All File Changes

v496_preview to v496_preview2 (2026-03-16 to 2026-03-23) v496

• confs/asia.hg.conf
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    5a1806a2620b4ac94254776f6bd3cbf2388b9009 Sun Mar 22 01:11:19 2026 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 2, context: html, text, full: html, text
    5a1806a2620b4ac94254776f6bd3cbf2388b9009 Sun Mar 22 01:11:19 2026 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 5, context: html, text, full: html, text
    5a1806a2620b4ac94254776f6bd3cbf2388b9009 Sun Mar 22 01:11:19 2026 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 2, context: html, text, full: html, text
    5a1806a2620b4ac94254776f6bd3cbf2388b9009 Sun Mar 22 01:11:19 2026 -0700
    Installing updated hg.conf files from UCSC servers
• docs/GBpandocHTMLrules.lua
  • lines changed 1, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• docs/hubs/hubBasics.md
  • lines changed 6, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• docs/staticPage.lua
  • lines changed 1, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/cartDump/cartDump.c
  • lines changed 98, context: html, text, full: html, text
    d99ea622f4024a17ea2cb5dbb4a4d81fd14395c7 Mon Mar 16 10:05:34 2026 -0700
    Moving cartDump vis adjustments for faceted tracks into its own function, per request. refs #37090
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 1, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/cirm/cdw/lib/cdwPageHeader.h
  • lines changed 1, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/hgBlat/hgBlat.c
  • lines changed 22, context: html, text, full: html, text
    651f959d7553ee0256b1e0b37ffa83d64709511d Mon Mar 16 17:57:16 2026 -0700
    Adding accessible labels to form controls across main CGI pages. Extends cheapcgi and hui libraries with aria-label support for track visibility dropdowns, and adds <label> elements to hgBlat, hgTables, hgPcr, and hgGateway form controls. Also adds Form Control Labels section to accessibility page. refs #37253
  • lines changed 2, context: html, text, full: html, text
    67f17c611fd3f1f8852cbdfcb706f099951b73cf Fri Mar 20 14:41:32 2026 -0700
    Remove visible label above hgBlat textarea per QA feedback. Replace with aria-label on the textarea element - the instructional text below already describes the field visually. refs #37253
• src/hg/hgConvert/hgConvert.c
  • lines changed 19, context: html, text, full: html, text
    d22f72049b67be2c8745828b1e6ebba9d5087ead Wed Mar 18 09:40:51 2026 -0700
    Add explanatory text and notes to hgConvert page, refs #36111 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/hgFetch/hgFetch.c
  • lines changed 54, context: html, text, full: html, text
    806f2d5c05d95f32fe2b1aadd8a70fbd9d0488ad Wed Mar 18 22:49:28 2026 -0700
    hgFetch gains support for retrieving local files from whitelisted trackDb settings, but only for locally defined tracks. refs #36320
• src/hg/hgGateway/hgGateway.html
  • lines changed 4, context: html, text, full: html, text
    651f959d7553ee0256b1e0b37ffa83d64709511d Mon Mar 16 17:57:16 2026 -0700
    Adding accessible labels to form controls across main CGI pages. Extends cheapcgi and hui libraries with aria-label support for track visibility dropdowns, and adds <label> elements to hgBlat, hgTables, hgPcr, and hgGateway form controls. Also adds Form Control Labels section to accessibility page. refs #37253
  • lines changed 1, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
  • lines changed 2, context: html, text, full: html, text
    a0b1ff8293644fb7d8cf5fa860312c29f31c2c67 Tue Mar 17 08:52:21 2026 -0700
    Merge branch 'lrnassar-accessibility-form-labels'
  • lines changed 2, context: html, text, full: html, text
    ff554a205dc0deb351a94778bda372ccd2ae3554 Wed Mar 18 13:50:21 2026 -0700
    Fix hgGateway label layout: add display:block to labels that replaced div elements, restoring the original block layout where Assembly dropdown and Position input appear below their labels. refs #37253
• src/hg/hgPcr/hgPcr.c
  • lines changed 14, context: html, text, full: html, text
    651f959d7553ee0256b1e0b37ffa83d64709511d Mon Mar 16 17:57:16 2026 -0700
    Adding accessible labels to form controls across main CGI pages. Extends cheapcgi and hui libraries with aria-label support for track visibility dropdowns, and adds <label> elements to hgBlat, hgTables, hgPcr, and hgGateway form controls. Also adds Form Control Labels section to accessibility page. refs #37253
• src/hg/hgTables/mainPage.c
  • lines changed 18, context: html, text, full: html, text
    651f959d7553ee0256b1e0b37ffa83d64709511d Mon Mar 16 17:57:16 2026 -0700
    Adding accessible labels to form controls across main CGI pages. Extends cheapcgi and hui libraries with aria-label support for track visibility dropdowns, and adds <label> elements to hgBlat, hgTables, hgPcr, and hgGateway form controls. Also adds Form Control Labels section to accessibility page. refs #37253
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 33, context: html, text, full: html, text
    da33d70c10ddaae6c3290cb900d7d0cc2b6ee01b Tue Mar 17 13:57:24 2026 -0700
    allow calculation of GC percent on the fly with code help from claude refs #35958
  • lines changed 2, context: html, text, full: html, text
    fa3c5feacf9d226310d8c7c775b8e8690aa4baf3 Tue Mar 17 14:39:15 2026 -0700
    add in the rest of the wiggle configurations for this onTheFly track refs #35958
  • lines changed 2, context: html, text, full: html, text
    7eb59a7b92b6256391c21256af4033ae03fff257 Fri Mar 20 16:39:11 2026 -0700
    minor issues discovered by claude code review
  • lines changed 4, context: html, text, full: html, text
    d543bdd5f9407b7373c73a3cab930c389971287b Mon Mar 23 09:27:15 2026 -0700
    Ongoing faceted composite modifications - collapsible facets, chips for selected facets, moving the show-only-selected element. Also first pass at using a CGI to fetch the metadata file, refs #36320
• src/hg/hgTracks/bigWigTrack.c
  • lines changed 155, context: html, text, full: html, text
    da33d70c10ddaae6c3290cb900d7d0cc2b6ee01b Tue Mar 17 13:57:24 2026 -0700
    allow calculation of GC percent on the fly with code help from claude refs #35958
  • lines changed 8, context: html, text, full: html, text
    3d4620f77d5ee2dca36cef39359e756c6a3624a0 Mon Mar 23 09:20:55 2026 -0700
    reset the GC on the fly to default off and same other defaults as the regular track refs #35958
• src/hg/hgTracks/config.c
  • lines changed 3, context: html, text, full: html, text
    651f959d7553ee0256b1e0b37ffa83d64709511d Mon Mar 16 17:57:16 2026 -0700
    Adding accessible labels to form controls across main CGI pages. Extends cheapcgi and hui libraries with aria-label support for track visibility dropdowns, and adds <label> elements to hgBlat, hgTables, hgPcr, and hgGateway form controls. Also adds Form Control Labels section to accessibility page. refs #37253
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    651f959d7553ee0256b1e0b37ffa83d64709511d Mon Mar 16 17:57:16 2026 -0700
    Adding accessible labels to form controls across main CGI pages. Extends cheapcgi and hui libraries with aria-label support for track visibility dropdowns, and adds <label> elements to hgBlat, hgTables, hgPcr, and hgGateway form controls. Also adds Form Control Labels section to accessibility page. refs #37253
  • lines changed 14, context: html, text, full: html, text
    da33d70c10ddaae6c3290cb900d7d0cc2b6ee01b Tue Mar 17 13:57:24 2026 -0700
    allow calculation of GC percent on the fly with code help from claude refs #35958
  • lines changed 1, context: html, text, full: html, text
    e30f8b3d5580f0be19ce22334dd97ccb497c49dc Thu Mar 19 11:40:59 2026 -0700
    Handle empty highlight cart variable appropriately (i.e. don't crash), refs #37268
• src/hg/hgTracks/hgTracks.h
  • lines changed 5, context: html, text, full: html, text
    da33d70c10ddaae6c3290cb900d7d0cc2b6ee01b Tue Mar 17 13:57:24 2026 -0700
    allow calculation of GC percent on the fly with code help from claude refs #35958
• src/hg/hgTracks/menu.c
  • lines changed 1, context: html, text, full: html, text
    ade21ee4e0109c70e29860d5393306e48e6a44d3 Mon Mar 16 16:38:58 2026 -0700
    Adding keyboard navigation accessibility to the Genome Browser menu bar and all main CGI pages. Converts non-focusable menu bar span elements to keyboard-accessible buttons using the W3C disclosure navigation pattern, adds aria-expanded state for screen readers, skip navigation link, and main content landmark. Also adds a Keyboard Navigation section to the accessibility page with screenshots. refs #37252
• src/hg/hgVai/hgVai.c
  • lines changed 1, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/hgc/bigBedClick.c
  • lines changed 89, context: html, text, full: html, text
    b33425c626414803bbddc702caecc256c5022277 Fri Mar 20 09:10:59 2026 -0700
    defining detailsHistogram tdb statements and an example histogram drawing code for it, used in the trexplorer track, refs #37273
  • lines changed 17, context: html, text, full: html, text
    cc9a51b3c9de74d78a0c7eeedb2b83d6336108c5 Mon Mar 23 04:36:13 2026 -0700
    automated code review found that we already have an escape function, so asked Claude to us it, refs #37273
• src/hg/hgc/hgc.c
  • lines changed 37, context: html, text, full: html, text
    da33d70c10ddaae6c3290cb900d7d0cc2b6ee01b Tue Mar 17 13:57:24 2026 -0700
    allow calculation of GC percent on the fly with code help from claude refs #35958
  • lines changed 21, context: html, text, full: html, text
    b33425c626414803bbddc702caecc256c5022277 Fri Mar 20 09:10:59 2026 -0700
    defining detailsHistogram tdb statements and an example histogram drawing code for it, used in the trexplorer track, refs #37273
• src/hg/hgc/hgc.h
  • lines changed 4, context: html, text, full: html, text
    b33425c626414803bbddc702caecc256c5022277 Fri Mar 20 09:10:59 2026 -0700
    defining detailsHistogram tdb statements and an example histogram drawing code for it, used in the trexplorer track, refs #37273
• src/hg/hgc/togaClick.c
  • lines changed 4, context: html, text, full: html, text
    da33d70c10ddaae6c3290cb900d7d0cc2b6ee01b Tue Mar 17 13:57:24 2026 -0700
    allow calculation of GC percent on the fly with code help from claude refs #35958
• src/hg/htdocs/ENCODE/aboutScaleup.html
  • lines changed 1, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/ENCODE/analysis.html
  • lines changed 2, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixInclude.html
