All File Changes

v498_preview to v498_preview2 (2026-04-27 to 2026-05-04) v498

• confs/asia.hg.conf
  • lines changed 6, context: html, text, full: html, text
    5fbb3fbaa31bbe6a068f98f73924d7512a26b389 Sun May 3 01:11:20 2026 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 6, context: html, text, full: html, text
    5fbb3fbaa31bbe6a068f98f73924d7512a26b389 Sun May 3 01:11:20 2026 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 3, context: html, text, full: html, text
    5fbb3fbaa31bbe6a068f98f73924d7512a26b389 Sun May 3 01:11:20 2026 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 6, context: html, text, full: html, text
    5fbb3fbaa31bbe6a068f98f73924d7512a26b389 Sun May 3 01:11:20 2026 -0700
    Installing updated hg.conf files from UCSC servers
• docs/index.md
  • lines changed 15, context: html, text, full: html, text
    06b9de0132c8653afc3c2d91cbc386c2f3967e72 Tue Apr 28 12:05:20 2026 -0700
    QA cleanup of /docs/ landing page and staticPage.lua writer. refs #36894 docs/index.md: fix /docs/contacts.html -> /contacts.html (was 404), correct "Hubs Basics" -> "Hub Basics", drop stray "?" in fragment-only URLs (/cgi-bin/hgHubConnect?#hubDeveloper etc.), convert section headings to sentence case per GB convention, rewrite tutorial-table descriptions in a consistent imperative voice, and replace the fragmented "Checked using our hub development tools" bullet with "Validate your hub with our hub development tools". docs/staticPage.lua: extend Link() to add target="_blank" rel="noopener" on http(s):// absolute URLs, and stop emitting empty title='' on every link. Modernize Table() output to drop deprecated HTML4 attributes: <col width="X%"> -> <col style="width: X%">, and align="left|right|center" on <th>/<td> replaced with style="text-align: ..." (omitted for the default left alignment). Renames html_align() -> html_align_style() to reflect the new return value.
  • lines changed 121, context: html, text, full: html, text
    61438453e9f8be7a5949725a688ac6cf709add28 Tue Apr 28 13:06:10 2026 -0700
    Restructure /docs/ landing page for new users; add docs-page styling. refs #36894 docs/index.md: rewrite as a beginner-first landing page. Replace the prior five-section structure with a flat five-H2 outline -- Tutorials, Visualize your own data, Share your work, Download data, Get help -- so every entry in the sidebar TOC maps to specific content rather than to a vague grouping. Promote the tutorial table from a buried H3 to top-level content. Drop sections that don't serve new users (the "Understanding assemblies/annotations" primer, the MySQL bullet, the mirror paragraph, the Multi-Region View specific mention, and the four scattered "Relevant FAQs" lists). Consolidate help into a single closer with contact, FAQ, workshops, and the suggestion form. Distinguish custom tracks vs track hubs ("simpler option" vs "more powerful and configurable"). Make tutorial titles the table links and drop the redundant Link column. docs/staticPage.lua: add a docs-page class to the row wrapper so /docs/- only CSS can be scoped without affecting other gbsPage static pages. src/hg/htdocs/staticStyle/gbStatic.css: add scoped .docs-page styles for the sidebar TOC ("On this page" label) and tables (roomier padding, zebra striping using the existing tr.even/tr.odd classes, subtle hover). All new rules are namespaced under .docs-page so the rest of the site is untouched.
• docs/staticPage.html
  • lines changed 34, context: html, text, full: html, text
    da335975e0d5712f47ee0d19b0eb5003d1a1b7f0 Mon Apr 27 14:16:44 2026 -0700
    Add sticky sidebar table of contents to /docs/ pages, ReadTheDocs-style. refs #36894 staticPage.lua: wrap doc body in a Bootstrap row with a col-md-2 sidebar holding a .docs-toc nav list and a col-md-10 content column. Collect both lev==1 and lev==2 headings into the TOC and emit id attributes on <h2> elements (replacing the prior inline <a name=> anchors). staticPage.html: add a small vanilla-JS scroll-spy that toggles .active on the TOC <li> matching the section currently scrolled past the top. No-ops on pages without #docs-toc. gbStatic.css: add styles for .docs-toc / .docs-toc-row (position: sticky, flex row for equal-height columns, link styling with active-state border). All rules are scoped to the .docs-toc class so non-docs pages sharing gbStatic.css are unaffected.
• docs/staticPage.lua
  • lines changed 22, context: html, text, full: html, text
    da335975e0d5712f47ee0d19b0eb5003d1a1b7f0 Mon Apr 27 14:16:44 2026 -0700
    Add sticky sidebar table of contents to /docs/ pages, ReadTheDocs-style. refs #36894 staticPage.lua: wrap doc body in a Bootstrap row with a col-md-2 sidebar holding a .docs-toc nav list and a col-md-10 content column. Collect both lev==1 and lev==2 headings into the TOC and emit id attributes on <h2> elements (replacing the prior inline <a name=> anchors). staticPage.html: add a small vanilla-JS scroll-spy that toggles .active on the TOC <li> matching the section currently scrolled past the top. No-ops on pages without #docs-toc. gbStatic.css: add styles for .docs-toc / .docs-toc-row (position: sticky, flex row for equal-height columns, link styling with active-state border). All rules are scoped to the .docs-toc class so non-docs pages sharing gbStatic.css are unaffected.
  • lines changed 1, context: html, text, full: html, text
    881e822ef9c0be6de740f46db251c96a202dd3b8 Tue Apr 28 11:09:54 2026 -0700
    Fix incorrect comment in staticPage.lua; closing div is col-md-10, not col-md-9. Per CR feedback. refs #36894
  • lines changed 22, context: html, text, full: html, text
    06b9de0132c8653afc3c2d91cbc386c2f3967e72 Tue Apr 28 12:05:20 2026 -0700
    QA cleanup of /docs/ landing page and staticPage.lua writer. refs #36894 docs/index.md: fix /docs/contacts.html -> /contacts.html (was 404), correct "Hubs Basics" -> "Hub Basics", drop stray "?" in fragment-only URLs (/cgi-bin/hgHubConnect?#hubDeveloper etc.), convert section headings to sentence case per GB convention, rewrite tutorial-table descriptions in a consistent imperative voice, and replace the fragmented "Checked using our hub development tools" bullet with "Validate your hub with our hub development tools". docs/staticPage.lua: extend Link() to add target="_blank" rel="noopener" on http(s):// absolute URLs, and stop emitting empty title='' on every link. Modernize Table() output to drop deprecated HTML4 attributes: <col width="X%"> -> <col style="width: X%">, and align="left|right|center" on <th>/<td> replaced with style="text-align: ..." (omitted for the default left alignment). Renames html_align() -> html_align_style() to reflect the new return value.
  • lines changed 3, context: html, text, full: html, text
    61438453e9f8be7a5949725a688ac6cf709add28 Tue Apr 28 13:06:10 2026 -0700
    Restructure /docs/ landing page for new users; add docs-page styling. refs #36894 docs/index.md: rewrite as a beginner-first landing page. Replace the prior five-section structure with a flat five-H2 outline -- Tutorials, Visualize your own data, Share your work, Download data, Get help -- so every entry in the sidebar TOC maps to specific content rather than to a vague grouping. Promote the tutorial table from a buried H3 to top-level content. Drop sections that don't serve new users (the "Understanding assemblies/annotations" primer, the MySQL bullet, the mirror paragraph, the Multi-Region View specific mention, and the four scattered "Relevant FAQs" lists). Consolidate help into a single closer with contact, FAQ, workshops, and the suggestion form. Distinguish custom tracks vs track hubs ("simpler option" vs "more powerful and configurable"). Make tutorial titles the table links and drop the redundant Link column. docs/staticPage.lua: add a docs-page class to the row wrapper so /docs/- only CSS can be scoped without affecting other gbsPage static pages. src/hg/htdocs/staticStyle/gbStatic.css: add scoped .docs-page styles for the sidebar TOC ("On this page" label) and tables (roomier padding, zebra striping using the existing tr.even/tr.odd classes, subtle hover). All new rules are namespaced under .docs-page so the rest of the site is untouched.
• src/hg/hgCustom/hgCustom.c
  • lines changed 99, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 8, context: html, text, full: html, text
    0750648bee41e57d7f1cbc3de8e3d9177bfd4c70 Fri May 1 10:02:25 2026 -0700
    Initial support for ripples seach in usher-sampled-server. Enabled by config param ripplesEnabled. If enabled, there is a new checkbox for the user to click if they want the extra search. Currently hardcoded to max of 10 sequences, otherwise extra search is not done (too slow). Ripples results, if any, are displayed in a table before the usual summary table.
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 116, context: html, text, full: html, text
    0750648bee41e57d7f1cbc3de8e3d9177bfd4c70 Fri May 1 10:02:25 2026 -0700
    Initial support for ripples seach in usher-sampled-server. Enabled by config param ripplesEnabled. If enabled, there is a new checkbox for the user to click if they want the extra search. Currently hardcoded to max of 10 sequences, otherwise extra search is not done (too slow). Ripples results, if any, are displayed in a table before the usual summary table.
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 34, context: html, text, full: html, text
    0750648bee41e57d7f1cbc3de8e3d9177bfd4c70 Fri May 1 10:02:25 2026 -0700
    Initial support for ripples seach in usher-sampled-server. Enabled by config param ripplesEnabled. If enabled, there is a new checkbox for the user to click if they want the extra search. Currently hardcoded to max of 10 sequences, otherwise extra search is not done (too slow). Ripples results, if any, are displayed in a table before the usual summary table.
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 346, context: html, text, full: html, text
    0750648bee41e57d7f1cbc3de8e3d9177bfd4c70 Fri May 1 10:02:25 2026 -0700
    Initial support for ripples seach in usher-sampled-server. Enabled by config param ripplesEnabled. If enabled, there is a new checkbox for the user to click if they want the extra search. Currently hardcoded to max of 10 sequences, otherwise extra search is not done (too slow). Ripples results, if any, are displayed in a table before the usual summary table.
• src/hg/hgTables/all.joiner
  • lines changed 1, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/hgTables/custom.c
  • lines changed 7, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/hgTables/filterFields.c
  • lines changed 2, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/hgTables/hgTables.c
  • lines changed 11, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/hgTables/joining.c
  • lines changed 7, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/hgTables/schema.c
  • lines changed 3, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    ca9c863b4422bb49521f37b6a29397d03d57f17a Mon Apr 27 13:42:24 2026 -0700
    Bump up size of readableWidth for track description pages from 50chars to 70chars. Also make hgTrackUi use the same width for the track descriptions, refs #37430
  • lines changed 9, context: html, text, full: html, text
    33d86ed28182f6dc7903ac522f4d94bf9906274d Wed Apr 29 01:44:21 2026 -0700
    add submit button to superTrack filters, refs #36258
  • lines changed 96, context: html, text, full: html, text
    b53a97d26633a1f174a7031559a69d37e393379f Fri May 1 14:19:19 2026 -0700
    Allow myVariants tracks to be shared similar to google docs, read only and read+edit access by username or for all. Last write wins. Currently no history of changes, leaving that for the next version of the feature
  • lines changed 24, context: html, text, full: html, text
    28b0357b2f17050e591d3d21e3fe2511e2ad0b55 Mon May 4 05:50:49 2026 -0700
    hgTrackUi: address #37426 QA feedback - Drop the unconditional bottom Submit button (introduced in 33d86ed) — it duplicated the existing top Submit on composites like refSeqComposite. Gate it on tdbIsSuperTrack so only superTracks get the bottom Submit (the case the original commit was meant to address). - Render the "Reset to defaults" link on superTrack pages too. Wire up the cart-clear path: superTrack children live in tdb->children (slRef), not tdb->subtracks, so cartRemoveAllForTdbAndChildren wouldn't reach them — walk children explicitly. - Filters heading: "Filters " → "Filters:" (matches the "Apply visibility:" / "Show or hide ...:" style elsewhere on the page). - Reword the Filters info tooltip per Gerardo's QA suggestion. refs #37426
  • lines changed 1, context: html, text, full: html, text
    e375b6261547192b9aebef00662d48fb7256c032 Mon May 4 09:00:02 2026 -0700
    Fix a comment typo and some potential XSS vectors pointed out in code review email
• src/hg/hgTracks/bamTrack.c
  • lines changed 1, context: html, text, full: html, text
    0e174ffaab04a16af6cbb3b368495772b57a24f5 Wed Apr 29 14:54:10 2026 -0700
    hgTracks: route bigDataUrl through hReplaceGbdb in parallel-loading code paths so gbdbLoc1/gbdbLoc2 rewrites apply to bigBed, bigWig, and bamWig tracks. refs #37479
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 2, context: html, text, full: html, text
    0e174ffaab04a16af6cbb3b368495772b57a24f5 Wed Apr 29 14:54:10 2026 -0700
    hgTracks: route bigDataUrl through hReplaceGbdb in parallel-loading code paths so gbdbLoc1/gbdbLoc2 rewrites apply to bigBed, bigWig, and bamWig tracks. refs #37479
• src/hg/hgTracks/bigWigTrack.c
  • lines changed 1, context: html, text, full: html, text
    0e174ffaab04a16af6cbb3b368495772b57a24f5 Wed Apr 29 14:54:10 2026 -0700
    hgTracks: route bigDataUrl through hReplaceGbdb in parallel-loading code paths so gbdbLoc1/gbdbLoc2 rewrites apply to bigBed, bigWig, and bamWig tracks. refs #37479
• src/hg/hgTracks/config.c
  • lines changed 29, context: html, text, full: html, text
    b53a97d26633a1f174a7031559a69d37e393379f Fri May 1 14:19:19 2026 -0700
    Allow myVariants tracks to be shared similar to google docs, read only and read+edit access by username or for all. Last write wins. Currently no history of changes, leaving that for the next version of the feature
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    c4559e7ed9e720d0101ac6839cd1772a611b44d1 Mon Apr 27 16:07:25 2026 -0700
    hgTracks: emit printTrackTiming() on the trackImgOnly fast path, refs #37445 When hgTracks is called with hgt.trackImgOnly=1 and !ideogramToo it takes an early-return path at hgTracks.c:9469 that emits the image and map but skipped the per-track timing block. With measureTiming=1 set, emit printTrackTiming() before returning so per-track load/draw times are available to clients of the JS-redraw fast path. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 7, context: html, text, full: html, text
    14cb2006a261922f27924e0fed14f067ce90fd1e Tue Apr 28 14:17:58 2026 -0700
    Move chromAlias info icon next to chromosome position, refs #29201 Relocate the icon from the right side of the search bar to between the Multi-region button and the chromosome position display, per reviewer feedback that the prior location read ambiguously next to the search box. Show only the (i) glyph (drop the "Aliases" label), bump font-size to 110%, tighten margins, and rename the tooltip from "Also known as:" to "Alternate sequence names:".
  • lines changed 5, context: html, text, full: html, text
    52ef51261a5be2ca2dea9e73642240cd46b6d865 Tue Apr 28 15:16:24 2026 -0700
    Extend chromAlias info icon mouseover with usage description and docs link, refs #29201 Per Max's feedback on the ticket, expand the tooltip to explain where alternative chromosome names can be used (position box, custom tracks, track hubs, bigBed/bigWig) and link to the assembly hub help docs page. Bold the "Alternate sequence names" header.
  • lines changed 12, context: html, text, full: html, text
    0b7b4c7700268abd9705dc8feef9f284ffdff350 Fri May 1 09:01:40 2026 -0700
    hgTracks: let quickLift tracks join the parallel-fetch worker pool When a track has a quickLiftDb setting, validate its bigDataUrl against the source db rather than the current target db, so the /gbdb/<sourceDb>/ prefix check in customFactoryParallelLoad accepts it. Previously quickLift tracks fell through to serial load, costing ~5 s per track on the main thread. refs #37470
  • lines changed 7, context: html, text, full: html, text
    a44642a3a2f8ce803f75233cbc67b50a04a7614b Fri May 1 12:46:58 2026 -0700
    hgTracks: validate decorator bigDataUrl against quickLiftDb when present loadDecorators was passing the current target db to isValidBigDataUrl, but quickLifted tracks have decorator bigDataUrls under /gbdb/<sourceDb>/..., matching the source assembly. Mirror the substitution already done in isTrackForParallelLoad so decorator validation does not errAbort on quickLifted tracks.
