utils/qa/weeklybld/doZip.csh
  • lines changed 44, context: html, text, full: html, text
    88f4f3286f2b21c8fb65b3502adbbc2e7eaf60f1 Fri Jul 10 06:14:13 2026 -0700
    Automate GitHub source-archive upload with submodules, refs #37741 makeZip.csh now also builds jksrc.vNN.tar.gz next to the zip (both from the recurse-submodules clone, so both include the htslib submodule). doZip.csh hardlinks these to kent.src.zip / kent.src.tar.gz and uploads them to the GitHub release (creating it if needed). This works around git-archive omitting submodule contents, which is why GitHub's own auto-generated source archives are not buildable. autoBuild.sh now runs release-markdown before the zip step so the release doZip creates carries the real notes.
• src/utils/qa/weeklybld/makeZip.csh
  • lines changed 14, context: html, text, full: html, text
    88f4f3286f2b21c8fb65b3502adbbc2e7eaf60f1 Fri Jul 10 06:14:13 2026 -0700
    Automate GitHub source-archive upload with submodules, refs #37741 makeZip.csh now also builds jksrc.vNN.tar.gz next to the zip (both from the recurse-submodules clone, so both include the htslib submodule). doZip.csh hardlinks these to kent.src.zip / kent.src.tar.gz and uploads them to the GitHub release (creating it if needed). This works around git-archive omitting submodule contents, which is why GitHub's own auto-generated source archives are not buildable. autoBuild.sh now runs release-markdown before the zip step so the release doZip creates carries the real notes.

• lines changed: 6456
• files changed: 135