  • lines changed 1, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/ENCODE/dataPlansMouse.html
  • lines changed 4, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/ENCODE/fileFormats.html
  • lines changed 2, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/ENCODE/index.html
  • lines changed 4, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 2, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/ENCODE/usageResources.html
  • lines changed 2, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 1, context: html, text, full: html, text
    5e6748ef77c3ede258c0ae362b0a1e626e62555c Wed Mar 18 17:17:25 2026 -0700
    Adding link to the heatmap docs in the format FAQ, refs #36176
  • lines changed 2, context: html, text, full: html, text
    c97646fc4092a0111ad9725d6da3334cb5cc64bc Mon Mar 23 08:51:13 2026 -0700
    retiring the redmine widget from all htdocs pages, refs #37279
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 0, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/FAQ/index.html
  • lines changed 2, context: html, text, full: html, text
    c97646fc4092a0111ad9725d6da3334cb5cc64bc Mon Mar 23 08:51:13 2026 -0700
    retiring the redmine widget from all htdocs pages, refs #37279
• src/hg/htdocs/accessibility.html
  • lines changed 37, context: html, text, full: html, text
    ade21ee4e0109c70e29860d5393306e48e6a44d3 Mon Mar 16 16:38:58 2026 -0700
    Adding keyboard navigation accessibility to the Genome Browser menu bar and all main CGI pages. Converts non-focusable menu bar span elements to keyboard-accessible buttons using the W3C disclosure navigation pattern, adds aria-expanded state for screen readers, skip navigation link, and main content landmark. Also adds a Keyboard Navigation section to the accessibility page with screenshots. refs #37252
  • lines changed 17, context: html, text, full: html, text
    651f959d7553ee0256b1e0b37ffa83d64709511d Mon Mar 16 17:57:16 2026 -0700
    Adding accessible labels to form controls across main CGI pages. Extends cheapcgi and hui libraries with aria-label support for track visibility dropdowns, and adds <label> elements to hgBlat, hgTables, hgPcr, and hgGateway form controls. Also adds Form Control Labels section to accessibility page. refs #37253
  • lines changed 9, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
  • lines changed 1, context: html, text, full: html, text
    5be4aee1392162b38bbd1318ea87d40f2ec63eb3 Fri Mar 20 14:29:52 2026 -0700
    Minor punctuation fix on accessibility page per QA feedback. refs #37254
• src/hg/htdocs/allTipsRaw.html
  • lines changed 2, context: html, text, full: html, text
    55f13dc0c9d9cec2e3b95521e22b191e134273df Mon Mar 16 16:12:26 2026 -0700
    Fixing 404 links for the 2026-03-15 Static Page Cronjob, No RM
• src/hg/htdocs/april1.html
  • lines changed 1, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/contacts.html
  • lines changed 6, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
  • lines changed 5, context: html, text, full: html, text
    89d1d7fce810632e8b2b1bc221a3af8924bd2226 Wed Mar 18 14:15:31 2026 -0700
    Feedback from CR: fix icon-only links with alt="" in contacts.html and pubs.html to have descriptive alt text (WCAG 1.1.1 requires alt when image is sole link content), and fix version number badges in liftOver.html to have alt="17" and alt="18" instead of empty alt. refs #37254
  • lines changed 2, context: html, text, full: html, text
    c97646fc4092a0111ad9725d6da3334cb5cc64bc Mon Mar 23 08:51:13 2026 -0700
    retiring the redmine widget from all htdocs pages, refs #37279
• src/hg/htdocs/covid19.html
  • lines changed 2, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/ebolaPortal/index.html
  • lines changed 3, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/GBsurvey507.html
  • lines changed 2, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/api.html
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    55f13dc0c9d9cec2e3b95521e22b191e134273df Mon Mar 16 16:12:26 2026 -0700
    Fixing 404 links for the 2026-03-15 Static Page Cronjob, No RM
• src/hg/htdocs/goldenPath/help/assemblyHubGuidelines.html
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    55f13dc0c9d9cec2e3b95521e22b191e134273df Mon Mar 16 16:12:26 2026 -0700
    Fixing 404 links for the 2026-03-15 Static Page Cronjob, No RM
• src/hg/htdocs/goldenPath/help/bedMethyl.html
  • lines changed 1, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/bigLolly.html
  • lines changed 2, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/bigRmsk.html
  • lines changed 8, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/covidBrowser.html
  • lines changed 1, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/cram.html
  • lines changed 1, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/decorator.html
  • lines changed 4, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/docker.html
  • lines changed 4, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/fileSearch.html
  • lines changed 1, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/gcOnFly.html
  • lines changed 18, context: html, text, full: html, text
    da33d70c10ddaae6c3290cb900d7d0cc2b6ee01b Tue Mar 17 13:57:24 2026 -0700
    allow calculation of GC percent on the fly with code help from claude refs #35958
• src/hg/htdocs/goldenPath/help/geneSearchBox.html
  • lines changed 1, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/genomeEuro.html
  • lines changed 1, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/heatmap.html
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    d33f10692e329f5f6a10508ed1c4d1123bf7a0e0 Mon Mar 16 10:54:29 2026 -0700
    Tweaking the sentence based on feedback from Jonathan, refs #36176
  • lines changed 2, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
  • lines changed 2, context: html, text, full: html, text
    17cda45b082befcc4b38faa51661b519e5669752 Tue Mar 17 10:53:48 2026 -0700
    Feedback from CR, refs #37247
• src/hg/htdocs/goldenPath/help/hgConvert.html
  • lines changed 3, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
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    019256d07c6f791954ecb76e3e40a4da960098ef Wed Mar 18 16:43:19 2026 -0700
    Fixing small issues I noticed in commits, refs #37243
• src/hg/htdocs/goldenPath/help/hgGeneGraph.html
  • lines changed 12, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/hgIntegratorHelp.html
  • lines changed 1, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 1, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/hgTablesHelp.html
  • lines changed 4, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 13, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 10, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
  • lines changed 2, context: html, text, full: html, text
    c97646fc4092a0111ad9725d6da3334cb5cc64bc Mon Mar 23 08:51:13 2026 -0700
    retiring the redmine widget from all htdocs pages, refs #37279
• src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html
  • lines changed 10, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/hic.html
  • lines changed 1, context: html, text, full: html, text
    17cda45b082befcc4b38faa51661b519e5669752 Tue Mar 17 10:53:48 2026 -0700
    Feedback from CR, refs #37247
• src/hg/htdocs/goldenPath/help/hubBasics.html
  • lines changed 6, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/hubQuickStart.html
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    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/hubQuickStartFilter.html
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    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/hubQuickStartSearch.html
  • lines changed 4, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/interact.html
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    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/liftOver.html
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    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
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    89d1d7fce810632e8b2b1bc221a3af8924bd2226 Wed Mar 18 14:15:31 2026 -0700
    Feedback from CR: fix icon-only links with alt="" in contacts.html and pubs.html to have descriptive alt text (WCAG 1.1.1 requires alt when image is sole link content), and fix version number badges in liftOver.html to have alt="17" and alt="18" instead of empty alt. refs #37254
• src/hg/htdocs/goldenPath/help/metadata.html
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    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/multiRegionHelp.html
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    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/quickLiftChain.html
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    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/sessions.html
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    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 58, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
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    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 51, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/help/trackSearch.html
  • lines changed 2, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/goldenPath/newsarch.html
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    5dbf9093ef09955761609bf2a591181b3d96a621 Mon Mar 16 16:57:16 2026 -0700
    Updating links to show track description page, #36826
  • lines changed 67, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
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    991b3c0bd4ec5909fd16b34ed7cc68c6f37afee4 Tue Mar 17 11:19:32 2026 -0700
    Announcing the updated SuperTrack Configuration Page, refs #36917
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    7b04ac35f781339fff38728a518bd641f0982a02 Tue Mar 17 14:44:21 2026 -0700
    Adding a comma for the SuperTrack Configuration Page announcement, refs #36917
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    0a31aa4f296a134f6f5e8966db98f23559e2e5b9 Tue Mar 17 15:20:18 2026 -0700
    Fixing title capitalization, refs #36917
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    c97646fc4092a0111ad9725d6da3334cb5cc64bc Mon Mar 23 08:51:13 2026 -0700
    retiring the redmine widget from all htdocs pages, refs #37279
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 1, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
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    e91e5efa506da2397a272d2b3c6e4dbe64508052 Thu Mar 19 12:31:13 2026 -0700
    Feedback from CR.