  • lines changed 99, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/hgTracks/hgTracks.h
  • lines changed 31, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/hgTracks/mainMain.c
  • lines changed 5, context: html, text, full: html, text
    b53a97d26633a1f174a7031559a69d37e393379f Fri May 1 14:19:19 2026 -0700
    Allow myVariants tracks to be shared similar to google docs, read only and read+edit access by username or for all. Last write wins. Currently no history of changes, leaving that for the next version of the feature
• src/hg/hgTracks/makeItemsTrack.c
  • lines changed 221, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/hgTracks/myVariantsTrack.c
  • lines changed 921, context: html, text, full: html, text
    5e26e73c8e71bfdcc0b96ee6ec3b480ea04867ec Mon May 4 08:37:03 2026 -0700
    Add missing file for myVariants feature, refs build email
• src/hg/hgc/hgc.c
  • lines changed 5, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/hgc/hgc.h
  • lines changed 1, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
  • lines changed 1, context: html, text, full: html, text
    e375b6261547192b9aebef00662d48fb7256c032 Mon May 4 09:00:02 2026 -0700
    Fix a comment typo and some potential XSS vectors pointed out in code review email
• src/hg/hgc/makeItemsClick.c
  • lines changed 86, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/hgc/makefile
  • lines changed 1, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/hgc/myVariantsClick.c
  • lines changed 338, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
  • lines changed 2, context: html, text, full: html, text
    e375b6261547192b9aebef00662d48fb7256c032 Mon May 4 09:00:02 2026 -0700
    Fix a comment typo and some potential XSS vectors pointed out in code review email
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 2, context: html, text, full: html, text
    e53713685bee07a91be62ffb8354d7478ce2ce7a Wed Apr 29 15:05:45 2026 -0700
    NMD Escape: switch default to MANE+Gencode, add MANE to descriptions and news. refs #33737 - nmd.ra: nmdEscMane on/pack and nmdEscGencode on/dense as the new defaults; nmdEscNcbiRefSeq off/hide. Fix "FIlter" typo in the RefSeq filterLabel. - nmd.html and nmdEscTranscripts.html: list MANE alongside Gencode and RefSeq ("Three transcript sets" / "Three versions"), with a short description of the MANE Select Plus Clinical set. - newsarch.html (Apr. 22, 2026 entry): add MANE Select Plus Clinical to the list of NMD escape ruleset tracks.
  • lines changed 91, context: html, text, full: html, text
    46f88622e6ec2bbc09f403eeb9ec6122eb05931f Thu Apr 30 15:41:01 2026 -0700
    Releasing PrimateAI-3D and PromoterAI tracks to beta and RR. refs #37274 refs #37278 Drops the alpha tag from both tracks under predictionScoresSuper. Adds 'New' pennantIcons on primateAi and promoterAi pointing at the May 1, 2026 newsarch anchor, and an 'Updated' pennantIcon on the predictionScoresSuper supertrack. Adds a combined release post to newsarch.html with an HBB hg38 screenshot illustrating PrimateAI-3D coding-region calls alongside PromoterAI per-allele scores in the proximal promoter, and updates the indexNews.html sidebar.
  • lines changed 5, context: html, text, full: html, text
    0f8c134e2fb577bb6cd39bc3d8233af4c3e0b122 Mon May 4 08:52:48 2026 -0700
    Fix unit spacing and entity encodings in NMD Escape descriptions per CR feedback. refs #33737 nmd.html / nmdEscTranscripts.html / newsarch.html (Apr. 22, 2026 entry): normalize 50bp/100bp/400nt to '50 bp' / '100 bp' / '400 nt' for consistent unit spacing; replace 3&#8242;UTR with plain 3'UTR; replace &nbsp; between numbers and units with a regular space.
• src/hg/htdocs/images/illuminaPrimatePromoterNewsImage.png
  • lines changed 0, context: html, text, full: html, text
    46f88622e6ec2bbc09f403eeb9ec6122eb05931f Thu Apr 30 15:41:01 2026 -0700
    Releasing PrimateAI-3D and PromoterAI tracks to beta and RR. refs #37274 refs #37278 Drops the alpha tag from both tracks under predictionScoresSuper. Adds 'New' pennantIcons on primateAi and promoterAi pointing at the May 1, 2026 newsarch anchor, and an 'Updated' pennantIcon on the predictionScoresSuper supertrack. Adds a combined release post to newsarch.html with an HBB hg38 screenshot illustrating PrimateAI-3D coding-region calls alongside PromoterAI per-allele scores in the proximal promoter, and updates the indexNews.html sidebar.
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    46f88622e6ec2bbc09f403eeb9ec6122eb05931f Thu Apr 30 15:41:01 2026 -0700
    Releasing PrimateAI-3D and PromoterAI tracks to beta and RR. refs #37274 refs #37278 Drops the alpha tag from both tracks under predictionScoresSuper. Adds 'New' pennantIcons on primateAi and promoterAi pointing at the May 1, 2026 newsarch anchor, and an 'Updated' pennantIcon on the predictionScoresSuper supertrack. Adds a combined release post to newsarch.html with an HBB hg38 screenshot illustrating PrimateAI-3D coding-region calls alongside PromoterAI per-allele scores in the proximal promoter, and updates the indexNews.html sidebar.
• src/hg/htdocs/staticStyle/gbStatic.css
  • lines changed 52, context: html, text, full: html, text
    da335975e0d5712f47ee0d19b0eb5003d1a1b7f0 Mon Apr 27 14:16:44 2026 -0700
    Add sticky sidebar table of contents to /docs/ pages, ReadTheDocs-style. refs #36894 staticPage.lua: wrap doc body in a Bootstrap row with a col-md-2 sidebar holding a .docs-toc nav list and a col-md-10 content column. Collect both lev==1 and lev==2 headings into the TOC and emit id attributes on <h2> elements (replacing the prior inline <a name=> anchors). staticPage.html: add a small vanilla-JS scroll-spy that toggles .active on the TOC <li> matching the section currently scrolled past the top. No-ops on pages without #docs-toc. gbStatic.css: add styles for .docs-toc / .docs-toc-row (position: sticky, flex row for equal-height columns, link styling with active-state border). All rules are scoped to the .docs-toc class so non-docs pages sharing gbStatic.css are unaffected.
  • lines changed 41, context: html, text, full: html, text
    61438453e9f8be7a5949725a688ac6cf709add28 Tue Apr 28 13:06:10 2026 -0700
    Restructure /docs/ landing page for new users; add docs-page styling. refs #36894 docs/index.md: rewrite as a beginner-first landing page. Replace the prior five-section structure with a flat five-H2 outline -- Tutorials, Visualize your own data, Share your work, Download data, Get help -- so every entry in the sidebar TOC maps to specific content rather than to a vague grouping. Promote the tutorial table from a buried H3 to top-level content. Drop sections that don't serve new users (the "Understanding assemblies/annotations" primer, the MySQL bullet, the mirror paragraph, the Multi-Region View specific mention, and the four scattered "Relevant FAQs" lists). Consolidate help into a single closer with contact, FAQ, workshops, and the suggestion form. Distinguish custom tracks vs track hubs ("simpler option" vs "more powerful and configurable"). Make tutorial titles the table links and drop the redundant Link column. docs/staticPage.lua: add a docs-page class to the row wrapper so /docs/- only CSS can be scoped without affecting other gbsPage static pages. src/hg/htdocs/staticStyle/gbStatic.css: add scoped .docs-page styles for the sidebar TOC ("On this page" label) and tables (roomier padding, zebra striping using the existing tr.even/tr.odd classes, subtle hover). All new rules are namespaced under .docs-page so the rest of the site is untouched.
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    ca9c863b4422bb49521f37b6a29397d03d57f17a Mon Apr 27 13:42:24 2026 -0700
    Bump up size of readableWidth for track description pages from 50chars to 70chars. Also make hgTrackUi use the same width for the track descriptions, refs #37430
  • lines changed 4, context: html, text, full: html, text
    14cb2006a261922f27924e0fed14f067ce90fd1e Tue Apr 28 14:17:58 2026 -0700
    Move chromAlias info icon next to chromosome position, refs #29201 Relocate the icon from the right side of the search bar to between the Multi-region button and the chromosome position display, per reviewer feedback that the prior location read ambiguously next to the search box. Show only the (i) glyph (drop the "Aliases" label), bump font-size to 110%, tighten margins, and rename the tooltip from "Also known as:" to "Alternate sequence names:".
  • lines changed 67, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/hubApi/dataApi.h
  • lines changed 8, context: html, text, full: html, text
    779b0a67557941da1d0402d9d6f2952ff54fb479 Mon Apr 27 16:48:42 2026 -0700
    add API assemblyRequest endpoint properly manage requests from the assemblySearch page system refs #31811
• src/hg/hubApi/findGenome.c
  • lines changed 91, context: html, text, full: html, text
    779b0a67557941da1d0402d9d6f2952ff54fb479 Mon Apr 27 16:48:42 2026 -0700
    add API assemblyRequest endpoint properly manage requests from the assemblySearch page system refs #31811
  • lines changed 25, context: html, text, full: html, text
    3eff31a9084b4a8a1587ba2fc43ab4e055e70979 Tue Apr 28 14:53:55 2026 -0700
    eliminate the HTTP_REFERER check and depend just on the userId cookie for security refs #31811
• src/hg/hubApi/hubApi.c
  • lines changed 2, context: html, text, full: html, text
    779b0a67557941da1d0402d9d6f2952ff54fb479 Mon Apr 27 16:48:42 2026 -0700
    add API assemblyRequest endpoint properly manage requests from the assemblySearch page system refs #31811
• src/hg/hubApi/liftOver.c
  • lines changed 15, context: html, text, full: html, text
    3eff31a9084b4a8a1587ba2fc43ab4e055e70979 Tue Apr 28 14:53:55 2026 -0700
    eliminate the HTTP_REFERER check and depend just on the userId cookie for security refs #31811
• src/hg/inc/hgFind.h
  • lines changed 12, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/inc/makeItemsItem.h
  • lines changed 94, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/inc/myVariants.h
  • lines changed 117, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/inc/myVariantsShare.h
  • lines changed 126, context: html, text, full: html, text
    b53a97d26633a1f174a7031559a69d37e393379f Fri May 1 14:19:19 2026 -0700
    Allow myVariants tracks to be shared similar to google docs, read only and read+edit access by username or for all. Last write wins. Currently no history of changes, leaving that for the next version of the feature
• src/hg/inc/userdata.h
  • lines changed 3, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/inc/wikiLink.h
  • lines changed 2, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/js/assemblySearch.js
  • lines changed 19, context: html, text, full: html, text
    779b0a67557941da1d0402d9d6f2952ff54fb479 Mon Apr 27 16:48:42 2026 -0700
    add API assemblyRequest endpoint properly manage requests from the assemblySearch page system refs #31811
• src/hg/js/hgTracks.js
  • lines changed 8, context: html, text, full: html, text
    9bab882abcb4115c3e43e5c9b49de5ccbdb91c9f Tue Apr 28 14:47:14 2026 -0700
    Make hgTrackUi popup scroll vertically when content would overflow the regular size of the dialog, like in the case of toggling the density graph option, refs #37443
  • lines changed 911, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
  • lines changed 28, context: html, text, full: html, text
    a375b8f8c4c56f9932180441032b45a2316c856b Fri May 1 14:30:01 2026 -0700
    Oops forgot to omit the create item button from the highlight menu when the hg.conf variable is off
• src/hg/js/hgc.js
  • lines changed 118, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/js/hui.js
  • lines changed 145, context: html, text, full: html, text
    b53a97d26633a1f174a7031559a69d37e393379f Fri May 1 14:19:19 2026 -0700
    Allow myVariants tracks to be shared similar to google docs, read only and read+edit access by username or for all. Last write wins. Currently no history of changes, leaving that for the next version of the feature
• src/hg/js/liftRequest.js
  • lines changed 8, context: html, text, full: html, text
    5be923c37e690d54b6d5c8e5835c3ebdb62f5f0c Mon Apr 27 16:00:13 2026 -0700
    correctly supply callback to autocomplete so it will indicate "No genomes found" when there is no match refs #31811
• src/hg/js/utils.js
  • lines changed 20, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/lib/cart.c
  • lines changed 11, context: html, text, full: html, text
    b53a97d26633a1f174a7031559a69d37e393379f Fri May 1 14:19:19 2026 -0700
    Allow myVariants tracks to be shared similar to google docs, read only and read+edit access by username or for all. Last write wins. Currently no history of changes, leaving that for the next version of the feature
• src/hg/lib/customAdjacency.c
  • lines changed 1, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/lib/customFactory.c
  • lines changed 77, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/lib/hui.c
  • lines changed 9, context: html, text, full: html, text
    166abc2cdfefcaa86521ee296e9ede826c5354ac Fri May 1 13:02:09 2026 -0700
    hgc: resolve dataVersion path for quickLifted tracks, refs #37489 checkDataVersion() skipped path resolution when tdb->table looked like a hub track, so a quickLifted ClinVar stanza with dataVersion /gbdb/$D/bbi/clinvar/version.txt displayed the raw setting (with literal $D) instead of opening the file. When quickLiftDb is set, allow the path-substitution branch and use the source assembly for $D so /gbdb/<srcDb>/... resolves.
  • lines changed 3, context: html, text, full: html, text
    b53a97d26633a1f174a7031559a69d37e393379f Fri May 1 14:19:19 2026 -0700
    Allow myVariants tracks to be shared similar to google docs, read only and read+edit access by username or for all. Last write wins. Currently no history of changes, leaving that for the next version of the feature
  • lines changed 31, context: html, text, full: html, text
    24fece8377dedf184e8e872325ff2af175076552 Mon May 4 05:51:05 2026 -0700
    hui: fix duplicated filter UI on bigGenePred; tighten supertrack filter changes Two issues, both surfaced reviewing #37426: 1. bigGenePred tracks (e.g. openprot) rendered every filterBy/highlightBy <select> twice with the same id. dropdownchecklist.js binds the first instance only, leaving the second copy display:none — users saw filter labels under the second copy with no input fields under them. The duplication was pre-existing (since 7d9e5c172d1b reorganized genePredCfgUi/scoreCfgUi): genePredCfgUi rendered filterBy inline, then for bigGenePred called scoreCfgUi which rendered filterBy again. Skip the inline rendering for bigGenePred and let scoreCfgUi own it; plain genePred (which doesn't reach scoreCfgUi here) is unchanged. 2. Tighten the supertrack filter changes from 66ea6cb4eaf: - cfgBeginBoxAndTitle: revert the title==NULL "emit nothing" branch. The supertrack flow exits scoreCfgUi before reaching this anyway, so the change was only affecting other title==NULL callers like interactUi.c — pure unintended side effect. - numericFiltersShowAll: revert the title==NULL <BR> suppression for the same reason. The supertrack <h3> heading already provides enough separation. - buildFilterBy: tighten the errAbort relaxation. The previous condition (as != NULL && getLabelSetting == NULL) let a typo'd filterValues.<field> on a regular subtrack silently render a useless filter whenever a matching filterLabel.<field> was present. Restrict the relaxation to as==NULL (the supertrack / noData case). Add a warn() before errAbort so hub makers reading the page see an actionable hint, not just an opaque abort. refs #37426
• src/hg/lib/makeItemsItem.as
  • lines changed 16, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/lib/makeItemsItem.c
  • lines changed 243, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/lib/makeItemsItem.sql
  • lines changed 23, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/lib/myVariants.as
  • lines changed 21, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/lib/myVariants.c
  • lines changed 706, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/lib/myVariants.sql
  • lines changed 25, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/lib/myVariantsShare.as
  • lines changed 13, context: html, text, full: html, text
    b53a97d26633a1f174a7031559a69d37e393379f Fri May 1 14:19:19 2026 -0700
    Allow myVariants tracks to be shared similar to google docs, read only and read+edit access by username or for all. Last write wins. Currently no history of changes, leaving that for the next version of the feature
• src/hg/lib/myVariantsShare.c
  • lines changed 369, context: html, text, full: html, text
    b53a97d26633a1f174a7031559a69d37e393379f Fri May 1 14:19:19 2026 -0700
    Allow myVariants tracks to be shared similar to google docs, read only and read+edit access by username or for all. Last write wins. Currently no history of changes, leaving that for the next version of the feature
• src/hg/lib/myVariantsShare.sql
  • lines changed 22, context: html, text, full: html, text
    b53a97d26633a1f174a7031559a69d37e393379f Fri May 1 14:19:19 2026 -0700
    Allow myVariants tracks to be shared similar to google docs, read only and read+edit access by username or for all. Last write wins. Currently no history of changes, leaving that for the next version of the feature
• src/hg/lib/trackDbCache.c
  • lines changed 12, context: html, text, full: html, text
    2029e9afd93f32973619c48e111bdf1a8f8219b5 Wed Apr 29 13:39:56 2026 -0700
    trackDbCache: bail out gracefully when /dev/shm is full instead of SIGBUS Use posix_fallocate() instead of ftruncate() so tmpfs commits the pages synchronously; on ENOSPC we log to stderr, drop the temp file, and return without writing the cache. Previously hgTracks would die from SIGBUS on the first write into the mmap'd region (e.g. Docker's default 64 MB /dev/shm), truncating the page mid-render. refs #37475 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/lib/trackHub.c
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    c4e77d5b638be84e6f6c5dbc4bcf6e47684831e8 Fri May 1 12:29:29 2026 -0700
    hgConvert quickLift: don't list hidden composite subtracks as not liftable validateTdbChildren walked every subtrack in a composite and reported any non-liftable types in the user-facing warning, even subtracks the user had not made visible. Skip subtracks where isParentVisible/isSubtrackVisible is false so only tracks the user actually asked to lift are validated. refs #37491 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/lib/userdata.c
  • lines changed 6, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/lib/wikiLink.c
  • lines changed 6, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/hg/makeDb/doc/TP53.txt
  • lines changed 428, context: html, text, full: html, text
    25a17db6de34b4884d273b88ad3d0aecb08f08d8 Tue Apr 28 18:41:26 2026 -0700
    Adding TP53 VCEP track hub makedoc. refs #37399 Build documentation for the 16 scripts in scripts/tp53/. Documents the canonical transcript (NM_000546.6 / NP_000537.3), source files in tp53_downloads/, per-track build commands with their data dependency order (AF + FLOSSIES + per-paper functional must build before Provisional and FuncPrelim), one-shot rebuild loop, hubCheck verification, ASCII safety check, otto weekly cron setup, hgdownload deployment, and RTS session creation. Mirrors the InSiGHT.txt makedoc structure.
• src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
  • lines changed 3, context: html, text, full: html, text
    b17a43e2a64efaca2ee008e7e466764fea60407a Fri May 1 12:44:21 2026 -0700
    explicit path names to allow function on cron jobs refs #31811
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
  • lines changed 1, context: html, text, full: html, text
    b17a43e2a64efaca2ee008e7e466764fea60407a Fri May 1 12:44:21 2026 -0700
    explicit path names to allow function on cron jobs refs #31811
• src/hg/makeDb/doc/asmHubs/trackData.pl
  • lines changed 3, context: html, text, full: html, text
    b17a43e2a64efaca2ee008e7e466764fea60407a Fri May 1 12:44:21 2026 -0700
    explicit path names to allow function on cron jobs refs #31811
• src/hg/makeDb/doc/hg38/mpra.txt
  • lines changed 24, context: html, text, full: html, text
    2087dbbb5adafd3219e2dfbbbe23d10a758e2828 Fri May 1 15:48:00 2026 -0700
    Update mprabase description page and stanza per QA pass. refs #37359 Description page (mprabase.html): added library-composition framing (curated union of study-specific libraries, not a uniform enhancer atlas), element-size note covering 144-200 bp tiles, 354-678 bp Klein 2020 length sub-experiments, and 1 bp SNP-coordinate markers, sharpened Mattioli mESC cell-line note (mouse orthologous sequence assayed in mouse cells), cell-line biological-context table, scoring-methodology paragraph noting that cross-experiment percentile comparisons are approximate, "Interpreting the raw score" subsection with the log2-to- fold-change translation, coordinate-provenance sentence, and Arnold et al. 2013 row in the Experiments table. References for all seven source publications added. trackDb stanza (mpra.ra): HTML mouseOver with bold field names and line breaks, plus dataVersion "MPRA Base v4.9.3 (Mar 2026)". Parent superTrack description page (mpra.html) opening paragraph rewritten to clarify the barcoded reporter-RNA mechanism and fold the variant-MPRA case in cleanly. Makedoc (mpra.txt): bundled Mattioli title rebuild ask with AutoSQL percentile_rank text fix and name disambiguation (149 of 625 unique names reused across PMIDs); added the open Klein 2020 sub-design question for Varda; updated Arnold orphan note to reflect Varda's confirmation that the HeLa STARR-seq element is a valid Stark Lab proof-of-concept.
  • lines changed 46, context: html, text, full: html, text
    899f9da8129add8c64c86b405c87b3a97738a2ad Fri May 1 17:12:18 2026 -0700
    Update mpraVarDb description page and trackDb stanza per QA pass. refs #37359 Description page (mpraVarDb.html): - Primary citation corrected from a fabricated "Wang T, Matreyek KA, Yang X." entry to Jin et al., 2024 (PMID 39325859, the actual published Bioinformatics paper for MPRAVarDB). - References for all 18 source studies added. - Studies-table counts corrected to match the data: Tewhey 27,138 to 23,430 (the biggest gap, ~14%), Griesemer 72,588 to 72,546, Abell 29,582 to 29,564, Mouri 14,551 to 14,549, McAfee 10,310 to 10,302, Cooper 5,340 to 5,330, Lu 1,038 to 1,036. - Color counts on Display Conventions corrected to actual post-liftOver values: 22,451 dark red / 17,773 orange / 198,804 grey = 239,028. - "Note on study type" paragraph clarifying that ~41% of variants (Griesemer + Schuster 3'UTR) measure post-transcriptional regulation rather than transcription. - "Cell-type specificity" reminder, "Note on Kircher 2019" saturation- mutagenesis structure, "Interpreting log2FC" subsection with the linear-fold-change translation, and "Significance thresholds across studies" Methods paragraph noting that source studies use a mix of FDR thresholds (0.05/0.10) and that Kircher reports raw regression p-values rather than FDR. - Kircher element list reworded to avoid double-counting UC88 as both a named element and "an ultraconserved enhancer". trackDb stanza (mpra.ra, mpraVarDb subtrack): - filterValues.cellLine fixed: PC3 was hiding 26,546 Schuster rows (data has "PC3 cell"), SF7996 was hiding 3,896 Kircher GBM rows (data has bundled "HEK293T,SF7996"), and SK-MEL-28 (1,510) and K562+GATA1 (31) were missing entirely. Added comma-escape syntax (HEK293T,,SF7996) per slNameListFromCommaEscaped. Recovers ~31,983 hidden rows. - HTML mouseOver with bold field names and line breaks. - urls rsid="https://www.ncbi.nlm.nih.gov/snp/$$" added so rsIDs are clickable linkouts to dbSNP. - dataVersion "MPRAVarDB snapshot 2026-03-10" added. Makedoc (mpra.txt): QA review note added with the trackDb-only fixes and the items punted to upstream / next rebuild for Tao Wang.
• src/hg/makeDb/doc/hg38/nmd.txt
  • lines changed 5, context: html, text, full: html, text
    7dae59171ebf9d462438202cc85ae434e8080fe8 Tue Apr 28 06:30:43 2026 -0700
    NMD Escape MANE: dedicated .as for cleaner labelFields dropdown. refs #33737 The MANE bigBed now ships with its own autoSql, so the labelFields dropdown in the track config shows "Gene Symbol", "Gencode Accession (ENST)" and "RefSeq Accession (NM_/NR_)" - the descriptions QA asked for. The shared nmdEscCollapsed.as keeps its generic wording for the Gencode and RefSeq subtracks, where the "transcripts" column holds different accession families and a single hard-coded label would not fit both.
• src/hg/makeDb/doc/hg38/rnaMod.txt
  • lines changed 62, context: html, text, full: html, text
    a54f86a21a62394f88021eefccba67f18a4a27e6 Thu Apr 30 05:45:35 2026 -0700
    Adding new "DRACH motif sites" track under rnaMod superTrack on hg38: every occurrence of the m6A consensus motif (DRACH) in MANE Select v1.5 transcripts, projected onto the genome via pslMap. New scripts under makeDb/scripts/rnaMod, makeDoc under makeDb/doc/hg38/rnaMod.txt. Refreshed the parent rnaMod.html. Track is alpha-only (rnaMod.ra is already alpha-included), refs #36613 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 34, context: html, text, full: html, text
    63653eb7f4fcccfedec87fe115ed0a954012c3ad Thu Apr 30 05:46:04 2026 -0700
    Adding new "m6A-Atlas v2 sites" track under rnaMod superTrack on hg38: 427760 high-confidence base-resolution m6A sites compiled by m6A-Atlas v2 (Liang 2024) from 12 detection technologies across 24 cell lines / tissues. Filters on region, technique, cell line, biotype, #techniques, #cell lines. Track lives in its own m6aAtlas.ra file, included alpha-only via trackDb.ra, refs #36613 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/hg38/varFreqs.txt
  • lines changed 64, context: html, text, full: html, text
    37a5b97198453bd06cb03d2092cae239f368e84c Wed Apr 29 05:49:14 2026 -0700
    varFreqs: add tishkoff180 subtrack (Fan et al. 2023, 180 indigenous African WGS, hg19 lift) Sites-only SNP VCF with aggregate AC/AF/AN from 180 individuals (15 each from 12 populations across Ethiopia, Tanzania, Cameroon, Botswana), sequenced at >30x on HiSeq X Ten. hg19 calls supplied by the Tishkoff lab (UPenn) and lifted to hg38 with CrossMap. Redistribution is not permitted, so tableBrowser is disabled. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>, refs #36642
• src/hg/makeDb/scripts/insight/buildInsightClinVar.py
  • lines changed 31, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/insight/insightAFfrequencies.py
  • lines changed 43, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/insight/insightClinDomains.py
  • lines changed 17, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/insight/insightFunctionalAssays.py
  • lines changed 24, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/insight/insightHCIPriors.py
  • lines changed 24, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/insight/insightPVS1.py
  • lines changed 23, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/lrSv/databases.tsv
  • lines changed 32, context: html, text, full: html, text
    9fbdfa3416ffde377072fafd2de44059155c3b44 Thu Apr 30 06:57:35 2026 -0700
    lrSv: add lrSvAll merged track combining all long-read SV subtracks Variants are merged on exact (chrom, start, end, svType, svLen, insLen). Per-database AC columns are stored as strings; "unknown" is used where the source dataset has only placeholder AC values (deCODE, SVatalog 101, 1KG ONT 100). Kim PD Brain is split into affected (PD+ILBD) and healthy (HC) AC columns. Gustafson contributes sampleCount instead of AC. Output: 2,694,871 unique SVs from 3,706,100 input rows across 15 subtracks (27% dedup). The merged track sits as the first subtrack of the lrSv supertrack with filters on sources, svType, svLen, insLen, maxAF/minAF, AC, and sourceCount. The trackDb stanza is generated by the build script directly into human/lrSvAll.ra and pulled in via 'include lrSvAll.ra' from lrSv.ra, so labels in databases.tsv stay the single source of truth. lrSv.html: add a "Disease cases" column to the dataset summary, strip parenthesized internal track names from the section headers, and shorten exact SV counts to ~Nk / ~N.NM in the prose. refs #36642
• src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py
  • lines changed 643, context: html, text, full: html, text
    9fbdfa3416ffde377072fafd2de44059155c3b44 Thu Apr 30 06:57:35 2026 -0700
    lrSv: add lrSvAll merged track combining all long-read SV subtracks Variants are merged on exact (chrom, start, end, svType, svLen, insLen). Per-database AC columns are stored as strings; "unknown" is used where the source dataset has only placeholder AC values (deCODE, SVatalog 101, 1KG ONT 100). Kim PD Brain is split into affected (PD+ILBD) and healthy (HC) AC columns. Gustafson contributes sampleCount instead of AC. Output: 2,694,871 unique SVs from 3,706,100 input rows across 15 subtracks (27% dedup). The merged track sits as the first subtrack of the lrSv supertrack with filters on sources, svType, svLen, insLen, maxAF/minAF, AC, and sourceCount. The trackDb stanza is generated by the build script directly into human/lrSvAll.ra and pulled in via 'include lrSvAll.ra' from lrSv.ra, so labels in databases.tsv stay the single source of truth. lrSv.html: add a "Disease cases" column to the dataset summary, strip parenthesized internal track names from the section headers, and shorten exact SV counts to ~Nk / ~N.NM in the prose. refs #36642
• src/hg/makeDb/scripts/mpravardb/mpravardbToBed.py
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    09f347da2873b42ab1b5c6f5684e429dc4e321d5 Mon May 4 08:52:54 2026 -0700
    Switch mpravardbToBed sanitize map to str.maketrans with \u escape keys per CR feedback. refs #37359 Replaces literal UTF-8 characters in the dictionary keys (curly quotes, primes, dashes, NBSP, mojibake) with their \uXXXX escape forms so an editor can't silently re-encode them and break the pipeline. Translation now uses str.translate(), and the whitespace-collapse regex is precompiled at module level.
• src/hg/makeDb/scripts/nmd/nmdEscManeCollapsed.as
  • lines changed 16, context: html, text, full: html, text
    7dae59171ebf9d462438202cc85ae434e8080fe8 Tue Apr 28 06:30:43 2026 -0700
    NMD Escape MANE: dedicated .as for cleaner labelFields dropdown. refs #33737 The MANE bigBed now ships with its own autoSql, so the labelFields dropdown in the track config shows "Gene Symbol", "Gencode Accession (ENST)" and "RefSeq Accession (NM_/NR_)" - the descriptions QA asked for. The shared nmdEscCollapsed.as keeps its generic wording for the Gencode and RefSeq subtracks, where the "transcripts" column holds different accession families and a single hard-coded label would not fit both.
• src/hg/makeDb/scripts/rnaMod/drach.as
  • lines changed 21, context: html, text, full: html, text
    a54f86a21a62394f88021eefccba67f18a4a27e6 Thu Apr 30 05:45:35 2026 -0700
    Adding new "DRACH motif sites" track under rnaMod superTrack on hg38: every occurrence of the m6A consensus motif (DRACH) in MANE Select v1.5 transcripts, projected onto the genome via pslMap. New scripts under makeDb/scripts/rnaMod, makeDoc under makeDb/doc/hg38/rnaMod.txt. Refreshed the parent rnaMod.html. Track is alpha-only (rnaMod.ra is already alpha-included), refs #36613 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/rnaMod/drachBedToBigBed.py
  • lines changed 149, context: html, text, full: html, text
    a54f86a21a62394f88021eefccba67f18a4a27e6 Thu Apr 30 05:45:35 2026 -0700
    Adding new "DRACH motif sites" track under rnaMod superTrack on hg38: every occurrence of the m6A consensus motif (DRACH) in MANE Select v1.5 transcripts, projected onto the genome via pslMap. New scripts under makeDb/scripts/rnaMod, makeDoc under makeDb/doc/hg38/rnaMod.txt. Refreshed the parent rnaMod.html. Track is alpha-only (rnaMod.ra is already alpha-included), refs #36613 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/rnaMod/drachFromFasta.py
  • lines changed 77, context: html, text, full: html, text
    a54f86a21a62394f88021eefccba67f18a4a27e6 Thu Apr 30 05:45:35 2026 -0700
    Adding new "DRACH motif sites" track under rnaMod superTrack on hg38: every occurrence of the m6A consensus motif (DRACH) in MANE Select v1.5 transcripts, projected onto the genome via pslMap. New scripts under makeDb/scripts/rnaMod, makeDoc under makeDb/doc/hg38/rnaMod.txt. Refreshed the parent rnaMod.html. Track is alpha-only (rnaMod.ra is already alpha-included), refs #36613 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/rnaMod/m6aAtlas.as
  • lines changed 28, context: html, text, full: html, text
    63653eb7f4fcccfedec87fe115ed0a954012c3ad Thu Apr 30 05:46:04 2026 -0700
    Adding new "m6A-Atlas v2 sites" track under rnaMod superTrack on hg38: 427760 high-confidence base-resolution m6A sites compiled by m6A-Atlas v2 (Liang 2024) from 12 detection technologies across 24 cell lines / tissues. Filters on region, technique, cell line, biotype, #techniques, #cell lines. Track lives in its own m6aAtlas.ra file, included alpha-only via trackDb.ra, refs #36613 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/rnaMod/m6aAtlasToBed.py
  • lines changed 155, context: html, text, full: html, text
    63653eb7f4fcccfedec87fe115ed0a954012c3ad Thu Apr 30 05:46:04 2026 -0700
    Adding new "m6A-Atlas v2 sites" track under rnaMod superTrack on hg38: 427760 high-confidence base-resolution m6A sites compiled by m6A-Atlas v2 (Liang 2024) from 12 detection technologies across 24 cell lines / tissues. Filters on region, technique, cell line, biotype, #techniques, #cell lines. Track lives in its own m6aAtlas.ra file, included alpha-only via trackDb.ra, refs #36613 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/rnaMod/makeDrach.sh
  • lines changed 91, context: html, text, full: html, text
    a54f86a21a62394f88021eefccba67f18a4a27e6 Thu Apr 30 05:45:35 2026 -0700
    Adding new "DRACH motif sites" track under rnaMod superTrack on hg38: every occurrence of the m6A consensus motif (DRACH) in MANE Select v1.5 transcripts, projected onto the genome via pslMap. New scripts under makeDb/scripts/rnaMod, makeDoc under makeDb/doc/hg38/rnaMod.txt. Refreshed the parent rnaMod.html. Track is alpha-only (rnaMod.ra is already alpha-included), refs #36613 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/tp53/tp53AFfrequencies.py
  • lines changed 279, context: html, text, full: html, text
    f24ea956ba3b7a8c7ee8be0826d66489b85e0bbc Tue Apr 28 18:22:48 2026 -0700
    Adding TP53 VCEP track hub build scripts. refs #37399 16 Python scripts that build the 15 bigBed tracks for the ClinGen TP53 VCEP track hub (CSpec GN009 v2.4.0, NM_000546.6 / NP_000537.3). Includes the NON-FINAL Provisional Classification (Tavtigian point sum across PM1 + PS3/BS3 + PP3/BP4 + AF + BS2 + splicing PP3), gnomAD v4.1 AF codes, FLOSSIES BS2 evidence, Bioinformatic PP3/BP4 (missense + single-aa in-frame del), VCEP curated variants from EvRepo with ClinVar VCV backfill, PM1 (clinical domains + cancerhotspots), PVS1 regions and splice sites, and the Functional Evidence composite (VCEP preliminary PS3/BS3 with per-paper raw scores from Kato/Giacomelli/Kawaguchi/Funk).