• src/hg/htdocs/goldenPath/trackDescriptions/bigRmskTrackDesc.html
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    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/gtex.html
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    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/images/keyboardMenuNav.png
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    ade21ee4e0109c70e29860d5393306e48e6a44d3 Mon Mar 16 16:38:58 2026 -0700
    Adding keyboard navigation accessibility to the Genome Browser menu bar and all main CGI pages. Converts non-focusable menu bar span elements to keyboard-accessible buttons using the W3C disclosure navigation pattern, adds aria-expanded state for screen readers, skip navigation link, and main content landmark. Also adds a Keyboard Navigation section to the accessibility page with screenshots. refs #37252
• src/hg/htdocs/images/newsArchImages/superTrackUi.png
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    991b3c0bd4ec5909fd16b34ed7cc68c6f37afee4 Tue Mar 17 11:19:32 2026 -0700
    Announcing the updated SuperTrack Configuration Page, refs #36917
• src/hg/htdocs/images/skipNavLink.png
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    ade21ee4e0109c70e29860d5393306e48e6a44d3 Mon Mar 16 16:38:58 2026 -0700
    Adding keyboard navigation accessibility to the Genome Browser menu bar and all main CGI pages. Converts non-focusable menu bar span elements to keyboard-accessible buttons using the W3C disclosure navigation pattern, adds aria-expanded state for screen readers, skip navigation link, and main content landmark. Also adds a Keyboard Navigation section to the accessibility page with screenshots. refs #37252
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 12, context: html, text, full: html, text
    ade21ee4e0109c70e29860d5393306e48e6a44d3 Mon Mar 16 16:38:58 2026 -0700
    Adding keyboard navigation accessibility to the Genome Browser menu bar and all main CGI pages. Converts non-focusable menu bar span elements to keyboard-accessible buttons using the W3C disclosure navigation pattern, adds aria-expanded state for screen readers, skip navigation link, and main content landmark. Also adds a Keyboard Navigation section to the accessibility page with screenshots. refs #37252
  • lines changed 1, context: html, text, full: html, text
    353da0efd7a5e331086b109f5ea4a14c30854269 Wed Mar 18 14:04:15 2026 -0700
    Fix skip nav link appearing in hgc popups: use tabindex=-1 to prevent auto-focus, with JS in jquery.plugins.js to enable the link on first Tab keypress. Reverts :focus-visible approach which didn't work due to browser auto-focus being treated as keyboard focus. refs #37252
• src/hg/htdocs/inc/hgCollectionHelpInclude.html
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    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/inc/hgMyData.html
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    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/index.html
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    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
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    c97646fc4092a0111ad9725d6da3334cb5cc64bc Mon Mar 23 08:51:13 2026 -0700
    retiring the redmine widget from all htdocs pages, refs #37279
• src/hg/htdocs/indexIntro.html
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    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/indexMeetings.html
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    55f13dc0c9d9cec2e3b95521e22b191e134273df Mon Mar 16 16:12:26 2026 -0700
    Fixing 404 links for the 2026-03-15 Static Page Cronjob, No RM
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    991b3c0bd4ec5909fd16b34ed7cc68c6f37afee4 Tue Mar 17 11:19:32 2026 -0700
    Announcing the updated SuperTrack Configuration Page, refs #36917
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    0a31aa4f296a134f6f5e8966db98f23559e2e5b9 Tue Mar 17 15:20:18 2026 -0700
    Fixing title capitalization, refs #36917
• src/hg/htdocs/redmineWidget.html
  • lines changed 32, context: html, text, full: html, text
    c97646fc4092a0111ad9725d6da3334cb5cc64bc Mon Mar 23 08:51:13 2026 -0700
    retiring the redmine widget from all htdocs pages, refs #37279
• src/hg/htdocs/singlecell.html
  • lines changed 2, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/staff.html
  • lines changed 2, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
  • lines changed 2, context: html, text, full: html, text
    c97646fc4092a0111ad9725d6da3334cb5cc64bc Mon Mar 23 08:51:13 2026 -0700
    retiring the redmine widget from all htdocs pages, refs #37279
• src/hg/htdocs/store.html
  • lines changed 2, context: html, text, full: html, text
    c97646fc4092a0111ad9725d6da3334cb5cc64bc Mon Mar 23 08:51:13 2026 -0700
    retiring the redmine widget from all htdocs pages, refs #37279
• src/hg/htdocs/style/facetedComposite.css
  • lines changed 119, context: html, text, full: html, text
    d543bdd5f9407b7373c73a3cab930c389971287b Mon Mar 23 09:27:15 2026 -0700
    Ongoing faceted composite modifications - collapsible facets, chips for selected facets, moving the show-only-selected element. Also first pass at using a CGI to fetch the metadata file, refs #36320
• src/hg/htdocs/style/nice_menu.css
  • lines changed 44, context: html, text, full: html, text
    ade21ee4e0109c70e29860d5393306e48e6a44d3 Mon Mar 16 16:38:58 2026 -0700
    Adding keyboard navigation accessibility to the Genome Browser menu bar and all main CGI pages. Converts non-focusable menu bar span elements to keyboard-accessible buttons using the W3C disclosure navigation pattern, adds aria-expanded state for screen readers, skip navigation link, and main content landmark. Also adds a Keyboard Navigation section to the accessibility page with screenshots. refs #37252
  • lines changed 1, context: html, text, full: html, text
    687677c1289ec87a034edf59effe5323c572ad41 Wed Mar 18 13:59:09 2026 -0700
    Fix skip nav link appearing in hgc popups: change :focus to :focus-visible so the skip link only appears on keyboard Tab navigation, not on programmatic/auto-focus when a popup window opens. refs #37252
• src/hg/htdocs/template.html
  • lines changed 1, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/htdocs/training/index.html
  • lines changed 1, context: html, text, full: html, text
    c97646fc4092a0111ad9725d6da3334cb5cc64bc Mon Mar 23 08:51:13 2026 -0700
    retiring the redmine widget from all htdocs pages, refs #37279
• src/hg/htdocs/training/openHouse.html
  • lines changed 1, context: html, text, full: html, text
    5709a7858d5c197721be66d5218a79124abadb70 Tue Mar 17 08:46:31 2026 -0700
    Adding alt text to images across static documentation pages, CGI headers, markdown docs, and Pandoc templates. Content images receive AI-generated descriptive alt text; decorative images (icons, spacers, toggles) receive alt="" per WCAG best practice. Also adds Image Descriptions section to the accessibility page, and fixes Pandoc Lua writers to output alt attributes. 67 files, covering help docs, news archive, ENCODE pages, portal pages, and session examples. refs #37254
• src/hg/hubApi/getData.c
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    e6389247d87dbd7b448a74f910033bceb9555633 Tue Mar 17 15:20:34 2026 -0700
    Changes from code review, refs #37212
• src/hg/inc/hui.h
  • lines changed 8, context: html, text, full: html, text
    651f959d7553ee0256b1e0b37ffa83d64709511d Mon Mar 16 17:57:16 2026 -0700
    Adding accessible labels to form controls across main CGI pages. Extends cheapcgi and hui libraries with aria-label support for track visibility dropdowns, and adds <label> elements to hgBlat, hgTables, hgPcr, and hgGateway form controls. Also adds Form Control Labels section to accessibility page. refs #37253
  • lines changed 13, context: html, text, full: html, text
    da33d70c10ddaae6c3290cb900d7d0cc2b6ee01b Tue Mar 17 13:57:24 2026 -0700
    allow calculation of GC percent on the fly with code help from claude refs #35958
• src/hg/js/autocomplete.js
  • lines changed 4, context: html, text, full: html, text
    da2089fb286b3119d62399a747a23fc22fa3ad70 Wed Mar 18 16:53:36 2026 -0700
    Add plain position searches to the recents search stack on hgTracks/hgGateway, refs #34588
• src/hg/js/autocompleteCat.js
  • lines changed 6, context: html, text, full: html, text
    da2089fb286b3119d62399a747a23fc22fa3ad70 Wed Mar 18 16:53:36 2026 -0700
    Add plain position searches to the recents search stack on hgTracks/hgGateway, refs #34588