  • lines changed 11, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/tp53/tp53Bioinformatic.py
  • lines changed 206, context: html, text, full: html, text
    f24ea956ba3b7a8c7ee8be0826d66489b85e0bbc Tue Apr 28 18:22:48 2026 -0700
    Adding TP53 VCEP track hub build scripts. refs #37399 16 Python scripts that build the 15 bigBed tracks for the ClinGen TP53 VCEP track hub (CSpec GN009 v2.4.0, NM_000546.6 / NP_000537.3). Includes the NON-FINAL Provisional Classification (Tavtigian point sum across PM1 + PS3/BS3 + PP3/BP4 + AF + BS2 + splicing PP3), gnomAD v4.1 AF codes, FLOSSIES BS2 evidence, Bioinformatic PP3/BP4 (missense + single-aa in-frame del), VCEP curated variants from EvRepo with ClinVar VCV backfill, PM1 (clinical domains + cancerhotspots), PVS1 regions and splice sites, and the Functional Evidence composite (VCEP preliminary PS3/BS3 with per-paper raw scores from Kato/Giacomelli/Kawaguchi/Funk).
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    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/tp53/tp53BioinformaticDel.py
  • lines changed 232, context: html, text, full: html, text
    f24ea956ba3b7a8c7ee8be0826d66489b85e0bbc Tue Apr 28 18:22:48 2026 -0700
    Adding TP53 VCEP track hub build scripts. refs #37399 16 Python scripts that build the 15 bigBed tracks for the ClinGen TP53 VCEP track hub (CSpec GN009 v2.4.0, NM_000546.6 / NP_000537.3). Includes the NON-FINAL Provisional Classification (Tavtigian point sum across PM1 + PS3/BS3 + PP3/BP4 + AF + BS2 + splicing PP3), gnomAD v4.1 AF codes, FLOSSIES BS2 evidence, Bioinformatic PP3/BP4 (missense + single-aa in-frame del), VCEP curated variants from EvRepo with ClinVar VCV backfill, PM1 (clinical domains + cancerhotspots), PVS1 regions and splice sites, and the Functional Evidence composite (VCEP preliminary PS3/BS3 with per-paper raw scores from Kato/Giacomelli/Kawaguchi/Funk).
  • lines changed 2, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/tp53/tp53CancerHotspots.py
  • lines changed 179, context: html, text, full: html, text
    f24ea956ba3b7a8c7ee8be0826d66489b85e0bbc Tue Apr 28 18:22:48 2026 -0700
    Adding TP53 VCEP track hub build scripts. refs #37399 16 Python scripts that build the 15 bigBed tracks for the ClinGen TP53 VCEP track hub (CSpec GN009 v2.4.0, NM_000546.6 / NP_000537.3). Includes the NON-FINAL Provisional Classification (Tavtigian point sum across PM1 + PS3/BS3 + PP3/BP4 + AF + BS2 + splicing PP3), gnomAD v4.1 AF codes, FLOSSIES BS2 evidence, Bioinformatic PP3/BP4 (missense + single-aa in-frame del), VCEP curated variants from EvRepo with ClinVar VCV backfill, PM1 (clinical domains + cancerhotspots), PVS1 regions and splice sites, and the Functional Evidence composite (VCEP preliminary PS3/BS3 with per-paper raw scores from Kato/Giacomelli/Kawaguchi/Funk).
  • lines changed 1, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/tp53/tp53ClinDomains.py
  • lines changed 159, context: html, text, full: html, text
    f24ea956ba3b7a8c7ee8be0826d66489b85e0bbc Tue Apr 28 18:22:48 2026 -0700
    Adding TP53 VCEP track hub build scripts. refs #37399 16 Python scripts that build the 15 bigBed tracks for the ClinGen TP53 VCEP track hub (CSpec GN009 v2.4.0, NM_000546.6 / NP_000537.3). Includes the NON-FINAL Provisional Classification (Tavtigian point sum across PM1 + PS3/BS3 + PP3/BP4 + AF + BS2 + splicing PP3), gnomAD v4.1 AF codes, FLOSSIES BS2 evidence, Bioinformatic PP3/BP4 (missense + single-aa in-frame del), VCEP curated variants from EvRepo with ClinVar VCV backfill, PM1 (clinical domains + cancerhotspots), PVS1 regions and splice sites, and the Functional Evidence composite (VCEP preliminary PS3/BS3 with per-paper raw scores from Kato/Giacomelli/Kawaguchi/Funk).
  • lines changed 1, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/tp53/tp53Flossies.py
  • lines changed 253, context: html, text, full: html, text
    f24ea956ba3b7a8c7ee8be0826d66489b85e0bbc Tue Apr 28 18:22:48 2026 -0700
    Adding TP53 VCEP track hub build scripts. refs #37399 16 Python scripts that build the 15 bigBed tracks for the ClinGen TP53 VCEP track hub (CSpec GN009 v2.4.0, NM_000546.6 / NP_000537.3). Includes the NON-FINAL Provisional Classification (Tavtigian point sum across PM1 + PS3/BS3 + PP3/BP4 + AF + BS2 + splicing PP3), gnomAD v4.1 AF codes, FLOSSIES BS2 evidence, Bioinformatic PP3/BP4 (missense + single-aa in-frame del), VCEP curated variants from EvRepo with ClinVar VCV backfill, PM1 (clinical domains + cancerhotspots), PVS1 regions and splice sites, and the Functional Evidence composite (VCEP preliminary PS3/BS3 with per-paper raw scores from Kato/Giacomelli/Kawaguchi/Funk).
  • lines changed 2, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/tp53/tp53FuncLib.py
  • lines changed 211, context: html, text, full: html, text
    f24ea956ba3b7a8c7ee8be0826d66489b85e0bbc Tue Apr 28 18:22:48 2026 -0700
    Adding TP53 VCEP track hub build scripts. refs #37399 16 Python scripts that build the 15 bigBed tracks for the ClinGen TP53 VCEP track hub (CSpec GN009 v2.4.0, NM_000546.6 / NP_000537.3). Includes the NON-FINAL Provisional Classification (Tavtigian point sum across PM1 + PS3/BS3 + PP3/BP4 + AF + BS2 + splicing PP3), gnomAD v4.1 AF codes, FLOSSIES BS2 evidence, Bioinformatic PP3/BP4 (missense + single-aa in-frame del), VCEP curated variants from EvRepo with ClinVar VCV backfill, PM1 (clinical domains + cancerhotspots), PVS1 regions and splice sites, and the Functional Evidence composite (VCEP preliminary PS3/BS3 with per-paper raw scores from Kato/Giacomelli/Kawaguchi/Funk).
  • lines changed 20, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/tp53/tp53FuncPrelim.py
  • lines changed 212, context: html, text, full: html, text
    f24ea956ba3b7a8c7ee8be0826d66489b85e0bbc Tue Apr 28 18:22:48 2026 -0700
    Adding TP53 VCEP track hub build scripts. refs #37399 16 Python scripts that build the 15 bigBed tracks for the ClinGen TP53 VCEP track hub (CSpec GN009 v2.4.0, NM_000546.6 / NP_000537.3). Includes the NON-FINAL Provisional Classification (Tavtigian point sum across PM1 + PS3/BS3 + PP3/BP4 + AF + BS2 + splicing PP3), gnomAD v4.1 AF codes, FLOSSIES BS2 evidence, Bioinformatic PP3/BP4 (missense + single-aa in-frame del), VCEP curated variants from EvRepo with ClinVar VCV backfill, PM1 (clinical domains + cancerhotspots), PVS1 regions and splice sites, and the Functional Evidence composite (VCEP preliminary PS3/BS3 with per-paper raw scores from Kato/Giacomelli/Kawaguchi/Funk).
  • lines changed 1, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/tp53/tp53Func_funk.py
  • lines changed 192, context: html, text, full: html, text
    f24ea956ba3b7a8c7ee8be0826d66489b85e0bbc Tue Apr 28 18:22:48 2026 -0700
    Adding TP53 VCEP track hub build scripts. refs #37399 16 Python scripts that build the 15 bigBed tracks for the ClinGen TP53 VCEP track hub (CSpec GN009 v2.4.0, NM_000546.6 / NP_000537.3). Includes the NON-FINAL Provisional Classification (Tavtigian point sum across PM1 + PS3/BS3 + PP3/BP4 + AF + BS2 + splicing PP3), gnomAD v4.1 AF codes, FLOSSIES BS2 evidence, Bioinformatic PP3/BP4 (missense + single-aa in-frame del), VCEP curated variants from EvRepo with ClinVar VCV backfill, PM1 (clinical domains + cancerhotspots), PVS1 regions and splice sites, and the Functional Evidence composite (VCEP preliminary PS3/BS3 with per-paper raw scores from Kato/Giacomelli/Kawaguchi/Funk).
  • lines changed 1, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/tp53/tp53Func_giacomelli.py
  • lines changed 182, context: html, text, full: html, text
    f24ea956ba3b7a8c7ee8be0826d66489b85e0bbc Tue Apr 28 18:22:48 2026 -0700
    Adding TP53 VCEP track hub build scripts. refs #37399 16 Python scripts that build the 15 bigBed tracks for the ClinGen TP53 VCEP track hub (CSpec GN009 v2.4.0, NM_000546.6 / NP_000537.3). Includes the NON-FINAL Provisional Classification (Tavtigian point sum across PM1 + PS3/BS3 + PP3/BP4 + AF + BS2 + splicing PP3), gnomAD v4.1 AF codes, FLOSSIES BS2 evidence, Bioinformatic PP3/BP4 (missense + single-aa in-frame del), VCEP curated variants from EvRepo with ClinVar VCV backfill, PM1 (clinical domains + cancerhotspots), PVS1 regions and splice sites, and the Functional Evidence composite (VCEP preliminary PS3/BS3 with per-paper raw scores from Kato/Giacomelli/Kawaguchi/Funk).
  • lines changed 1, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/tp53/tp53Func_kato.py
  • lines changed 185, context: html, text, full: html, text
    f24ea956ba3b7a8c7ee8be0826d66489b85e0bbc Tue Apr 28 18:22:48 2026 -0700
    Adding TP53 VCEP track hub build scripts. refs #37399 16 Python scripts that build the 15 bigBed tracks for the ClinGen TP53 VCEP track hub (CSpec GN009 v2.4.0, NM_000546.6 / NP_000537.3). Includes the NON-FINAL Provisional Classification (Tavtigian point sum across PM1 + PS3/BS3 + PP3/BP4 + AF + BS2 + splicing PP3), gnomAD v4.1 AF codes, FLOSSIES BS2 evidence, Bioinformatic PP3/BP4 (missense + single-aa in-frame del), VCEP curated variants from EvRepo with ClinVar VCV backfill, PM1 (clinical domains + cancerhotspots), PVS1 regions and splice sites, and the Functional Evidence composite (VCEP preliminary PS3/BS3 with per-paper raw scores from Kato/Giacomelli/Kawaguchi/Funk).
  • lines changed 1, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/tp53/tp53Func_kawaguchi.py
  • lines changed 156, context: html, text, full: html, text
    f24ea956ba3b7a8c7ee8be0826d66489b85e0bbc Tue Apr 28 18:22:48 2026 -0700
    Adding TP53 VCEP track hub build scripts. refs #37399 16 Python scripts that build the 15 bigBed tracks for the ClinGen TP53 VCEP track hub (CSpec GN009 v2.4.0, NM_000546.6 / NP_000537.3). Includes the NON-FINAL Provisional Classification (Tavtigian point sum across PM1 + PS3/BS3 + PP3/BP4 + AF + BS2 + splicing PP3), gnomAD v4.1 AF codes, FLOSSIES BS2 evidence, Bioinformatic PP3/BP4 (missense + single-aa in-frame del), VCEP curated variants from EvRepo with ClinVar VCV backfill, PM1 (clinical domains + cancerhotspots), PVS1 regions and splice sites, and the Functional Evidence composite (VCEP preliminary PS3/BS3 with per-paper raw scores from Kato/Giacomelli/Kawaguchi/Funk).
  • lines changed 1, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/tp53/tp53PVS1.py
  • lines changed 115, context: html, text, full: html, text
    f24ea956ba3b7a8c7ee8be0826d66489b85e0bbc Tue Apr 28 18:22:48 2026 -0700
    Adding TP53 VCEP track hub build scripts. refs #37399 16 Python scripts that build the 15 bigBed tracks for the ClinGen TP53 VCEP track hub (CSpec GN009 v2.4.0, NM_000546.6 / NP_000537.3). Includes the NON-FINAL Provisional Classification (Tavtigian point sum across PM1 + PS3/BS3 + PP3/BP4 + AF + BS2 + splicing PP3), gnomAD v4.1 AF codes, FLOSSIES BS2 evidence, Bioinformatic PP3/BP4 (missense + single-aa in-frame del), VCEP curated variants from EvRepo with ClinVar VCV backfill, PM1 (clinical domains + cancerhotspots), PVS1 regions and splice sites, and the Functional Evidence composite (VCEP preliminary PS3/BS3 with per-paper raw scores from Kato/Giacomelli/Kawaguchi/Funk).
  • lines changed 1, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/tp53/tp53PVS1Splice.py
  • lines changed 219, context: html, text, full: html, text
    f24ea956ba3b7a8c7ee8be0826d66489b85e0bbc Tue Apr 28 18:22:48 2026 -0700
    Adding TP53 VCEP track hub build scripts. refs #37399 16 Python scripts that build the 15 bigBed tracks for the ClinGen TP53 VCEP track hub (CSpec GN009 v2.4.0, NM_000546.6 / NP_000537.3). Includes the NON-FINAL Provisional Classification (Tavtigian point sum across PM1 + PS3/BS3 + PP3/BP4 + AF + BS2 + splicing PP3), gnomAD v4.1 AF codes, FLOSSIES BS2 evidence, Bioinformatic PP3/BP4 (missense + single-aa in-frame del), VCEP curated variants from EvRepo with ClinVar VCV backfill, PM1 (clinical domains + cancerhotspots), PVS1 regions and splice sites, and the Functional Evidence composite (VCEP preliminary PS3/BS3 with per-paper raw scores from Kato/Giacomelli/Kawaguchi/Funk).
  • lines changed 1, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/tp53/tp53ProvisionalClass.py
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    f24ea956ba3b7a8c7ee8be0826d66489b85e0bbc Tue Apr 28 18:22:48 2026 -0700
    Adding TP53 VCEP track hub build scripts. refs #37399 16 Python scripts that build the 15 bigBed tracks for the ClinGen TP53 VCEP track hub (CSpec GN009 v2.4.0, NM_000546.6 / NP_000537.3). Includes the NON-FINAL Provisional Classification (Tavtigian point sum across PM1 + PS3/BS3 + PP3/BP4 + AF + BS2 + splicing PP3), gnomAD v4.1 AF codes, FLOSSIES BS2 evidence, Bioinformatic PP3/BP4 (missense + single-aa in-frame del), VCEP curated variants from EvRepo with ClinVar VCV backfill, PM1 (clinical domains + cancerhotspots), PVS1 regions and splice sites, and the Functional Evidence composite (VCEP preliminary PS3/BS3 with per-paper raw scores from Kato/Giacomelli/Kawaguchi/Funk).
  • lines changed 1, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/scripts/tp53/tp53VCEPClinVar.py
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    f24ea956ba3b7a8c7ee8be0826d66489b85e0bbc Tue Apr 28 18:22:48 2026 -0700
    Adding TP53 VCEP track hub build scripts. refs #37399 16 Python scripts that build the 15 bigBed tracks for the ClinGen TP53 VCEP track hub (CSpec GN009 v2.4.0, NM_000546.6 / NP_000537.3). Includes the NON-FINAL Provisional Classification (Tavtigian point sum across PM1 + PS3/BS3 + PP3/BP4 + AF + BS2 + splicing PP3), gnomAD v4.1 AF codes, FLOSSIES BS2 evidence, Bioinformatic PP3/BP4 (missense + single-aa in-frame del), VCEP curated variants from EvRepo with ClinVar VCV backfill, PM1 (clinical domains + cancerhotspots), PVS1 regions and splice sites, and the Functional Evidence composite (VCEP preliminary PS3/BS3 with per-paper raw scores from Kato/Giacomelli/Kawaguchi/Funk).
  • lines changed 21, context: html, text, full: html, text
    a56d88e05670b759ff3b32829542537ccc790c57 Tue Apr 28 19:18:20 2026 -0700
    Address CR feedback on insight + tp53 hub scripts. refs #37418 Drop duplicated bash() wrappers in favor of subprocess.run / check_output with list args, eliminating shell=True, embedded-quote concerns, and stderr-into-stdout merging. Centralize common operations as run_sort_bed/run_liftOver in tp53FuncLib alongside existing run_bedToBigBed. Switch HTML escaping to stdlib html.escape() consistently. insightHCIPriors mouseover (previously unescaped) now escapes HGVS fields, addressing the specific c.123A>G case Jonathan flagged. Replace invalid </br> tags with <br> across all five affected mouseover sites.