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    68bc2fb0b79a074d3a0050db46bcb8b46a11600d Mon Mar 23 09:31:49 2026 -0700
    fix by claude, strip html highlighting markup when populating the input box with the text selections refs there is some RM but I can not find that
• src/hg/js/detailsHistogram.js
  • lines changed 132, context: html, text, full: html, text
    b33425c626414803bbddc702caecc256c5022277 Fri Mar 20 09:10:59 2026 -0700
    defining detailsHistogram tdb statements and an example histogram drawing code for it, used in the trexplorer track, refs #37273
• src/hg/js/facetedComposite.js
  • lines changed 176, context: html, text, full: html, text
    d543bdd5f9407b7373c73a3cab930c389971287b Mon Mar 23 09:27:15 2026 -0700
    Ongoing faceted composite modifications - collapsible facets, chips for selected facets, moving the show-only-selected element. Also first pass at using a CGI to fetch the metadata file, refs #36320
• src/hg/js/hgSearch.js
  • lines changed 30, context: html, text, full: html, text
    161ce497109c05416bfe719cb391667d64c580b2 Tue Mar 17 15:15:18 2026 -0700
    Merge hgSearch results by trackName before looping over results, which prevents having multiple sections per hgFindSpec as some tracks have multiple hgFindSpecs that can match for a given term. Also fix category display in a similar way so that the same track does not show up in the tree multiple times which breaks checkbox selection, refs #34334 and #37078
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    2490e8607ac86b0d23962ee8c0f9b47716ee9e3d Wed Mar 18 16:56:56 2026 -0700
    woops forgot to add position saving to hgSearch, refs #34588
• src/hg/js/hgTracks.js
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    cca2b17b47cb702ca0a1bf45c8a68559c37e5b0a Tue Mar 17 09:05:42 2026 -0700
    Default to with headers for download data in region menu on hgTracks, refs #36802
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    da2089fb286b3119d62399a747a23fc22fa3ad70 Wed Mar 18 16:53:36 2026 -0700
    Add plain position searches to the recents search stack on hgTracks/hgGateway, refs #34588
• src/hg/js/jquery.plugins.js
  • lines changed 99, context: html, text, full: html, text
    ade21ee4e0109c70e29860d5393306e48e6a44d3 Mon Mar 16 16:38:58 2026 -0700
    Adding keyboard navigation accessibility to the Genome Browser menu bar and all main CGI pages. Converts non-focusable menu bar span elements to keyboard-accessible buttons using the W3C disclosure navigation pattern, adds aria-expanded state for screen readers, skip navigation link, and main content landmark. Also adds a Keyboard Navigation section to the accessibility page with screenshots. refs #37252
  • lines changed 9, context: html, text, full: html, text
    353da0efd7a5e331086b109f5ea4a14c30854269 Wed Mar 18 14:04:15 2026 -0700
    Fix skip nav link appearing in hgc popups: use tabindex=-1 to prevent auto-focus, with JS in jquery.plugins.js to enable the link on first Tab keypress. Reverts :focus-visible approach which didn't work due to browser auto-focus being treated as keyboard focus. refs #37252
  • lines changed 1, context: html, text, full: html, text
    52069d415878530954cc12f10810612ab4011856 Fri Mar 20 14:27:55 2026 -0700
    Fix Tab to Tools dropdown not opening after Escape on Genomes/Genome Browser links. The suppressFocus flag was not being reset when focus moved to an <a> parent item, causing the next button focus handler to skip. refs #37252
• src/hg/js/makefile
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    b33425c626414803bbddc702caecc256c5022277 Fri Mar 20 09:10:59 2026 -0700
    defining detailsHistogram tdb statements and an example histogram drawing code for it, used in the trexplorer track, refs #37273
• src/hg/js/utils.js
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    da2089fb286b3119d62399a747a23fc22fa3ad70 Wed Mar 18 16:53:36 2026 -0700
    Add plain position searches to the recents search stack on hgTracks/hgGateway, refs #34588
• src/hg/lib/cart.c
  • lines changed 2, context: html, text, full: html, text
    ade21ee4e0109c70e29860d5393306e48e6a44d3 Mon Mar 16 16:38:58 2026 -0700
    Adding keyboard navigation accessibility to the Genome Browser menu bar and all main CGI pages. Converts non-focusable menu bar span elements to keyboard-accessible buttons using the W3C disclosure navigation pattern, adds aria-expanded state for screen readers, skip navigation link, and main content landmark. Also adds a Keyboard Navigation section to the accessibility page with screenshots. refs #37252
• src/hg/lib/hui.c
  • lines changed 13, context: html, text, full: html, text
    651f959d7553ee0256b1e0b37ffa83d64709511d Mon Mar 16 17:57:16 2026 -0700
    Adding accessible labels to form controls across main CGI pages. Extends cheapcgi and hui libraries with aria-label support for track visibility dropdowns, and adds <label> elements to hgBlat, hgTables, hgPcr, and hgGateway form controls. Also adds Form Control Labels section to accessibility page. refs #37253
  • lines changed 12, context: html, text, full: html, text
    da33d70c10ddaae6c3290cb900d7d0cc2b6ee01b Tue Mar 17 13:57:24 2026 -0700
    allow calculation of GC percent on the fly with code help from claude refs #35958
• src/hg/lib/trackHub.c
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    5bf51515b69bd518b2154df5476bc7ed319e33bd Sun Mar 22 21:05:42 2026 -0700
    Add bigMethyl to the list of valid tracktyopes to check. Generate a warning rather than error for halSnake tracks when when HAL support is not compiled in. Added danger comments about duplicated track name checking
• src/hg/lib/web.c
  • lines changed 5, context: html, text, full: html, text
    ade21ee4e0109c70e29860d5393306e48e6a44d3 Mon Mar 16 16:38:58 2026 -0700
    Adding keyboard navigation accessibility to the Genome Browser menu bar and all main CGI pages. Converts non-focusable menu bar span elements to keyboard-accessible buttons using the W3C disclosure navigation pattern, adds aria-expanded state for screen readers, skip navigation link, and main content landmark. Also adds a Keyboard Navigation section to the accessibility page with screenshots. refs #37252
  • lines changed 1, context: html, text, full: html, text
    e6389247d87dbd7b448a74f910033bceb9555633 Tue Mar 17 15:20:34 2026 -0700
    Changes from code review, refs #37212
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
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    a55016e7b323196b8a41e1f98fb511f70aaf4271 Fri Mar 20 11:15:58 2026 -0700
    VGP update in progress
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
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    a55016e7b323196b8a41e1f98fb511f70aaf4271 Fri Mar 20 11:15:58 2026 -0700
    VGP update in progress
• src/hg/makeDb/doc/hg38/primateAi.txt
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    e82f973dc7a5a814f0fd23999aa27222fa1260da Fri Mar 20 09:56:15 2026 -0700
    primateAI track, refs #37274
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    59e0ac66496c36893df2b1440a037557fed23ff4 Mon Mar 23 04:31:33 2026 -0700
    fixing up primateai makedoc, refs #37274
• src/hg/makeDb/doc/hg38/strVar.txt
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    f163cd6d8b443276863daa47c386072244dacc88 Tue Mar 17 07:27:58 2026 -0700
    Adding TRExplorer V2 tandem repeat catalog track to strVar supertrack, max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/hg38/varFreqs.txt
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    9503ddb81a5f54677116bdf1b6d059350441c711 Wed Mar 18 09:00:18 2026 -0700
    str var docs update 2
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    165a15d6a94d53f8162a01e69f3912a7a23a3b50 Mon Mar 23 06:47:55 2026 -0700
    mostly done with the variant frequencies track, refs#36642
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
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    a55016e7b323196b8a41e1f98fb511f70aaf4271 Fri Mar 20 11:15:58 2026 -0700
    VGP update in progress
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
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    a55016e7b323196b8a41e1f98fb511f70aaf4271 Fri Mar 20 11:15:58 2026 -0700
    VGP update in progress
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
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    a55016e7b323196b8a41e1f98fb511f70aaf4271 Fri Mar 20 11:15:58 2026 -0700
    VGP update in progress
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
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    a55016e7b323196b8a41e1f98fb511f70aaf4271 Fri Mar 20 11:15:58 2026 -0700
    VGP update in progress
• src/hg/makeDb/scripts/primateAiToBigBed.py
  • lines changed 57, context: html, text, full: html, text
    e82f973dc7a5a814f0fd23999aa27222fa1260da Fri Mar 20 09:56:15 2026 -0700
    primateAI track, refs #37274
• src/hg/makeDb/scripts/primateai/primateAi.as
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    59e0ac66496c36893df2b1440a037557fed23ff4 Mon Mar 23 04:31:33 2026 -0700
    fixing up primateai makedoc, refs #37274
• src/hg/makeDb/scripts/primateai/primateAiToBigBed.py
  • lines changed 57, context: html, text, full: html, text
    59e0ac66496c36893df2b1440a037557fed23ff4 Mon Mar 23 04:31:33 2026 -0700
    fixing up primateai makedoc, refs #37274
• src/hg/makeDb/scripts/trexplorer/trexplorer.as
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    f163cd6d8b443276863daa47c386072244dacc88 Tue Mar 17 07:27:58 2026 -0700
    Adding TRExplorer V2 tandem repeat catalog track to strVar supertrack, max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/trexplorer/trexplorerToBed.py
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    f163cd6d8b443276863daa47c386072244dacc88 Tue Mar 17 07:27:58 2026 -0700
    Adding TRExplorer V2 tandem repeat catalog track to strVar supertrack, max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/abraomToVcf.py
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/alfa_to_vcf.py
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/finngen_to_vcf.py
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/hrcToVcf.py
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/kovaToVcf.py
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/saudiToVcf.py
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/schema_addAcAnAf.py
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/sparkMergeVcfAddCounts.sh
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/webstr/webstrToBed.py
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    d2b7a0b56d985859c5deed015119edce22449b91 Wed Mar 18 03:45:53 2026 -0700
    Change webstr track name to motifxCopyCount format to match trexplorer, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/abraom.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/alfaVcf.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/allofus.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/encodeEgaspUpdate.html
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    17cda45b082befcc4b38faa51661b519e5669752 Tue Mar 17 10:53:48 2026 -0700
    Feedback from CR, refs #37247
• src/hg/makeDb/trackDb/human/finngen.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/gasp.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/gregor.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/cactus447way.html
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    17cda45b082befcc4b38faa51661b519e5669752 Tue Mar 17 10:53:48 2026 -0700
    Feedback from CR, refs #37247
• src/hg/makeDb/trackDb/human/hg38/gencNcOrfs.html
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    480184bd87fd28bc6979a6614994d8e5d32408d4 Fri Mar 20 16:10:47 2026 -0700
    finishing up the ncOrfs track, refs #35101
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
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    fb0b01e877831e8d82d2ccf9a7e2686caf0fb46d Thu Mar 19 15:51:47 2026 -0700
    Updating the mouseOver for the gnomAD STR track, refs #35420
• src/hg/makeDb/trackDb/human/hg38/gnomadV4.1.html
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    7ee933ee520cbb5fb38a80c3e73104e3b183c4a9 Mon Mar 16 07:56:03 2026 -0700
    fixing typos found by Claude and adding some info from gnomad.html
• src/hg/makeDb/trackDb/human/hg38/metamorf.html
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    480184bd87fd28bc6979a6614994d8e5d32408d4 Fri Mar 20 16:10:47 2026 -0700
    finishing up the ncOrfs track, refs #35101
• src/hg/makeDb/trackDb/human/hg38/ncOrfs.html
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    32210ea1b735a49d95ab5a8f7263e9dc13d47c8b Wed Mar 18 09:41:30 2026 -0700
    adding ncOrf docs page, refs #37036
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    480184bd87fd28bc6979a6614994d8e5d32408d4 Fri Mar 20 16:10:47 2026 -0700
    finishing up the ncOrfs track, refs #35101
• src/hg/makeDb/trackDb/human/hg38/ncOrfs.ra
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    480184bd87fd28bc6979a6614994d8e5d32408d4 Fri Mar 20 16:10:47 2026 -0700
    finishing up the ncOrfs track, refs #35101
• src/hg/makeDb/trackDb/human/hg38/nuorfdb.html
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    480184bd87fd28bc6979a6614994d8e5d32408d4 Fri Mar 20 16:10:47 2026 -0700
    finishing up the ncOrfs track, refs #35101
• src/hg/makeDb/trackDb/human/hg38/openprot.html
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    480184bd87fd28bc6979a6614994d8e5d32408d4 Fri Mar 20 16:10:47 2026 -0700
    finishing up the ncOrfs track, refs #35101
• src/hg/makeDb/trackDb/human/hg38/strVar.html
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    f163cd6d8b443276863daa47c386072244dacc88 Tue Mar 17 07:27:58 2026 -0700
    Adding TRExplorer V2 tandem repeat catalog track to strVar supertrack, max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    f7c829bade73527f309fe014daffc593426520c7 Tue Mar 17 07:46:51 2026 -0700
    strVar docs update
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    5f7b866b6b7036475f9631251398b895d910149d Wed Mar 18 03:43:06 2026 -0700
    str var docs update
• src/hg/makeDb/trackDb/human/hg38/strVar.ra
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    f163cd6d8b443276863daa47c386072244dacc88 Tue Mar 17 07:27:58 2026 -0700
    Adding TRExplorer V2 tandem repeat catalog track to strVar supertrack, max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    b3e96ef681c8f0325c9dc1da380eb35eedad6c63 Thu Mar 19 17:26:25 2026 -0700
    Chaning the mouseOver for the STR supertrack, refs #36652
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    6ca2d6d95a4e6862eff89b169ffc310e98e1569c Thu Mar 19 17:29:49 2026 -0700
    Changing the Repeat Motif to include the bp instead of having its own line, refs #36652
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    8bc3d5c597d9a4a29dad3804e97752cbfb40629a Fri Mar 20 07:47:14 2026 -0700
    adding trexplorer track with special tdb tags, no redmine yet
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    b33425c626414803bbddc702caecc256c5022277 Fri Mar 20 09:10:59 2026 -0700
    defining detailsHistogram tdb statements and an example histogram drawing code for it, used in the trexplorer track, refs #37273
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    12c3c77b9d4fbcff74f37816dbcfbc80fa5c1b90 Fri Mar 20 15:09:23 2026 -0700
    Fixing a typo in the mouseOver (HRPC to HPRC), no redmine
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    1bc19e88d777c2ae6c16d36052b584b3a67503ca Fri Mar 20 15:51:56 2026 -0700
    Staging the STR tracks for hg38 on hgwbeta. The tracks will go out with the v496 CGI release, refs #36652
• src/hg/makeDb/trackDb/human/hg38/trexplorer.html
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    f163cd6d8b443276863daa47c386072244dacc88 Tue Mar 17 07:27:58 2026 -0700
    Adding TRExplorer V2 tandem repeat catalog track to strVar supertrack, max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    9503ddb81a5f54677116bdf1b6d059350441c711 Wed Mar 18 09:00:18 2026 -0700
    str var docs update 2
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hgdp1kFreq.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hrc.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/indigenomes.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/kova.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/methylationAtlasSignals.html
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    019256d07c6f791954ecb76e3e40a4da960098ef Wed Mar 18 16:43:19 2026 -0700
    Fixing small issues I noticed in commits, refs #37243
• src/hg/makeDb/trackDb/human/mgrb.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/mxbFreq.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/npm.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/predictionScoresSuper.html
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    e82f973dc7a5a814f0fd23999aa27222fa1260da Fri Mar 20 09:56:15 2026 -0700
    primateAI track, refs #37274
• src/hg/makeDb/trackDb/human/predictionScoresSuper.ra