• src/hg/makeDb/trackDb/encode4RegLayeredDisplay.shared.html
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    b4808fac05f88a0170f2642a1670d571ceca4b7e Mon May 4 10:08:39 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - Added Andrews 2023 reference (PMID 37104580) to wgEncodeReg4.html supertrack page. - Added 16 missing organ rows to 5 hg38 multiWig organ availability tables (Dnase +nose; Atac +bone marrow, skin; H3K4me3 +bone, epithelium, mouth; H3K27ac +bone, epithelium, eye, mouth; Ctcf +bone, bone marrow, embryo, epithelium, mouth, penis). - Added colored Organ/Tissue cell to organ tables across 12 multiWig HTMLs (5 hg38 + 5 mm10 standard + 2 Txn) using RGB from .ra color settings. - Restructured Txn organ tables to a 4-column Organ/Source/Plus/Minus layout, removing the "all X" row prefix encoding. - Rewrote the "two versions" Description block across 12 multiWig HTMLs with parallel 3-bullet conditional logic and ENCODE-standard biosample terminology. - Updated DNase/ATAC/Histone/CTCF (Indiv.) Epigenetics composite pages on both assemblies with 5-bullet Description and explicit per-assay color legend in Display Conventions. - Added encode4RegLayeredDisplay.shared.html and replaced the inline Display Conventions block in 10 multiWig HTMLs with an SSI include.
• src/hg/makeDb/trackDb/human/clinvar.ra
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    41fdf8f63b9a1bd2c3a6c3010c0fc0b08bd41495 Tue Apr 28 05:45:32 2026 -0700
    fixing dataversion statement on clinvar, refs #37467
• src/hg/makeDb/trackDb/human/cloneEnd.trackDb.ra
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    5c12c955bfbf5428bfe5f0932df7c16110020d28 Wed Apr 29 16:31:03 2026 -0700
    Moving the new track to next to the other Chori track. Chaning the priority so they are grouped together on the UI page, refs #35059
• src/hg/makeDb/trackDb/human/cloneEndSuper.html
  • lines changed 3, context: html, text, full: html, text
    23a1d303af11df08a568807aa65c21d973b4fc1a Wed Apr 29 16:32:15 2026 -0700
    Fixing the table layout, refs #35059
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    294e9bf7a3169d3dd8c176fb896cbd0c5066ea22 Thu Apr 30 02:10:35 2026 -0700
    docs updates, refs #35059
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    db75ac2f74d3149efdb945d1efe966b27ec0def8 Thu Apr 30 15:39:17 2026 -0700
    Adding a note about Pieter de Jong's contribution to the BAC tracks, refs #35059
• src/hg/makeDb/trackDb/human/dbVarCommon.html
  • lines changed 124, context: html, text, full: html, text
    b85c12cf9af0ee1a954b8cced961bcbd909b7979 Wed Apr 29 12:04:36 2026 -0700
    Expand dbVar tracks to expose all six nstd186 source studies and add new Somatic and Other composites. refs #37406 Restructure the dbVar supertrack: - Renamed from "dbVar Common Struct Var" to "dbVar Struct Var". - dbVar Common SV: added subtracks for Lee, Abel, and Byrska-Bishop (the three nstd186 source studies that were missing from our Curated Common track), and for the American/East Asian/South Asian/Other populations. - dbVar Conflict SV: description page refreshed; subtrack longLabel clarified. - dbVar Somatic SV (new): single subtrack pulling somatic_sv.bb from the dbVar hub. Default hidden. - dbVar Other SV (new): residual bucket for dbVar SVs not classified as common, somatic, or clinical, split into Healthy and Phenotype subtracks. Default hidden. NCBI sometimes calls this "presumed normal"; the description page notes the equivalence. mergeSpannedItems on for the dense subtracks (normal_healthy ~5.6M items, normal_phenotype ~410K, somatic_sv ~67K). - ClinVar SVs are not duplicated; description pages cross-link to the existing ClinVar track instead. Description pages: rewrite dbVarCommon.html and dbVarCurated.html, refresh dbVarConflict.html, add dbVarSomatic.html and dbVarOther.html. Retire the unused dbVar_common.html. Methods links now point at NCBI's dbVar Overview rather than the FTP directory listing. searchTable termRegex widened to ^[den]ssv[0-9]+ so dssv* accessions in normal_healthy resolve. Otto: stage downloads to release/\${db}.new/, validate per file (size floor and 10% itemCount delta vs the current live copy), then atomically swap via directory rename with a one-cycle .prev rollback. On validation failure, leave .new/ in place for human inspection and exit non-zero so the wrapper emails. On no-op runs the wrapper now stays silent. checkNstd175.sh's "update done" message moved inside the update branch so silence is honoured. New-file detection (via a knownFiles.txt manifest) emails when NCBI adds a file we don't yet expose. knownFiles.txt itself lives only at the deployment path under /hive/data/outside/otto/dbVar/, not in the tree.
• src/hg/makeDb/trackDb/human/dbVarConflict.html
  • lines changed 35, context: html, text, full: html, text
    b85c12cf9af0ee1a954b8cced961bcbd909b7979 Wed Apr 29 12:04:36 2026 -0700
    Expand dbVar tracks to expose all six nstd186 source studies and add new Somatic and Other composites. refs #37406 Restructure the dbVar supertrack: - Renamed from "dbVar Common Struct Var" to "dbVar Struct Var". - dbVar Common SV: added subtracks for Lee, Abel, and Byrska-Bishop (the three nstd186 source studies that were missing from our Curated Common track), and for the American/East Asian/South Asian/Other populations. - dbVar Conflict SV: description page refreshed; subtrack longLabel clarified. - dbVar Somatic SV (new): single subtrack pulling somatic_sv.bb from the dbVar hub. Default hidden. - dbVar Other SV (new): residual bucket for dbVar SVs not classified as common, somatic, or clinical, split into Healthy and Phenotype subtracks. Default hidden. NCBI sometimes calls this "presumed normal"; the description page notes the equivalence. mergeSpannedItems on for the dense subtracks (normal_healthy ~5.6M items, normal_phenotype ~410K, somatic_sv ~67K). - ClinVar SVs are not duplicated; description pages cross-link to the existing ClinVar track instead. Description pages: rewrite dbVarCommon.html and dbVarCurated.html, refresh dbVarConflict.html, add dbVarSomatic.html and dbVarOther.html. Retire the unused dbVar_common.html. Methods links now point at NCBI's dbVar Overview rather than the FTP directory listing. searchTable termRegex widened to ^[den]ssv[0-9]+ so dssv* accessions in normal_healthy resolve. Otto: stage downloads to release/\${db}.new/, validate per file (size floor and 10% itemCount delta vs the current live copy), then atomically swap via directory rename with a one-cycle .prev rollback. On validation failure, leave .new/ in place for human inspection and exit non-zero so the wrapper emails. On no-op runs the wrapper now stays silent. checkNstd175.sh's "update done" message moved inside the update branch so silence is honoured. New-file detection (via a knownFiles.txt manifest) emails when NCBI adds a file we don't yet expose. knownFiles.txt itself lives only at the deployment path under /hive/data/outside/otto/dbVar/, not in the tree.
• src/hg/makeDb/trackDb/human/dbVarCurated.html
  • lines changed 110, context: html, text, full: html, text
    b85c12cf9af0ee1a954b8cced961bcbd909b7979 Wed Apr 29 12:04:36 2026 -0700
    Expand dbVar tracks to expose all six nstd186 source studies and add new Somatic and Other composites. refs #37406 Restructure the dbVar supertrack: - Renamed from "dbVar Common Struct Var" to "dbVar Struct Var". - dbVar Common SV: added subtracks for Lee, Abel, and Byrska-Bishop (the three nstd186 source studies that were missing from our Curated Common track), and for the American/East Asian/South Asian/Other populations. - dbVar Conflict SV: description page refreshed; subtrack longLabel clarified. - dbVar Somatic SV (new): single subtrack pulling somatic_sv.bb from the dbVar hub. Default hidden. - dbVar Other SV (new): residual bucket for dbVar SVs not classified as common, somatic, or clinical, split into Healthy and Phenotype subtracks. Default hidden. NCBI sometimes calls this "presumed normal"; the description page notes the equivalence. mergeSpannedItems on for the dense subtracks (normal_healthy ~5.6M items, normal_phenotype ~410K, somatic_sv ~67K). - ClinVar SVs are not duplicated; description pages cross-link to the existing ClinVar track instead. Description pages: rewrite dbVarCommon.html and dbVarCurated.html, refresh dbVarConflict.html, add dbVarSomatic.html and dbVarOther.html. Retire the unused dbVar_common.html. Methods links now point at NCBI's dbVar Overview rather than the FTP directory listing. searchTable termRegex widened to ^[den]ssv[0-9]+ so dssv* accessions in normal_healthy resolve. Otto: stage downloads to release/\${db}.new/, validate per file (size floor and 10% itemCount delta vs the current live copy), then atomically swap via directory rename with a one-cycle .prev rollback. On validation failure, leave .new/ in place for human inspection and exit non-zero so the wrapper emails. On no-op runs the wrapper now stays silent. checkNstd175.sh's "update done" message moved inside the update branch so silence is honoured. New-file detection (via a knownFiles.txt manifest) emails when NCBI adds a file we don't yet expose. knownFiles.txt itself lives only at the deployment path under /hive/data/outside/otto/dbVar/, not in the tree.
• src/hg/makeDb/trackDb/human/dbVarOther.html
  • lines changed 130, context: html, text, full: html, text
    b85c12cf9af0ee1a954b8cced961bcbd909b7979 Wed Apr 29 12:04:36 2026 -0700
    Expand dbVar tracks to expose all six nstd186 source studies and add new Somatic and Other composites. refs #37406 Restructure the dbVar supertrack: - Renamed from "dbVar Common Struct Var" to "dbVar Struct Var". - dbVar Common SV: added subtracks for Lee, Abel, and Byrska-Bishop (the three nstd186 source studies that were missing from our Curated Common track), and for the American/East Asian/South Asian/Other populations. - dbVar Conflict SV: description page refreshed; subtrack longLabel clarified. - dbVar Somatic SV (new): single subtrack pulling somatic_sv.bb from the dbVar hub. Default hidden. - dbVar Other SV (new): residual bucket for dbVar SVs not classified as common, somatic, or clinical, split into Healthy and Phenotype subtracks. Default hidden. NCBI sometimes calls this "presumed normal"; the description page notes the equivalence. mergeSpannedItems on for the dense subtracks (normal_healthy ~5.6M items, normal_phenotype ~410K, somatic_sv ~67K). - ClinVar SVs are not duplicated; description pages cross-link to the existing ClinVar track instead. Description pages: rewrite dbVarCommon.html and dbVarCurated.html, refresh dbVarConflict.html, add dbVarSomatic.html and dbVarOther.html. Retire the unused dbVar_common.html. Methods links now point at NCBI's dbVar Overview rather than the FTP directory listing. searchTable termRegex widened to ^[den]ssv[0-9]+ so dssv* accessions in normal_healthy resolve. Otto: stage downloads to release/\${db}.new/, validate per file (size floor and 10% itemCount delta vs the current live copy), then atomically swap via directory rename with a one-cycle .prev rollback. On validation failure, leave .new/ in place for human inspection and exit non-zero so the wrapper emails. On no-op runs the wrapper now stays silent. checkNstd175.sh's "update done" message moved inside the update branch so silence is honoured. New-file detection (via a knownFiles.txt manifest) emails when NCBI adds a file we don't yet expose. knownFiles.txt itself lives only at the deployment path under /hive/data/outside/otto/dbVar/, not in the tree.
• src/hg/makeDb/trackDb/human/dbVarSomatic.html
  • lines changed 118, context: html, text, full: html, text
    b85c12cf9af0ee1a954b8cced961bcbd909b7979 Wed Apr 29 12:04:36 2026 -0700
    Expand dbVar tracks to expose all six nstd186 source studies and add new Somatic and Other composites. refs #37406 Restructure the dbVar supertrack: - Renamed from "dbVar Common Struct Var" to "dbVar Struct Var". - dbVar Common SV: added subtracks for Lee, Abel, and Byrska-Bishop (the three nstd186 source studies that were missing from our Curated Common track), and for the American/East Asian/South Asian/Other populations. - dbVar Conflict SV: description page refreshed; subtrack longLabel clarified. - dbVar Somatic SV (new): single subtrack pulling somatic_sv.bb from the dbVar hub. Default hidden. - dbVar Other SV (new): residual bucket for dbVar SVs not classified as common, somatic, or clinical, split into Healthy and Phenotype subtracks. Default hidden. NCBI sometimes calls this "presumed normal"; the description page notes the equivalence. mergeSpannedItems on for the dense subtracks (normal_healthy ~5.6M items, normal_phenotype ~410K, somatic_sv ~67K). - ClinVar SVs are not duplicated; description pages cross-link to the existing ClinVar track instead. Description pages: rewrite dbVarCommon.html and dbVarCurated.html, refresh dbVarConflict.html, add dbVarSomatic.html and dbVarOther.html. Retire the unused dbVar_common.html. Methods links now point at NCBI's dbVar Overview rather than the FTP directory listing. searchTable termRegex widened to ^[den]ssv[0-9]+ so dssv* accessions in normal_healthy resolve. Otto: stage downloads to release/\${db}.new/, validate per file (size floor and 10% itemCount delta vs the current live copy), then atomically swap via directory rename with a one-cycle .prev rollback. On validation failure, leave .new/ in place for human inspection and exit non-zero so the wrapper emails. On no-op runs the wrapper now stays silent. checkNstd175.sh's "update done" message moved inside the update branch so silence is honoured. New-file detection (via a knownFiles.txt manifest) emails when NCBI adds a file we don't yet expose. knownFiles.txt itself lives only at the deployment path under /hive/data/outside/otto/dbVar/, not in the tree.
• src/hg/makeDb/trackDb/human/dbVar_common.html
  • lines changed 20, context: html, text, full: html, text
    b85c12cf9af0ee1a954b8cced961bcbd909b7979 Wed Apr 29 12:04:36 2026 -0700
    Expand dbVar tracks to expose all six nstd186 source studies and add new Somatic and Other composites. refs #37406 Restructure the dbVar supertrack: - Renamed from "dbVar Common Struct Var" to "dbVar Struct Var". - dbVar Common SV: added subtracks for Lee, Abel, and Byrska-Bishop (the three nstd186 source studies that were missing from our Curated Common track), and for the American/East Asian/South Asian/Other populations. - dbVar Conflict SV: description page refreshed; subtrack longLabel clarified. - dbVar Somatic SV (new): single subtrack pulling somatic_sv.bb from the dbVar hub. Default hidden. - dbVar Other SV (new): residual bucket for dbVar SVs not classified as common, somatic, or clinical, split into Healthy and Phenotype subtracks. Default hidden. NCBI sometimes calls this "presumed normal"; the description page notes the equivalence. mergeSpannedItems on for the dense subtracks (normal_healthy ~5.6M items, normal_phenotype ~410K, somatic_sv ~67K). - ClinVar SVs are not duplicated; description pages cross-link to the existing ClinVar track instead. Description pages: rewrite dbVarCommon.html and dbVarCurated.html, refresh dbVarConflict.html, add dbVarSomatic.html and dbVarOther.html. Retire the unused dbVar_common.html. Methods links now point at NCBI's dbVar Overview rather than the FTP directory listing. searchTable termRegex widened to ^[den]ssv[0-9]+ so dssv* accessions in normal_healthy resolve. Otto: stage downloads to release/\${db}.new/, validate per file (size floor and 10% itemCount delta vs the current live copy), then atomically swap via directory rename with a one-cycle .prev rollback. On validation failure, leave .new/ in place for human inspection and exit non-zero so the wrapper emails. On no-op runs the wrapper now stays silent. checkNstd175.sh's "update done" message moved inside the update branch so silence is honoured. New-file detection (via a knownFiles.txt manifest) emails when NCBI adds a file we don't yet expose. knownFiles.txt itself lives only at the deployment path under /hive/data/outside/otto/dbVar/, not in the tree.