  • lines changed 1, context: html, text, full: html, text
    e82f973dc7a5a814f0fd23999aa27222fa1260da Fri Mar 20 09:56:15 2026 -0700
    primateAI track, refs #37274
• src/hg/makeDb/trackDb/human/primateAi.html
  • lines changed 86, context: html, text, full: html, text
    e82f973dc7a5a814f0fd23999aa27222fa1260da Fri Mar 20 09:56:15 2026 -0700
    primateAI track, refs #37274
• src/hg/makeDb/trackDb/human/primateAi.ra
  • lines changed 15, context: html, text, full: html, text
    e82f973dc7a5a814f0fd23999aa27222fa1260da Fri Mar 20 09:56:15 2026 -0700
    primateAI track, refs #37274
• src/hg/makeDb/trackDb/human/saudi.html
  • lines changed 51, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 3, context: html, text, full: html, text
    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/schema.html
  • lines changed 73, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 4, context: html, text, full: html, text
    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/sfariSparkExomes.html
  • lines changed 124, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/sgdpFreq.html
  • lines changed 69, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/swefreq.html
  • lines changed 68, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/tommo60kjpn.html
  • lines changed 50, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 3, context: html, text, full: html, text
    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/topmed.html
  • lines changed 53, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 3, context: html, text, full: html, text
    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/varFreqs.html
  • lines changed 739, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 55, context: html, text, full: html, text
    165a15d6a94d53f8162a01e69f3912a7a23a3b50 Mon Mar 23 06:47:55 2026 -0700
    mostly done with the variant frequencies track, refs#36642
• src/hg/makeDb/trackDb/human/varFreqs.ra
  • lines changed 226, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 185, context: html, text, full: html, text
    165a15d6a94d53f8162a01e69f3912a7a23a3b50 Mon Mar 23 06:47:55 2026 -0700
    mostly done with the variant frequencies track, refs#36642
• src/hg/makeDb/trackDb/human/varFreqsAll.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 151, context: html, text, full: html, text
    165a15d6a94d53f8162a01e69f3912a7a23a3b50 Mon Mar 23 06:47:55 2026 -0700
    mostly done with the variant frequencies track, refs#36642
• src/hg/makeDb/trackDb/relatedTracks.ra
  • lines changed 2, context: html, text, full: html, text
    ca100016955e808effb386de2e8905b9473790f3 Wed Mar 18 15:04:03 2026 -0700
    Editing the relatedTracks text shown for each STR track for hg38, refs #36652 #35420
• src/hg/makeDb/trackDb/tagTypes.tab
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    ddb0492ea27cc63662c636f901fee2490f738bab Mon Mar 16 14:30:42 2026 -0700
    Adding some faceted composite trackDb settings to tagTypes.tab for validity checks on native tracks, refs #36320
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    8bc3d5c597d9a4a29dad3804e97752cbfb40629a Fri Mar 20 07:47:14 2026 -0700
    adding trexplorer track with special tdb tags, no redmine yet
• src/hg/utils/bigChainToChain/bigChainToChain.c
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    15080c151c9929733fa2af71ce5dc98533c4f913 Fri Mar 20 18:45:40 2026 -0700
    The error messages are more detailed to help users, something MarkD wanted. It aborts by default if chromStart or chromEnd are greater than chromSize, unless the user has specified -skipChromCheck which skips both chrom name and chrom size checks now. Fixes issues with undetected overflowing integers issues, warns when they are too large instead of silently failing. Expanded the all the coordinates in the utils and the lib so that they use full range of unsigned integer space when querying and using GB for chromStart and chromEnd coordinates used by BED standard and supported by .2bit chroms. Fixed minor overflow issue with bigBed.c going past the end of the 4GB space. I made changes to bigBedToBed.c and then used CLAUDE prompt to refactor those changes into the 6 other utilities bigMafToMaf, bigChainToChain, bigGenePredToGenePred, bigPslToPsl, bigWigToBedGraph, bigWigToWig. refs #28109
• src/hg/utils/bigGenePredToGenePred/bigGenePredToGenePred.c
  • lines changed 41, context: html, text, full: html, text
    15080c151c9929733fa2af71ce5dc98533c4f913 Fri Mar 20 18:45:40 2026 -0700
    The error messages are more detailed to help users, something MarkD wanted. It aborts by default if chromStart or chromEnd are greater than chromSize, unless the user has specified -skipChromCheck which skips both chrom name and chrom size checks now. Fixes issues with undetected overflowing integers issues, warns when they are too large instead of silently failing. Expanded the all the coordinates in the utils and the lib so that they use full range of unsigned integer space when querying and using GB for chromStart and chromEnd coordinates used by BED standard and supported by .2bit chroms. Fixed minor overflow issue with bigBed.c going past the end of the 4GB space. I made changes to bigBedToBed.c and then used CLAUDE prompt to refactor those changes into the 6 other utilities bigMafToMaf, bigChainToChain, bigGenePredToGenePred, bigPslToPsl, bigWigToBedGraph, bigWigToWig. refs #28109
• src/hg/utils/bigMafToMaf/bigMafToMaf.c
  • lines changed 40, context: html, text, full: html, text
    15080c151c9929733fa2af71ce5dc98533c4f913 Fri Mar 20 18:45:40 2026 -0700
    The error messages are more detailed to help users, something MarkD wanted. It aborts by default if chromStart or chromEnd are greater than chromSize, unless the user has specified -skipChromCheck which skips both chrom name and chrom size checks now. Fixes issues with undetected overflowing integers issues, warns when they are too large instead of silently failing. Expanded the all the coordinates in the utils and the lib so that they use full range of unsigned integer space when querying and using GB for chromStart and chromEnd coordinates used by BED standard and supported by .2bit chroms. Fixed minor overflow issue with bigBed.c going past the end of the 4GB space. I made changes to bigBedToBed.c and then used CLAUDE prompt to refactor those changes into the 6 other utilities bigMafToMaf, bigChainToChain, bigGenePredToGenePred, bigPslToPsl, bigWigToBedGraph, bigWigToWig. refs #28109
• src/hg/utils/bigPslToPsl/bigPslToPsl.c
  • lines changed 41, context: html, text, full: html, text
    15080c151c9929733fa2af71ce5dc98533c4f913 Fri Mar 20 18:45:40 2026 -0700
    The error messages are more detailed to help users, something MarkD wanted. It aborts by default if chromStart or chromEnd are greater than chromSize, unless the user has specified -skipChromCheck which skips both chrom name and chrom size checks now. Fixes issues with undetected overflowing integers issues, warns when they are too large instead of silently failing. Expanded the all the coordinates in the utils and the lib so that they use full range of unsigned integer space when querying and using GB for chromStart and chromEnd coordinates used by BED standard and supported by .2bit chroms. Fixed minor overflow issue with bigBed.c going past the end of the 4GB space. I made changes to bigBedToBed.c and then used CLAUDE prompt to refactor those changes into the 6 other utilities bigMafToMaf, bigChainToChain, bigGenePredToGenePred, bigPslToPsl, bigWigToBedGraph, bigWigToWig. refs #28109
• src/hg/utils/hubCheck/hubCheck.c
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    5bf51515b69bd518b2154df5476bc7ed319e33bd Sun Mar 22 21:05:42 2026 -0700
    Add bigMethyl to the list of valid tracktyopes to check. Generate a warning rather than error for halSnake tracks when when HAL support is not compiled in. Added danger comments about duplicated track name checking
• src/hg/utils/hubCheck/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    5bf51515b69bd518b2154df5476bc7ed319e33bd Sun Mar 22 21:05:42 2026 -0700
    Add bigMethyl to the list of valid tracktyopes to check. Generate a warning rather than error for halSnake tracks when when HAL support is not compiled in. Added danger comments about duplicated track name checking
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    75a3d3c5cf3525a7a25dfd53cdd765daf8e32cef Fri Mar 20 11:06:36 2026 -0700
    123 new lineages and slight tweaks to several existing lineage definitions.
• src/inc/bigBedCmdSupport.h
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    15080c151c9929733fa2af71ce5dc98533c4f913 Fri Mar 20 18:45:40 2026 -0700
    The error messages are more detailed to help users, something MarkD wanted. It aborts by default if chromStart or chromEnd are greater than chromSize, unless the user has specified -skipChromCheck which skips both chrom name and chrom size checks now. Fixes issues with undetected overflowing integers issues, warns when they are too large instead of silently failing. Expanded the all the coordinates in the utils and the lib so that they use full range of unsigned integer space when querying and using GB for chromStart and chromEnd coordinates used by BED standard and supported by .2bit chroms. Fixed minor overflow issue with bigBed.c going past the end of the 4GB space. I made changes to bigBedToBed.c and then used CLAUDE prompt to refactor those changes into the 6 other utilities bigMafToMaf, bigChainToChain, bigGenePredToGenePred, bigPslToPsl, bigWigToBedGraph, bigWigToWig. refs #28109
• src/inc/cheapcgi.h
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    651f959d7553ee0256b1e0b37ffa83d64709511d Mon Mar 16 17:57:16 2026 -0700
    Adding accessible labels to form controls across main CGI pages. Extends cheapcgi and hui libraries with aria-label support for track visibility dropdowns, and adds <label> elements to hgBlat, hgTables, hgPcr, and hgGateway form controls. Also adds Form Control Labels section to accessibility page. refs #37253
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    21805a85e551d9688edb34683f955c8a41710e80 Wed Mar 18 22:17:44 2026 -0700
    Added a #defined-out version of cgiDecode that's much faster for large cart variables. Came up once years ago but was never put into practice. refs #37262
• src/inc/filePath.h
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    3d91dda86ff75aa59b6095ae6bcab96d72f99656 Wed Mar 18 22:45:15 2026 -0700
    eatExcessDotDotInPath does unexpected things with inputs like ../../ and /a/./.. . Adding an alternate version until we can assess the impacts of changing. refs #36320, #37263
• src/inc/portable.h
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    3d91dda86ff75aa59b6095ae6bcab96d72f99656 Wed Mar 18 22:45:15 2026 -0700
    eatExcessDotDotInPath does unexpected things with inputs like ../../ and /a/./.. . Adding an alternate version until we can assess the impacts of changing. refs #36320, #37263
• src/lib/bigBed.c
  • lines changed 2, context: html, text, full: html, text
    15080c151c9929733fa2af71ce5dc98533c4f913 Fri Mar 20 18:45:40 2026 -0700
    The error messages are more detailed to help users, something MarkD wanted. It aborts by default if chromStart or chromEnd are greater than chromSize, unless the user has specified -skipChromCheck which skips both chrom name and chrom size checks now. Fixes issues with undetected overflowing integers issues, warns when they are too large instead of silently failing. Expanded the all the coordinates in the utils and the lib so that they use full range of unsigned integer space when querying and using GB for chromStart and chromEnd coordinates used by BED standard and supported by .2bit chroms. Fixed minor overflow issue with bigBed.c going past the end of the 4GB space. I made changes to bigBedToBed.c and then used CLAUDE prompt to refactor those changes into the 6 other utilities bigMafToMaf, bigChainToChain, bigGenePredToGenePred, bigPslToPsl, bigWigToBedGraph, bigWigToWig. refs #28109
• src/lib/bigBedCmdSupport.c
  • lines changed 141, context: html, text, full: html, text
    15080c151c9929733fa2af71ce5dc98533c4f913 Fri Mar 20 18:45:40 2026 -0700
    The error messages are more detailed to help users, something MarkD wanted. It aborts by default if chromStart or chromEnd are greater than chromSize, unless the user has specified -skipChromCheck which skips both chrom name and chrom size checks now. Fixes issues with undetected overflowing integers issues, warns when they are too large instead of silently failing. Expanded the all the coordinates in the utils and the lib so that they use full range of unsigned integer space when querying and using GB for chromStart and chromEnd coordinates used by BED standard and supported by .2bit chroms. Fixed minor overflow issue with bigBed.c going past the end of the 4GB space. I made changes to bigBedToBed.c and then used CLAUDE prompt to refactor those changes into the 6 other utilities bigMafToMaf, bigChainToChain, bigGenePredToGenePred, bigPslToPsl, bigWigToBedGraph, bigWigToWig. refs #28109
• src/lib/cheapcgi.c
  • lines changed 13, context: html, text, full: html, text
    651f959d7553ee0256b1e0b37ffa83d64709511d Mon Mar 16 17:57:16 2026 -0700
    Adding accessible labels to form controls across main CGI pages. Extends cheapcgi and hui libraries with aria-label support for track visibility dropdowns, and adds <label> elements to hgBlat, hgTables, hgPcr, and hgGateway form controls. Also adds Form Control Labels section to accessibility page. refs #37253
  • lines changed 68, context: html, text, full: html, text
    21805a85e551d9688edb34683f955c8a41710e80 Wed Mar 18 22:17:44 2026 -0700
    Added a #defined-out version of cgiDecode that's much faster for large cart variables. Came up once years ago but was never put into practice. refs #37262
  • lines changed 3, context: html, text, full: html, text
    8094e7fe54b5d6725fc5c6a6fecb9efdde170967 Thu Mar 19 00:55:26 2026 -0700
    A few fixes in the ifdef'd alternate cgiDecode version; ensuring a length variable is appropriately set and used, refs #37262
• src/lib/filePath.c
  • lines changed 25, context: html, text, full: html, text
    3d91dda86ff75aa59b6095ae6bcab96d72f99656 Wed Mar 18 22:45:15 2026 -0700
    eatExcessDotDotInPath does unexpected things with inputs like ../../ and /a/./.. . Adding an alternate version until we can assess the impacts of changing. refs #36320, #37263
• src/lib/options.c
  • lines changed 10, context: html, text, full: html, text
    15080c151c9929733fa2af71ce5dc98533c4f913 Fri Mar 20 18:45:40 2026 -0700
    The error messages are more detailed to help users, something MarkD wanted. It aborts by default if chromStart or chromEnd are greater than chromSize, unless the user has specified -skipChromCheck which skips both chrom name and chrom size checks now. Fixes issues with undetected overflowing integers issues, warns when they are too large instead of silently failing. Expanded the all the coordinates in the utils and the lib so that they use full range of unsigned integer space when querying and using GB for chromStart and chromEnd coordinates used by BED standard and supported by .2bit chroms. Fixed minor overflow issue with bigBed.c going past the end of the 4GB space. I made changes to bigBedToBed.c and then used CLAUDE prompt to refactor those changes into the 6 other utilities bigMafToMaf, bigChainToChain, bigGenePredToGenePred, bigPslToPsl, bigWigToBedGraph, bigWigToWig. refs #28109
• src/lib/osunix.c
  • lines changed 89, context: html, text, full: html, text
    3d91dda86ff75aa59b6095ae6bcab96d72f99656 Wed Mar 18 22:45:15 2026 -0700
    eatExcessDotDotInPath does unexpected things with inputs like ../../ and /a/./.. . Adding an alternate version until we can assess the impacts of changing. refs #36320, #37263
  • lines changed 1, context: html, text, full: html, text
    6fffb6bc625848c354f044f0f1faed45c84c8f7d Wed Mar 18 23:01:31 2026 -0700
    Removing unused variable, refs #36320
• src/lib/udc.c
  • lines changed 6, context: html, text, full: html, text
    7d39d6e6cbd055195a34ad066be052dbc338b258 Sun Mar 22 21:12:13 2026 -0700
    added missing newlines in verbose() calls that led to hard to read message
• src/utils/bigBedToBed/bigBedToBed.c
  • lines changed 41, context: html, text, full: html, text
    15080c151c9929733fa2af71ce5dc98533c4f913 Fri Mar 20 18:45:40 2026 -0700
    The error messages are more detailed to help users, something MarkD wanted. It aborts by default if chromStart or chromEnd are greater than chromSize, unless the user has specified -skipChromCheck which skips both chrom name and chrom size checks now. Fixes issues with undetected overflowing integers issues, warns when they are too large instead of silently failing. Expanded the all the coordinates in the utils and the lib so that they use full range of unsigned integer space when querying and using GB for chromStart and chromEnd coordinates used by BED standard and supported by .2bit chroms. Fixed minor overflow issue with bigBed.c going past the end of the 4GB space. I made changes to bigBedToBed.c and then used CLAUDE prompt to refactor those changes into the 6 other utilities bigMafToMaf, bigChainToChain, bigGenePredToGenePred, bigPslToPsl, bigWigToBedGraph, bigWigToWig. refs #28109