• src/hg/makeDb/trackDb/human/hg19/gnomadMpc.html
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    ced625fd01d4a62ad02ed6be998a4d17058524e1 Wed Apr 29 01:08:47 2026 -0700
    update docs for the new MPC score and a warning on hg19. refs #37478
• src/hg/makeDb/trackDb/human/hg38/bacRearray32k.html
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    bfc0ac4ea2f3cc169bac73afc6511c07dd802a20 Wed Apr 29 14:41:53 2026 -0700
    Resolve OUP article-lookup links to canonical URLs in BAC track refs. refs #35059 bacRearray32k.html: Krzywinski 2004 NAR -> /nar/article/32/12/3651/2375827 choriCloneEnds.html: Schneider 2013 NAR -> /nar/article/41/D1/D1070/1065498 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    db75ac2f74d3149efdb945d1efe966b27ec0def8 Thu Apr 30 15:39:17 2026 -0700
    Adding a note about Pieter de Jong's contribution to the BAC tracks, refs #35059
• src/hg/makeDb/trackDb/human/hg38/gnomadMpc.html
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    ced625fd01d4a62ad02ed6be998a4d17058524e1 Wed Apr 29 01:08:47 2026 -0700
    update docs for the new MPC score and a warning on hg19. refs #37478
• src/hg/makeDb/trackDb/human/hg38/m6aAtlas.html
  • lines changed 122, context: html, text, full: html, text
    63653eb7f4fcccfedec87fe115ed0a954012c3ad Thu Apr 30 05:46:04 2026 -0700
    Adding new "m6A-Atlas v2 sites" track under rnaMod superTrack on hg38: 427760 high-confidence base-resolution m6A sites compiled by m6A-Atlas v2 (Liang 2024) from 12 detection technologies across 24 cell lines / tissues. Filters on region, technique, cell line, biotype, #techniques, #cell lines. Track lives in its own m6aAtlas.ra file, included alpha-only via trackDb.ra, refs #36613 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/m6aAtlas.ra
  • lines changed 26, context: html, text, full: html, text
    63653eb7f4fcccfedec87fe115ed0a954012c3ad Thu Apr 30 05:46:04 2026 -0700
    Adding new "m6A-Atlas v2 sites" track under rnaMod superTrack on hg38: 427760 high-confidence base-resolution m6A sites compiled by m6A-Atlas v2 (Liang 2024) from 12 detection technologies across 24 cell lines / tissues. Filters on region, technique, cell line, biotype, #techniques, #cell lines. Track lives in its own m6aAtlas.ra file, included alpha-only via trackDb.ra, refs #36613 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/mb2.ra
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    84ce1cd33d7b4cfdf5cc798d392a6594ba5a3c7a Wed Apr 29 10:07:45 2026 -0700
    Switching to local URLs for MethBase 2 track, refs #36320
• src/hg/makeDb/trackDb/human/hg38/mb2_2.ra
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    84ce1cd33d7b4cfdf5cc798d392a6594ba5a3c7a Wed Apr 29 10:07:45 2026 -0700
    Switching to local URLs for MethBase 2 track, refs #36320
• src/hg/makeDb/trackDb/human/hg38/mpra.html
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    2087dbbb5adafd3219e2dfbbbe23d10a758e2828 Fri May 1 15:48:00 2026 -0700
    Update mprabase description page and stanza per QA pass. refs #37359 Description page (mprabase.html): added library-composition framing (curated union of study-specific libraries, not a uniform enhancer atlas), element-size note covering 144-200 bp tiles, 354-678 bp Klein 2020 length sub-experiments, and 1 bp SNP-coordinate markers, sharpened Mattioli mESC cell-line note (mouse orthologous sequence assayed in mouse cells), cell-line biological-context table, scoring-methodology paragraph noting that cross-experiment percentile comparisons are approximate, "Interpreting the raw score" subsection with the log2-to- fold-change translation, coordinate-provenance sentence, and Arnold et al. 2013 row in the Experiments table. References for all seven source publications added. trackDb stanza (mpra.ra): HTML mouseOver with bold field names and line breaks, plus dataVersion "MPRA Base v4.9.3 (Mar 2026)". Parent superTrack description page (mpra.html) opening paragraph rewritten to clarify the barcoded reporter-RNA mechanism and fold the variant-MPRA case in cleanly. Makedoc (mpra.txt): bundled Mattioli title rebuild ask with AutoSQL percentile_rank text fix and name disambiguation (149 of 625 unique names reused across PMIDs); added the open Klein 2020 sub-design question for Varda; updated Arnold orphan note to reflect Varda's confirmation that the HeLa STARR-seq element is a valid Stark Lab proof-of-concept.
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    3115e4005436926896b8c3b4979a490a8190c023 Fri May 1 17:17:18 2026 -0700
    Polish mpra superTrack description page after subtrack QA. refs #37359 - Replace fabricated "Wang T, Matreyek KA, Yang X." citation with the actual published MPRAVarDB paper (Jin et al., 2024, PMID 39325859, Bioinformatics 40(10)) in both the inline link and References section. - Acknowledge the 5'-vs-3'UTR placement difference in the MPRA mechanism paragraph instead of stating every fragment is cloned upstream of the reporter; ~41% of mpraVarDb tests 3'UTR variants placed downstream to measure post-transcriptional effects. - Update MPRAVarDB description to read "transcriptional or post- transcriptional regulatory activity" to match the subtrack page. - Rewrite the cell-line note to clarify that Mattioli 2020 mESC rows test the mouse orthologous sequence in mouse cells, with hg38 coordinates derived from the orthologous human position by liftOver. - Move the cell-line note below the bulleted track list to fix a dangling colon on the list intro.
• src/hg/makeDb/trackDb/human/hg38/mpra.ra
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    2087dbbb5adafd3219e2dfbbbe23d10a758e2828 Fri May 1 15:48:00 2026 -0700
    Update mprabase description page and stanza per QA pass. refs #37359 Description page (mprabase.html): added library-composition framing (curated union of study-specific libraries, not a uniform enhancer atlas), element-size note covering 144-200 bp tiles, 354-678 bp Klein 2020 length sub-experiments, and 1 bp SNP-coordinate markers, sharpened Mattioli mESC cell-line note (mouse orthologous sequence assayed in mouse cells), cell-line biological-context table, scoring-methodology paragraph noting that cross-experiment percentile comparisons are approximate, "Interpreting the raw score" subsection with the log2-to- fold-change translation, coordinate-provenance sentence, and Arnold et al. 2013 row in the Experiments table. References for all seven source publications added. trackDb stanza (mpra.ra): HTML mouseOver with bold field names and line breaks, plus dataVersion "MPRA Base v4.9.3 (Mar 2026)". Parent superTrack description page (mpra.html) opening paragraph rewritten to clarify the barcoded reporter-RNA mechanism and fold the variant-MPRA case in cleanly. Makedoc (mpra.txt): bundled Mattioli title rebuild ask with AutoSQL percentile_rank text fix and name disambiguation (149 of 625 unique names reused across PMIDs); added the open Klein 2020 sub-design question for Varda; updated Arnold orphan note to reflect Varda's confirmation that the HeLa STARR-seq element is a valid Stark Lab proof-of-concept.
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    899f9da8129add8c64c86b405c87b3a97738a2ad Fri May 1 17:12:18 2026 -0700
    Update mpraVarDb description page and trackDb stanza per QA pass. refs #37359 Description page (mpraVarDb.html): - Primary citation corrected from a fabricated "Wang T, Matreyek KA, Yang X." entry to Jin et al., 2024 (PMID 39325859, the actual published Bioinformatics paper for MPRAVarDB). - References for all 18 source studies added. - Studies-table counts corrected to match the data: Tewhey 27,138 to 23,430 (the biggest gap, ~14%), Griesemer 72,588 to 72,546, Abell 29,582 to 29,564, Mouri 14,551 to 14,549, McAfee 10,310 to 10,302, Cooper 5,340 to 5,330, Lu 1,038 to 1,036. - Color counts on Display Conventions corrected to actual post-liftOver values: 22,451 dark red / 17,773 orange / 198,804 grey = 239,028. - "Note on study type" paragraph clarifying that ~41% of variants (Griesemer + Schuster 3'UTR) measure post-transcriptional regulation rather than transcription. - "Cell-type specificity" reminder, "Note on Kircher 2019" saturation- mutagenesis structure, "Interpreting log2FC" subsection with the linear-fold-change translation, and "Significance thresholds across studies" Methods paragraph noting that source studies use a mix of FDR thresholds (0.05/0.10) and that Kircher reports raw regression p-values rather than FDR. - Kircher element list reworded to avoid double-counting UC88 as both a named element and "an ultraconserved enhancer". trackDb stanza (mpra.ra, mpraVarDb subtrack): - filterValues.cellLine fixed: PC3 was hiding 26,546 Schuster rows (data has "PC3 cell"), SF7996 was hiding 3,896 Kircher GBM rows (data has bundled "HEK293T,SF7996"), and SK-MEL-28 (1,510) and K562+GATA1 (31) were missing entirely. Added comma-escape syntax (HEK293T,,SF7996) per slNameListFromCommaEscaped. Recovers ~31,983 hidden rows. - HTML mouseOver with bold field names and line breaks. - urls rsid="https://www.ncbi.nlm.nih.gov/snp/$$" added so rsIDs are clickable linkouts to dbSNP. - dataVersion "MPRAVarDB snapshot 2026-03-10" added. Makedoc (mpra.txt): QA review note added with the trackDb-only fixes and the items punted to upstream / next rebuild for Tao Wang.
• src/hg/makeDb/trackDb/human/hg38/mpraVarDb.html
  • lines changed 281, context: html, text, full: html, text
    899f9da8129add8c64c86b405c87b3a97738a2ad Fri May 1 17:12:18 2026 -0700
    Update mpraVarDb description page and trackDb stanza per QA pass. refs #37359 Description page (mpraVarDb.html): - Primary citation corrected from a fabricated "Wang T, Matreyek KA, Yang X." entry to Jin et al., 2024 (PMID 39325859, the actual published Bioinformatics paper for MPRAVarDB). - References for all 18 source studies added. - Studies-table counts corrected to match the data: Tewhey 27,138 to 23,430 (the biggest gap, ~14%), Griesemer 72,588 to 72,546, Abell 29,582 to 29,564, Mouri 14,551 to 14,549, McAfee 10,310 to 10,302, Cooper 5,340 to 5,330, Lu 1,038 to 1,036. - Color counts on Display Conventions corrected to actual post-liftOver values: 22,451 dark red / 17,773 orange / 198,804 grey = 239,028. - "Note on study type" paragraph clarifying that ~41% of variants (Griesemer + Schuster 3'UTR) measure post-transcriptional regulation rather than transcription. - "Cell-type specificity" reminder, "Note on Kircher 2019" saturation- mutagenesis structure, "Interpreting log2FC" subsection with the linear-fold-change translation, and "Significance thresholds across studies" Methods paragraph noting that source studies use a mix of FDR thresholds (0.05/0.10) and that Kircher reports raw regression p-values rather than FDR. - Kircher element list reworded to avoid double-counting UC88 as both a named element and "an ultraconserved enhancer". trackDb stanza (mpra.ra, mpraVarDb subtrack): - filterValues.cellLine fixed: PC3 was hiding 26,546 Schuster rows (data has "PC3 cell"), SF7996 was hiding 3,896 Kircher GBM rows (data has bundled "HEK293T,SF7996"), and SK-MEL-28 (1,510) and K562+GATA1 (31) were missing entirely. Added comma-escape syntax (HEK293T,,SF7996) per slNameListFromCommaEscaped. Recovers ~31,983 hidden rows. - HTML mouseOver with bold field names and line breaks. - urls rsid="https://www.ncbi.nlm.nih.gov/snp/$$" added so rsIDs are clickable linkouts to dbSNP. - dataVersion "MPRAVarDB snapshot 2026-03-10" added. Makedoc (mpra.txt): QA review note added with the trackDb-only fixes and the items punted to upstream / next rebuild for Tao Wang.
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    a040682f91470d94ede23575f556f33fc2c83fe0 Mon May 4 09:52:27 2026 -0700
    Fix stale Griesemer variant count in mpraVarDb.html study-type note. refs #37359 Inline mention in the 'Note on study type' paragraph still read 72,588; the studies table and the 99,092 3'UTR total were already on the corrected 72,546. Per CR feedback.
• src/hg/makeDb/trackDb/human/hg38/mprabase.html
  • lines changed 135, context: html, text, full: html, text
    2087dbbb5adafd3219e2dfbbbe23d10a758e2828 Fri May 1 15:48:00 2026 -0700
    Update mprabase description page and stanza per QA pass. refs #37359 Description page (mprabase.html): added library-composition framing (curated union of study-specific libraries, not a uniform enhancer atlas), element-size note covering 144-200 bp tiles, 354-678 bp Klein 2020 length sub-experiments, and 1 bp SNP-coordinate markers, sharpened Mattioli mESC cell-line note (mouse orthologous sequence assayed in mouse cells), cell-line biological-context table, scoring-methodology paragraph noting that cross-experiment percentile comparisons are approximate, "Interpreting the raw score" subsection with the log2-to- fold-change translation, coordinate-provenance sentence, and Arnold et al. 2013 row in the Experiments table. References for all seven source publications added. trackDb stanza (mpra.ra): HTML mouseOver with bold field names and line breaks, plus dataVersion "MPRA Base v4.9.3 (Mar 2026)". Parent superTrack description page (mpra.html) opening paragraph rewritten to clarify the barcoded reporter-RNA mechanism and fold the variant-MPRA case in cleanly. Makedoc (mpra.txt): bundled Mattioli title rebuild ask with AutoSQL percentile_rank text fix and name disambiguation (149 of 625 unique names reused across PMIDs); added the open Klein 2020 sub-design question for Varda; updated Arnold orphan note to reflect Varda's confirmation that the HeLa STARR-seq element is a valid Stark Lab proof-of-concept.
• src/hg/makeDb/trackDb/human/hg38/nmd.html
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    e53713685bee07a91be62ffb8354d7478ce2ce7a Wed Apr 29 15:05:45 2026 -0700
    NMD Escape: switch default to MANE+Gencode, add MANE to descriptions and news. refs #33737 - nmd.ra: nmdEscMane on/pack and nmdEscGencode on/dense as the new defaults; nmdEscNcbiRefSeq off/hide. Fix "FIlter" typo in the RefSeq filterLabel. - nmd.html and nmdEscTranscripts.html: list MANE alongside Gencode and RefSeq ("Three transcript sets" / "Three versions"), with a short description of the MANE Select Plus Clinical set. - newsarch.html (Apr. 22, 2026 entry): add MANE Select Plus Clinical to the list of NMD escape ruleset tracks.
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    0f8c134e2fb577bb6cd39bc3d8233af4c3e0b122 Mon May 4 08:52:48 2026 -0700
    Fix unit spacing and entity encodings in NMD Escape descriptions per CR feedback. refs #33737 nmd.html / nmdEscTranscripts.html / newsarch.html (Apr. 22, 2026 entry): normalize 50bp/100bp/400nt to '50 bp' / '100 bp' / '400 nt' for consistent unit spacing; replace 3&#8242;UTR with plain 3'UTR; replace &nbsp; between numbers and units with a regular space.
• src/hg/makeDb/trackDb/human/hg38/nmd.ra
  • lines changed 7, context: html, text, full: html, text
    e53713685bee07a91be62ffb8354d7478ce2ce7a Wed Apr 29 15:05:45 2026 -0700
    NMD Escape: switch default to MANE+Gencode, add MANE to descriptions and news. refs #33737 - nmd.ra: nmdEscMane on/pack and nmdEscGencode on/dense as the new defaults; nmdEscNcbiRefSeq off/hide. Fix "FIlter" typo in the RefSeq filterLabel. - nmd.html and nmdEscTranscripts.html: list MANE alongside Gencode and RefSeq ("Three transcript sets" / "Three versions"), with a short description of the MANE Select Plus Clinical set. - newsarch.html (Apr. 22, 2026 entry): add MANE Select Plus Clinical to the list of NMD escape ruleset tracks.
• src/hg/makeDb/trackDb/human/hg38/nmdEscTranscripts.html
  • lines changed 6, context: html, text, full: html, text
    e53713685bee07a91be62ffb8354d7478ce2ce7a Wed Apr 29 15:05:45 2026 -0700
    NMD Escape: switch default to MANE+Gencode, add MANE to descriptions and news. refs #33737 - nmd.ra: nmdEscMane on/pack and nmdEscGencode on/dense as the new defaults; nmdEscNcbiRefSeq off/hide. Fix "FIlter" typo in the RefSeq filterLabel. - nmd.html and nmdEscTranscripts.html: list MANE alongside Gencode and RefSeq ("Three transcript sets" / "Three versions"), with a short description of the MANE Select Plus Clinical set. - newsarch.html (Apr. 22, 2026 entry): add MANE Select Plus Clinical to the list of NMD escape ruleset tracks.
  • lines changed 7, context: html, text, full: html, text
    0f8c134e2fb577bb6cd39bc3d8233af4c3e0b122 Mon May 4 08:52:48 2026 -0700
    Fix unit spacing and entity encodings in NMD Escape descriptions per CR feedback. refs #33737 nmd.html / nmdEscTranscripts.html / newsarch.html (Apr. 22, 2026 entry): normalize 50bp/100bp/400nt to '50 bp' / '100 bp' / '400 nt' for consistent unit spacing; replace 3&#8242;UTR with plain 3'UTR; replace &nbsp; between numbers and units with a regular space.
• src/hg/makeDb/trackDb/human/hg38/rnaMod.html
  • lines changed 33, context: html, text, full: html, text
    a54f86a21a62394f88021eefccba67f18a4a27e6 Thu Apr 30 05:45:35 2026 -0700
    Adding new "DRACH motif sites" track under rnaMod superTrack on hg38: every occurrence of the m6A consensus motif (DRACH) in MANE Select v1.5 transcripts, projected onto the genome via pslMap. New scripts under makeDb/scripts/rnaMod, makeDoc under makeDb/doc/hg38/rnaMod.txt. Refreshed the parent rnaMod.html. Track is alpha-only (rnaMod.ra is already alpha-included), refs #36613 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 4, context: html, text, full: html, text
    63653eb7f4fcccfedec87fe115ed0a954012c3ad Thu Apr 30 05:46:04 2026 -0700
    Adding new "m6A-Atlas v2 sites" track under rnaMod superTrack on hg38: 427760 high-confidence base-resolution m6A sites compiled by m6A-Atlas v2 (Liang 2024) from 12 detection technologies across 24 cell lines / tissues. Filters on region, technique, cell line, biotype, #techniques, #cell lines. Track lives in its own m6aAtlas.ra file, included alpha-only via trackDb.ra, refs #36613 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/rnaMod.ra
  • lines changed 18, context: html, text, full: html, text
    a54f86a21a62394f88021eefccba67f18a4a27e6 Thu Apr 30 05:45:35 2026 -0700
    Adding new "DRACH motif sites" track under rnaMod superTrack on hg38: every occurrence of the m6A consensus motif (DRACH) in MANE Select v1.5 transcripts, projected onto the genome via pslMap. New scripts under makeDb/scripts/rnaMod, makeDoc under makeDb/doc/hg38/rnaMod.txt. Refreshed the parent rnaMod.html. Track is alpha-only (rnaMod.ra is already alpha-included), refs #36613 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    63653eb7f4fcccfedec87fe115ed0a954012c3ad Thu Apr 30 05:46:04 2026 -0700
    Adding new "m6A-Atlas v2 sites" track under rnaMod superTrack on hg38: 427760 high-confidence base-resolution m6A sites compiled by m6A-Atlas v2 (Liang 2024) from 12 detection technologies across 24 cell lines / tissues. Filters on region, technique, cell line, biotype, #techniques, #cell lines. Track lives in its own m6aAtlas.ra file, included alpha-only via trackDb.ra, refs #36613 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.html
  • lines changed 9, context: html, text, full: html, text
    b4808fac05f88a0170f2642a1670d571ceca4b7e Mon May 4 10:08:39 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - Added Andrews 2023 reference (PMID 37104580) to wgEncodeReg4.html supertrack page. - Added 16 missing organ rows to 5 hg38 multiWig organ availability tables (Dnase +nose; Atac +bone marrow, skin; H3K4me3 +bone, epithelium, mouth; H3K27ac +bone, epithelium, eye, mouth; Ctcf +bone, bone marrow, embryo, epithelium, mouth, penis). - Added colored Organ/Tissue cell to organ tables across 12 multiWig HTMLs (5 hg38 + 5 mm10 standard + 2 Txn) using RGB from .ra color settings. - Restructured Txn organ tables to a 4-column Organ/Source/Plus/Minus layout, removing the "all X" row prefix encoding. - Rewrote the "two versions" Description block across 12 multiWig HTMLs with parallel 3-bullet conditional logic and ENCODE-standard biosample terminology. - Updated DNase/ATAC/Histone/CTCF (Indiv.) Epigenetics composite pages on both assemblies with 5-bullet Description and explicit per-assay color legend in Display Conventions. - Added encode4RegLayeredDisplay.shared.html and replaced the inline Display Conventions block in 10 multiWig HTMLs with an SSI include.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Atac.html
  • lines changed 64, context: html, text, full: html, text
    b4808fac05f88a0170f2642a1670d571ceca4b7e Mon May 4 10:08:39 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - Added Andrews 2023 reference (PMID 37104580) to wgEncodeReg4.html supertrack page. - Added 16 missing organ rows to 5 hg38 multiWig organ availability tables (Dnase +nose; Atac +bone marrow, skin; H3K4me3 +bone, epithelium, mouth; H3K27ac +bone, epithelium, eye, mouth; Ctcf +bone, bone marrow, embryo, epithelium, mouth, penis). - Added colored Organ/Tissue cell to organ tables across 12 multiWig HTMLs (5 hg38 + 5 mm10 standard + 2 Txn) using RGB from .ra color settings. - Restructured Txn organ tables to a 4-column Organ/Source/Plus/Minus layout, removing the "all X" row prefix encoding. - Rewrote the "two versions" Description block across 12 multiWig HTMLs with parallel 3-bullet conditional logic and ENCODE-standard biosample terminology. - Updated DNase/ATAC/Histone/CTCF (Indiv.) Epigenetics composite pages on both assemblies with 5-bullet Description and explicit per-assay color legend in Display Conventions. - Added encode4RegLayeredDisplay.shared.html and replaced the inline Display Conventions block in 10 multiWig HTMLs with an SSI include.
  • lines changed 16, context: html, text, full: html, text
    dfa92621f4a734ac53cf35d13c6b9e2cda4b9c32 Mon May 4 10:56:43 2026 -0700
    Fix H3K27ac color hex and swapped checkmark columns in ENCODE4 Regulation HTML tables. refs #34923 Two QA fixes following Gerardo's description-page pass in b4808fac05f: - H3K27ac signal-color hex on Epigenetics description pages: #FFCD00 was the cCRE classification yellow; the assay color used by the composite (per /gbdb/{hg38,mm10}/encode4/regulation/epi_colors.json, after the contrast darkening in 46b52b437f5) is #B59100. Updated wgEncodeReg4Epigenetics.html and encode4RegEpigenetics.html. - "Available Organs and Tissues" tables on the 5 hg38 multiWig description pages had the Tissue and Primary Cell / All Biosamples columns swapped for organs that exist only as wgEncodeReg4XxxAll<Organ> in the .ra (introduced with the tp/ave fix in 0b65049e315). Inverse case: DNase lymphoid tissue showed both columns checked but only the tissue-only subtrack exists. Total 81 row corrections across DNase, ATAC, H3K4me3, H3K27ac, and CTCF. mm10 unaffected (no All-prefix subtracks).
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Dnase.html
  • lines changed 79, context: html, text, full: html, text
    b4808fac05f88a0170f2642a1670d571ceca4b7e Mon May 4 10:08:39 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - Added Andrews 2023 reference (PMID 37104580) to wgEncodeReg4.html supertrack page. - Added 16 missing organ rows to 5 hg38 multiWig organ availability tables (Dnase +nose; Atac +bone marrow, skin; H3K4me3 +bone, epithelium, mouth; H3K27ac +bone, epithelium, eye, mouth; Ctcf +bone, bone marrow, embryo, epithelium, mouth, penis). - Added colored Organ/Tissue cell to organ tables across 12 multiWig HTMLs (5 hg38 + 5 mm10 standard + 2 Txn) using RGB from .ra color settings. - Restructured Txn organ tables to a 4-column Organ/Source/Plus/Minus layout, removing the "all X" row prefix encoding. - Rewrote the "two versions" Description block across 12 multiWig HTMLs with parallel 3-bullet conditional logic and ENCODE-standard biosample terminology. - Updated DNase/ATAC/Histone/CTCF (Indiv.) Epigenetics composite pages on both assemblies with 5-bullet Description and explicit per-assay color legend in Display Conventions. - Added encode4RegLayeredDisplay.shared.html and replaced the inline Display Conventions block in 10 multiWig HTMLs with an SSI include.
  • lines changed 17, context: html, text, full: html, text
    dfa92621f4a734ac53cf35d13c6b9e2cda4b9c32 Mon May 4 10:56:43 2026 -0700
    Fix H3K27ac color hex and swapped checkmark columns in ENCODE4 Regulation HTML tables. refs #34923 Two QA fixes following Gerardo's description-page pass in b4808fac05f: - H3K27ac signal-color hex on Epigenetics description pages: #FFCD00 was the cCRE classification yellow; the assay color used by the composite (per /gbdb/{hg38,mm10}/encode4/regulation/epi_colors.json, after the contrast darkening in 46b52b437f5) is #B59100. Updated wgEncodeReg4Epigenetics.html and encode4RegEpigenetics.html. - "Available Organs and Tissues" tables on the 5 hg38 multiWig description pages had the Tissue and Primary Cell / All Biosamples columns swapped for organs that exist only as wgEncodeReg4XxxAll<Organ> in the .ra (introduced with the tp/ave fix in 0b65049e315). Inverse case: DNase lymphoid tissue showed both columns checked but only the tissue-only subtrack exists. Total 81 row corrections across DNase, ATAC, H3K4me3, H3K27ac, and CTCF. mm10 unaffected (no All-prefix subtracks).
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.html
  • lines changed 21, context: html, text, full: html, text
    b4808fac05f88a0170f2642a1670d571ceca4b7e Mon May 4 10:08:39 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - Added Andrews 2023 reference (PMID 37104580) to wgEncodeReg4.html supertrack page. - Added 16 missing organ rows to 5 hg38 multiWig organ availability tables (Dnase +nose; Atac +bone marrow, skin; H3K4me3 +bone, epithelium, mouth; H3K27ac +bone, epithelium, eye, mouth; Ctcf +bone, bone marrow, embryo, epithelium, mouth, penis). - Added colored Organ/Tissue cell to organ tables across 12 multiWig HTMLs (5 hg38 + 5 mm10 standard + 2 Txn) using RGB from .ra color settings. - Restructured Txn organ tables to a 4-column Organ/Source/Plus/Minus layout, removing the "all X" row prefix encoding. - Rewrote the "two versions" Description block across 12 multiWig HTMLs with parallel 3-bullet conditional logic and ENCODE-standard biosample terminology. - Updated DNase/ATAC/Histone/CTCF (Indiv.) Epigenetics composite pages on both assemblies with 5-bullet Description and explicit per-assay color legend in Display Conventions. - Added encode4RegLayeredDisplay.shared.html and replaced the inline Display Conventions block in 10 multiWig HTMLs with an SSI include.
  • lines changed 1, context: html, text, full: html, text
    dfa92621f4a734ac53cf35d13c6b9e2cda4b9c32 Mon May 4 10:56:43 2026 -0700
    Fix H3K27ac color hex and swapped checkmark columns in ENCODE4 Regulation HTML tables. refs #34923 Two QA fixes following Gerardo's description-page pass in b4808fac05f: - H3K27ac signal-color hex on Epigenetics description pages: #FFCD00 was the cCRE classification yellow; the assay color used by the composite (per /gbdb/{hg38,mm10}/encode4/regulation/epi_colors.json, after the contrast darkening in 46b52b437f5) is #B59100. Updated wgEncodeReg4Epigenetics.html and encode4RegEpigenetics.html. - "Available Organs and Tissues" tables on the 5 hg38 multiWig description pages had the Tissue and Primary Cell / All Biosamples columns swapped for organs that exist only as wgEncodeReg4XxxAll<Organ> in the .ra (introduced with the tp/ave fix in 0b65049e315). Inverse case: DNase lymphoid tissue showed both columns checked but only the tissue-only subtrack exists. Total 81 row corrections across DNase, ATAC, H3K4me3, H3K27ac, and CTCF. mm10 unaffected (no All-prefix subtracks).
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkCtcf.html
  • lines changed 74, context: html, text, full: html, text
    b4808fac05f88a0170f2642a1670d571ceca4b7e Mon May 4 10:08:39 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - Added Andrews 2023 reference (PMID 37104580) to wgEncodeReg4.html supertrack page. - Added 16 missing organ rows to 5 hg38 multiWig organ availability tables (Dnase +nose; Atac +bone marrow, skin; H3K4me3 +bone, epithelium, mouth; H3K27ac +bone, epithelium, eye, mouth; Ctcf +bone, bone marrow, embryo, epithelium, mouth, penis). - Added colored Organ/Tissue cell to organ tables across 12 multiWig HTMLs (5 hg38 + 5 mm10 standard + 2 Txn) using RGB from .ra color settings. - Restructured Txn organ tables to a 4-column Organ/Source/Plus/Minus layout, removing the "all X" row prefix encoding. - Rewrote the "two versions" Description block across 12 multiWig HTMLs with parallel 3-bullet conditional logic and ENCODE-standard biosample terminology. - Updated DNase/ATAC/Histone/CTCF (Indiv.) Epigenetics composite pages on both assemblies with 5-bullet Description and explicit per-assay color legend in Display Conventions. - Added encode4RegLayeredDisplay.shared.html and replaced the inline Display Conventions block in 10 multiWig HTMLs with an SSI include.
  • lines changed 15, context: html, text, full: html, text
    dfa92621f4a734ac53cf35d13c6b9e2cda4b9c32 Mon May 4 10:56:43 2026 -0700
    Fix H3K27ac color hex and swapped checkmark columns in ENCODE4 Regulation HTML tables. refs #34923 Two QA fixes following Gerardo's description-page pass in b4808fac05f: - H3K27ac signal-color hex on Epigenetics description pages: #FFCD00 was the cCRE classification yellow; the assay color used by the composite (per /gbdb/{hg38,mm10}/encode4/regulation/epi_colors.json, after the contrast darkening in 46b52b437f5) is #B59100. Updated wgEncodeReg4Epigenetics.html and encode4RegEpigenetics.html. - "Available Organs and Tissues" tables on the 5 hg38 multiWig description pages had the Tissue and Primary Cell / All Biosamples columns swapped for organs that exist only as wgEncodeReg4XxxAll<Organ> in the .ra (introduced with the tp/ave fix in 0b65049e315). Inverse case: DNase lymphoid tissue showed both columns checked but only the tissue-only subtrack exists. Total 81 row corrections across DNase, ATAC, H3K4me3, H3K27ac, and CTCF. mm10 unaffected (no All-prefix subtracks).
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k27ac.html
  • lines changed 76, context: html, text, full: html, text
    b4808fac05f88a0170f2642a1670d571ceca4b7e Mon May 4 10:08:39 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - Added Andrews 2023 reference (PMID 37104580) to wgEncodeReg4.html supertrack page. - Added 16 missing organ rows to 5 hg38 multiWig organ availability tables (Dnase +nose; Atac +bone marrow, skin; H3K4me3 +bone, epithelium, mouth; H3K27ac +bone, epithelium, eye, mouth; Ctcf +bone, bone marrow, embryo, epithelium, mouth, penis). - Added colored Organ/Tissue cell to organ tables across 12 multiWig HTMLs (5 hg38 + 5 mm10 standard + 2 Txn) using RGB from .ra color settings. - Restructured Txn organ tables to a 4-column Organ/Source/Plus/Minus layout, removing the "all X" row prefix encoding. - Rewrote the "two versions" Description block across 12 multiWig HTMLs with parallel 3-bullet conditional logic and ENCODE-standard biosample terminology. - Updated DNase/ATAC/Histone/CTCF (Indiv.) Epigenetics composite pages on both assemblies with 5-bullet Description and explicit per-assay color legend in Display Conventions. - Added encode4RegLayeredDisplay.shared.html and replaced the inline Display Conventions block in 10 multiWig HTMLs with an SSI include.
  • lines changed 17, context: html, text, full: html, text
    dfa92621f4a734ac53cf35d13c6b9e2cda4b9c32 Mon May 4 10:56:43 2026 -0700
    Fix H3K27ac color hex and swapped checkmark columns in ENCODE4 Regulation HTML tables. refs #34923 Two QA fixes following Gerardo's description-page pass in b4808fac05f: - H3K27ac signal-color hex on Epigenetics description pages: #FFCD00 was the cCRE classification yellow; the assay color used by the composite (per /gbdb/{hg38,mm10}/encode4/regulation/epi_colors.json, after the contrast darkening in 46b52b437f5) is #B59100. Updated wgEncodeReg4Epigenetics.html and encode4RegEpigenetics.html. - "Available Organs and Tissues" tables on the 5 hg38 multiWig description pages had the Tissue and Primary Cell / All Biosamples columns swapped for organs that exist only as wgEncodeReg4XxxAll<Organ> in the .ra (introduced with the tp/ave fix in 0b65049e315). Inverse case: DNase lymphoid tissue showed both columns checked but only the tissue-only subtrack exists. Total 81 row corrections across DNase, ATAC, H3K4me3, H3K27ac, and CTCF. mm10 unaffected (no All-prefix subtracks).
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k4me3.html
  • lines changed 76, context: html, text, full: html, text
    b4808fac05f88a0170f2642a1670d571ceca4b7e Mon May 4 10:08:39 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - Added Andrews 2023 reference (PMID 37104580) to wgEncodeReg4.html supertrack page. - Added 16 missing organ rows to 5 hg38 multiWig organ availability tables (Dnase +nose; Atac +bone marrow, skin; H3K4me3 +bone, epithelium, mouth; H3K27ac +bone, epithelium, eye, mouth; Ctcf +bone, bone marrow, embryo, epithelium, mouth, penis). - Added colored Organ/Tissue cell to organ tables across 12 multiWig HTMLs (5 hg38 + 5 mm10 standard + 2 Txn) using RGB from .ra color settings. - Restructured Txn organ tables to a 4-column Organ/Source/Plus/Minus layout, removing the "all X" row prefix encoding. - Rewrote the "two versions" Description block across 12 multiWig HTMLs with parallel 3-bullet conditional logic and ENCODE-standard biosample terminology. - Updated DNase/ATAC/Histone/CTCF (Indiv.) Epigenetics composite pages on both assemblies with 5-bullet Description and explicit per-assay color legend in Display Conventions. - Added encode4RegLayeredDisplay.shared.html and replaced the inline Display Conventions block in 10 multiWig HTMLs with an SSI include.