• src/utils/bigWigToBedGraph/bigWigToBedGraph.c
  • lines changed 41, context: html, text, full: html, text
    15080c151c9929733fa2af71ce5dc98533c4f913 Fri Mar 20 18:45:40 2026 -0700
    The error messages are more detailed to help users, something MarkD wanted. It aborts by default if chromStart or chromEnd are greater than chromSize, unless the user has specified -skipChromCheck which skips both chrom name and chrom size checks now. Fixes issues with undetected overflowing integers issues, warns when they are too large instead of silently failing. Expanded the all the coordinates in the utils and the lib so that they use full range of unsigned integer space when querying and using GB for chromStart and chromEnd coordinates used by BED standard and supported by .2bit chroms. Fixed minor overflow issue with bigBed.c going past the end of the 4GB space. I made changes to bigBedToBed.c and then used CLAUDE prompt to refactor those changes into the 6 other utilities bigMafToMaf, bigChainToChain, bigGenePredToGenePred, bigPslToPsl, bigWigToBedGraph, bigWigToWig. refs #28109
• src/utils/bigWigToWig/bigWigToWig.c
  • lines changed 42, context: html, text, full: html, text
    15080c151c9929733fa2af71ce5dc98533c4f913 Fri Mar 20 18:45:40 2026 -0700
    The error messages are more detailed to help users, something MarkD wanted. It aborts by default if chromStart or chromEnd are greater than chromSize, unless the user has specified -skipChromCheck which skips both chrom name and chrom size checks now. Fixes issues with undetected overflowing integers issues, warns when they are too large instead of silently failing. Expanded the all the coordinates in the utils and the lib so that they use full range of unsigned integer space when querying and using GB for chromStart and chromEnd coordinates used by BED standard and supported by .2bit chroms. Fixed minor overflow issue with bigBed.c going past the end of the 4GB space. I made changes to bigBedToBed.c and then used CLAUDE prompt to refactor those changes into the 6 other utilities bigMafToMaf, bigChainToChain, bigGenePredToGenePred, bigPslToPsl, bigWigToBedGraph, bigWigToWig. refs #28109
• src/utils/faCount/faCount.c
  • lines changed 14, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/makefile
  • lines changed 3, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/expected/allThree.txt
  • lines changed 6, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/expected/allThree_2bit.txt
  • lines changed 6, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/expected/mixed.txt
  • lines changed 10, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/expected/mixedDinuc.txt
  • lines changed 10, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/expected/mixedStrands.txt
  • lines changed 10, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/expected/mixedSummary.txt
  • lines changed 3, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/expected/s1.s2.dinuc.txt
  • lines changed 4, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/expected/s1.s2.strands.txt
  • lines changed 4, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/expected/s1.s2.summary.txt
  • lines changed 3, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/expected/s1.s2.txt
  • lines changed 4, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/expected/s1.s2_2bit.dinuc.txt
  • lines changed 4, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/expected/s1.s2_2bit.strands.txt
  • lines changed 4, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/expected/s1.s2_2bit.summary.txt
  • lines changed 3, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/expected/s1.s2_2bit.txt
  • lines changed 4, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/expected/s1.txt
  • lines changed 3, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/expected/s1Ands2.txt
  • lines changed 4, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/expected/s1Ands2_2bit.txt
  • lines changed 4, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/expected/s1_2bit.txt
  • lines changed 3, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/expected/s2.txt
  • lines changed 3, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/expected/s2_2bit.txt
  • lines changed 3, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/input/s1.2bit
  • lines changed 0, context: html, text, full: html, text
    10801162f7e4bbb3a4f704c7545043056ebaecb5 Mon Mar 16 14:43:44 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/input/s1.fa.gz
  • lines changed 0, context: html, text, full: html, text
    10801162f7e4bbb3a4f704c7545043056ebaecb5 Mon Mar 16 14:43:44 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/input/s1.s2.2bit
  • lines changed 0, context: html, text, full: html, text
    10801162f7e4bbb3a4f704c7545043056ebaecb5 Mon Mar 16 14:43:44 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/input/s1.s2.fa.gz
  • lines changed 0, context: html, text, full: html, text
    10801162f7e4bbb3a4f704c7545043056ebaecb5 Mon Mar 16 14:43:44 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/input/s2.2bit
  • lines changed 0, context: html, text, full: html, text
    10801162f7e4bbb3a4f704c7545043056ebaecb5 Mon Mar 16 14:43:44 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/input/s2.fa.gz
  • lines changed 0, context: html, text, full: html, text
    10801162f7e4bbb3a4f704c7545043056ebaecb5 Mon Mar 16 14:43:44 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faCount/tests/makefile
  • lines changed 100, context: html, text, full: html, text
    b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700
    enhanced command to allow 2bit inputs - code by claude assistance - no redmine
• src/utils/faSize/tests/expected/mixed.txt
  • lines changed 6, context: html, text, full: html, text
    a4d9c97c1a9bff4e6c0a7d54b02b89f11a4ee0fd Mon Mar 16 14:12:28 2026 -0700
    add mixed operation fasta and 2bit in one argument set no redmine
• src/utils/faSize/tests/expected/mixedDetailed.txt
  • lines changed 8, context: html, text, full: html, text
    a4d9c97c1a9bff4e6c0a7d54b02b89f11a4ee0fd Mon Mar 16 14:12:28 2026 -0700
    add mixed operation fasta and 2bit in one argument set no redmine
• src/utils/faSize/tests/expected/mixedVeryDetailed.txt
  • lines changed 8, context: html, text, full: html, text
    a4d9c97c1a9bff4e6c0a7d54b02b89f11a4ee0fd Mon Mar 16 14:12:28 2026 -0700
    add mixed operation fasta and 2bit in one argument set no redmine
• src/utils/faSize/tests/makefile
  • lines changed 15, context: html, text, full: html, text
    a4d9c97c1a9bff4e6c0a7d54b02b89f11a4ee0fd Mon Mar 16 14:12:28 2026 -0700
    add mixed operation fasta and 2bit in one argument set no redmine
• src/utils/makefile
  • lines changed 11, context: html, text, full: html, text
    a939f7e2ddc1a11f641e065b0d49a57f4ee8ae14 Mon Mar 23 06:21:52 2026 -0700
    moving genePredCompare tool to non-apps build, email from Hiram
• src/utils/qa/checkHTTPS
  • lines changed 2, context: html, text, full: html, text
    66e8e1c2647f443f0e8371d44f40266b6ff20abd Tue Mar 17 14:26:40 2026 -0700
    Changing certificate renewal warnings to 14 days ahead instead of 30
  • lines changed 2, context: html, text, full: html, text
    5ba2c58ea600a81b0f5f8bc38a5c43b1500d9099 Wed Mar 18 14:56:48 2026 -0700
    Adding psygene server to the certs check script, per Erich's request
• src/utils/qa/qaTestScript.py
  • lines changed 8, context: html, text, full: html, text
    845001c015716a49a2f316b8b349eef37a7b1e9d Mon Mar 23 09:30:48 2026 -0700
    Fixed qaTestScript ActionChains hang, updated two element selectors to match current UI, and increase HAL hub timeout, No RM
• src/utils/qa/staticpaths
  • lines changed 4, context: html, text, full: html, text
    c605596280a5b280f9cd1dca798cc45d0dc26229 Mon Mar 16 12:53:27 2026 -0700
    Removed eng and mgc directories since they do not have html files. Removed ENCODE and license directories since all the html files are in the linkCheckExclude file. No RM.

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• files changed: 330