  • lines changed 16, context: html, text, full: html, text
    dfa92621f4a734ac53cf35d13c6b9e2cda4b9c32 Mon May 4 10:56:43 2026 -0700
    Fix H3K27ac color hex and swapped checkmark columns in ENCODE4 Regulation HTML tables. refs #34923 Two QA fixes following Gerardo's description-page pass in b4808fac05f: - H3K27ac signal-color hex on Epigenetics description pages: #FFCD00 was the cCRE classification yellow; the assay color used by the composite (per /gbdb/{hg38,mm10}/encode4/regulation/epi_colors.json, after the contrast darkening in 46b52b437f5) is #B59100. Updated wgEncodeReg4Epigenetics.html and encode4RegEpigenetics.html. - "Available Organs and Tissues" tables on the 5 hg38 multiWig description pages had the Tissue and Primary Cell / All Biosamples columns swapped for organs that exist only as wgEncodeReg4XxxAll<Organ> in the .ra (introduced with the tp/ave fix in 0b65049e315). Inverse case: DNase lymphoid tissue showed both columns checked but only the tissue-only subtrack exists. Total 81 row corrections across DNase, ATAC, H3K4me3, H3K27ac, and CTCF. mm10 unaffected (no All-prefix subtracks).
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Txn.html
  • lines changed 89, context: html, text, full: html, text
    b4808fac05f88a0170f2642a1670d571ceca4b7e Mon May 4 10:08:39 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - Added Andrews 2023 reference (PMID 37104580) to wgEncodeReg4.html supertrack page. - Added 16 missing organ rows to 5 hg38 multiWig organ availability tables (Dnase +nose; Atac +bone marrow, skin; H3K4me3 +bone, epithelium, mouth; H3K27ac +bone, epithelium, eye, mouth; Ctcf +bone, bone marrow, embryo, epithelium, mouth, penis). - Added colored Organ/Tissue cell to organ tables across 12 multiWig HTMLs (5 hg38 + 5 mm10 standard + 2 Txn) using RGB from .ra color settings. - Restructured Txn organ tables to a 4-column Organ/Source/Plus/Minus layout, removing the "all X" row prefix encoding. - Rewrote the "two versions" Description block across 12 multiWig HTMLs with parallel 3-bullet conditional logic and ENCODE-standard biosample terminology. - Updated DNase/ATAC/Histone/CTCF (Indiv.) Epigenetics composite pages on both assemblies with 5-bullet Description and explicit per-assay color legend in Display Conventions. - Added encode4RegLayeredDisplay.shared.html and replaced the inline Display Conventions block in 10 multiWig HTMLs with an SSI include.
• src/hg/makeDb/trackDb/human/lrSv.html
  • lines changed 5, context: html, text, full: html, text
    7ad95a5c42dfbca5fcccf33d5410daf5512af04a Tue Apr 28 12:30:48 2026 -0700
    lrSv: note likely sample overlap across collections (e.g. 1KG in HPRC/CoLoRSdb). refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 68, context: html, text, full: html, text
    9fbdfa3416ffde377072fafd2de44059155c3b44 Thu Apr 30 06:57:35 2026 -0700
    lrSv: add lrSvAll merged track combining all long-read SV subtracks Variants are merged on exact (chrom, start, end, svType, svLen, insLen). Per-database AC columns are stored as strings; "unknown" is used where the source dataset has only placeholder AC values (deCODE, SVatalog 101, 1KG ONT 100). Kim PD Brain is split into affected (PD+ILBD) and healthy (HC) AC columns. Gustafson contributes sampleCount instead of AC. Output: 2,694,871 unique SVs from 3,706,100 input rows across 15 subtracks (27% dedup). The merged track sits as the first subtrack of the lrSv supertrack with filters on sources, svType, svLen, insLen, maxAF/minAF, AC, and sourceCount. The trackDb stanza is generated by the build script directly into human/lrSvAll.ra and pulled in via 'include lrSvAll.ra' from lrSv.ra, so labels in databases.tsv stay the single source of truth. lrSv.html: add a "Disease cases" column to the dataset summary, strip parenthesized internal track names from the section headers, and shorten exact SV counts to ~Nk / ~N.NM in the prose. refs #36642
• src/hg/makeDb/trackDb/human/lrSv.ra
  • lines changed 2, context: html, text, full: html, text
    9fbdfa3416ffde377072fafd2de44059155c3b44 Thu Apr 30 06:57:35 2026 -0700
    lrSv: add lrSvAll merged track combining all long-read SV subtracks Variants are merged on exact (chrom, start, end, svType, svLen, insLen). Per-database AC columns are stored as strings; "unknown" is used where the source dataset has only placeholder AC values (deCODE, SVatalog 101, 1KG ONT 100). Kim PD Brain is split into affected (PD+ILBD) and healthy (HC) AC columns. Gustafson contributes sampleCount instead of AC. Output: 2,694,871 unique SVs from 3,706,100 input rows across 15 subtracks (27% dedup). The merged track sits as the first subtrack of the lrSv supertrack with filters on sources, svType, svLen, insLen, maxAF/minAF, AC, and sourceCount. The trackDb stanza is generated by the build script directly into human/lrSvAll.ra and pulled in via 'include lrSvAll.ra' from lrSv.ra, so labels in databases.tsv stay the single source of truth. lrSv.html: add a "Disease cases" column to the dataset summary, strip parenthesized internal track names from the section headers, and shorten exact SV counts to ~Nk / ~N.NM in the prose. refs #36642
• src/hg/makeDb/trackDb/human/lrSvAll.ra
  • lines changed 41, context: html, text, full: html, text
    9fbdfa3416ffde377072fafd2de44059155c3b44 Thu Apr 30 06:57:35 2026 -0700
    lrSv: add lrSvAll merged track combining all long-read SV subtracks Variants are merged on exact (chrom, start, end, svType, svLen, insLen). Per-database AC columns are stored as strings; "unknown" is used where the source dataset has only placeholder AC values (deCODE, SVatalog 101, 1KG ONT 100). Kim PD Brain is split into affected (PD+ILBD) and healthy (HC) AC columns. Gustafson contributes sampleCount instead of AC. Output: 2,694,871 unique SVs from 3,706,100 input rows across 15 subtracks (27% dedup). The merged track sits as the first subtrack of the lrSv supertrack with filters on sources, svType, svLen, insLen, maxAF/minAF, AC, and sourceCount. The trackDb stanza is generated by the build script directly into human/lrSvAll.ra and pulled in via 'include lrSvAll.ra' from lrSv.ra, so labels in databases.tsv stay the single source of truth. lrSv.html: add a "Disease cases" column to the dataset summary, strip parenthesized internal track names from the section headers, and shorten exact SV counts to ~Nk / ~N.NM in the prose. refs #36642
• src/hg/makeDb/trackDb/human/predictionScoresSuper.ra
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    46f88622e6ec2bbc09f403eeb9ec6122eb05931f Thu Apr 30 15:41:01 2026 -0700
    Releasing PrimateAI-3D and PromoterAI tracks to beta and RR. refs #37274 refs #37278 Drops the alpha tag from both tracks under predictionScoresSuper. Adds 'New' pennantIcons on primateAi and promoterAi pointing at the May 1, 2026 newsarch anchor, and an 'Updated' pennantIcon on the predictionScoresSuper supertrack. Adds a combined release post to newsarch.html with an HBB hg38 screenshot illustrating PrimateAI-3D coding-region calls alongside PromoterAI per-allele scores in the proximal promoter, and updates the indexNews.html sidebar.
• src/hg/makeDb/trackDb/human/primateAi.ra
  • lines changed 1, context: html, text, full: html, text
    46f88622e6ec2bbc09f403eeb9ec6122eb05931f Thu Apr 30 15:41:01 2026 -0700
    Releasing PrimateAI-3D and PromoterAI tracks to beta and RR. refs #37274 refs #37278 Drops the alpha tag from both tracks under predictionScoresSuper. Adds 'New' pennantIcons on primateAi and promoterAi pointing at the May 1, 2026 newsarch anchor, and an 'Updated' pennantIcon on the predictionScoresSuper supertrack. Adds a combined release post to newsarch.html with an HBB hg38 screenshot illustrating PrimateAI-3D coding-region calls alongside PromoterAI per-allele scores in the proximal promoter, and updates the indexNews.html sidebar.
• src/hg/makeDb/trackDb/human/promoterAi.ra
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    46f88622e6ec2bbc09f403eeb9ec6122eb05931f Thu Apr 30 15:41:01 2026 -0700
    Releasing PrimateAI-3D and PromoterAI tracks to beta and RR. refs #37274 refs #37278 Drops the alpha tag from both tracks under predictionScoresSuper. Adds 'New' pennantIcons on primateAi and promoterAi pointing at the May 1, 2026 newsarch anchor, and an 'Updated' pennantIcon on the predictionScoresSuper supertrack. Adds a combined release post to newsarch.html with an HBB hg38 screenshot illustrating PrimateAI-3D coding-region calls alongside PromoterAI per-allele scores in the proximal promoter, and updates the indexNews.html sidebar.
• src/hg/makeDb/trackDb/human/tishkoff180.html
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    37a5b97198453bd06cb03d2092cae239f368e84c Wed Apr 29 05:49:14 2026 -0700
    varFreqs: add tishkoff180 subtrack (Fan et al. 2023, 180 indigenous African WGS, hg19 lift) Sites-only SNP VCF with aggregate AC/AF/AN from 180 individuals (15 each from 12 populations across Ethiopia, Tanzania, Cameroon, Botswana), sequenced at >30x on HiSeq X Ten. hg19 calls supplied by the Tishkoff lab (UPenn) and lifted to hg38 with CrossMap. Redistribution is not permitted, so tableBrowser is disabled. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>, refs #36642
• src/hg/makeDb/trackDb/human/trackDb.dbVar.ra
  • lines changed 226, context: html, text, full: html, text
    b85c12cf9af0ee1a954b8cced961bcbd909b7979 Wed Apr 29 12:04:36 2026 -0700
    Expand dbVar tracks to expose all six nstd186 source studies and add new Somatic and Other composites. refs #37406 Restructure the dbVar supertrack: - Renamed from "dbVar Common Struct Var" to "dbVar Struct Var". - dbVar Common SV: added subtracks for Lee, Abel, and Byrska-Bishop (the three nstd186 source studies that were missing from our Curated Common track), and for the American/East Asian/South Asian/Other populations. - dbVar Conflict SV: description page refreshed; subtrack longLabel clarified. - dbVar Somatic SV (new): single subtrack pulling somatic_sv.bb from the dbVar hub. Default hidden. - dbVar Other SV (new): residual bucket for dbVar SVs not classified as common, somatic, or clinical, split into Healthy and Phenotype subtracks. Default hidden. NCBI sometimes calls this "presumed normal"; the description page notes the equivalence. mergeSpannedItems on for the dense subtracks (normal_healthy ~5.6M items, normal_phenotype ~410K, somatic_sv ~67K). - ClinVar SVs are not duplicated; description pages cross-link to the existing ClinVar track instead. Description pages: rewrite dbVarCommon.html and dbVarCurated.html, refresh dbVarConflict.html, add dbVarSomatic.html and dbVarOther.html. Retire the unused dbVar_common.html. Methods links now point at NCBI's dbVar Overview rather than the FTP directory listing. searchTable termRegex widened to ^[den]ssv[0-9]+ so dssv* accessions in normal_healthy resolve. Otto: stage downloads to release/\${db}.new/, validate per file (size floor and 10% itemCount delta vs the current live copy), then atomically swap via directory rename with a one-cycle .prev rollback. On validation failure, leave .new/ in place for human inspection and exit non-zero so the wrapper emails. On no-op runs the wrapper now stays silent. checkNstd175.sh's "update done" message moved inside the update branch so silence is honoured. New-file detection (via a knownFiles.txt manifest) emails when NCBI adds a file we don't yet expose. knownFiles.txt itself lives only at the deployment path under /hive/data/outside/otto/dbVar/, not in the tree.
  • lines changed 40, context: html, text, full: html, text
    cea47d47e8b2d70f5655d5947669e15d59c079d6 Thu Apr 30 02:59:15 2026 -0700
    committing dbVar nr track, keeping it only on dev, may be useful one day when looking at a CNV and for comparing against the new normal dbVar track
• src/hg/makeDb/trackDb/human/varFreqs.html
  • lines changed 9, context: html, text, full: html, text
    37a5b97198453bd06cb03d2092cae239f368e84c Wed Apr 29 05:49:14 2026 -0700
    varFreqs: add tishkoff180 subtrack (Fan et al. 2023, 180 indigenous African WGS, hg19 lift) Sites-only SNP VCF with aggregate AC/AF/AN from 180 individuals (15 each from 12 populations across Ethiopia, Tanzania, Cameroon, Botswana), sequenced at >30x on HiSeq X Ten. hg19 calls supplied by the Tishkoff lab (UPenn) and lifted to hg38 with CrossMap. Redistribution is not permitted, so tableBrowser is disabled. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>, refs #36642
• src/hg/makeDb/trackDb/human/varFreqs.ra
  • lines changed 16, context: html, text, full: html, text
    37a5b97198453bd06cb03d2092cae239f368e84c Wed Apr 29 05:49:14 2026 -0700
    varFreqs: add tishkoff180 subtrack (Fan et al. 2023, 180 indigenous African WGS, hg19 lift) Sites-only SNP VCF with aggregate AC/AF/AN from 180 individuals (15 each from 12 populations across Ethiopia, Tanzania, Cameroon, Botswana), sequenced at >30x on HiSeq X Ten. hg19 calls supplied by the Tishkoff lab (UPenn) and lifted to hg38 with CrossMap. Redistribution is not permitted, so tableBrowser is disabled. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>, refs #36642
• src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html
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    6c22604d52ab423f3b84eb10a3d5e5bf64ce90a1 Wed Apr 29 12:31:41 2026 -0700
    mm10 ENCODE4 cCREs QA cleanups from qa-track SKILL.md pass: urlLabel trailing colon on 17 subtracks, pennantIcon simplified to text-only, removed broken encode4Reg links, plus minor description page fixes (heading case, en-dash, target="_blank", bigWigToWig in example, cgi-bin path). refs #37131 refs #37409
• src/hg/makeDb/trackDb/mouse/mm10/cCREsSuper.html
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    6c22604d52ab423f3b84eb10a3d5e5bf64ce90a1 Wed Apr 29 12:31:41 2026 -0700
    mm10 ENCODE4 cCREs QA cleanups from qa-track SKILL.md pass: urlLabel trailing colon on 17 subtracks, pennantIcon simplified to text-only, removed broken encode4Reg links, plus minor description page fixes (heading case, en-dash, target="_blank", bigWigToWig in example, cgi-bin path). refs #37131 refs #37409
• src/hg/makeDb/trackDb/mouse/mm10/coreCollection.html
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    6c22604d52ab423f3b84eb10a3d5e5bf64ce90a1 Wed Apr 29 12:31:41 2026 -0700
    mm10 ENCODE4 cCREs QA cleanups from qa-track SKILL.md pass: urlLabel trailing colon on 17 subtracks, pennantIcon simplified to text-only, removed broken encode4Reg links, plus minor description page fixes (heading case, en-dash, target="_blank", bigWigToWig in example, cgi-bin path). refs #37131 refs #37409
• src/hg/makeDb/trackDb/mouse/mm10/encode.cCREs.override.ra
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    6c22604d52ab423f3b84eb10a3d5e5bf64ce90a1 Wed Apr 29 12:31:41 2026 -0700
    mm10 ENCODE4 cCREs QA cleanups from qa-track SKILL.md pass: urlLabel trailing colon on 17 subtracks, pennantIcon simplified to text-only, removed broken encode4Reg links, plus minor description page fixes (heading case, en-dash, target="_blank", bigWigToWig in example, cgi-bin path). refs #37131 refs #37409
• src/hg/makeDb/trackDb/mouse/mm10/encode4.ccres.ra
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    6c22604d52ab423f3b84eb10a3d5e5bf64ce90a1 Wed Apr 29 12:31:41 2026 -0700
    mm10 ENCODE4 cCREs QA cleanups from qa-track SKILL.md pass: urlLabel trailing colon on 17 subtracks, pennantIcon simplified to text-only, removed broken encode4Reg links, plus minor description page fixes (heading case, en-dash, target="_blank", bigWigToWig in example, cgi-bin path). refs #37131 refs #37409
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegAtac.html
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    b4808fac05f88a0170f2642a1670d571ceca4b7e Mon May 4 10:08:39 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - Added Andrews 2023 reference (PMID 37104580) to wgEncodeReg4.html supertrack page. - Added 16 missing organ rows to 5 hg38 multiWig organ availability tables (Dnase +nose; Atac +bone marrow, skin; H3K4me3 +bone, epithelium, mouth; H3K27ac +bone, epithelium, eye, mouth; Ctcf +bone, bone marrow, embryo, epithelium, mouth, penis). - Added colored Organ/Tissue cell to organ tables across 12 multiWig HTMLs (5 hg38 + 5 mm10 standard + 2 Txn) using RGB from .ra color settings. - Restructured Txn organ tables to a 4-column Organ/Source/Plus/Minus layout, removing the "all X" row prefix encoding. - Rewrote the "two versions" Description block across 12 multiWig HTMLs with parallel 3-bullet conditional logic and ENCODE-standard biosample terminology. - Updated DNase/ATAC/Histone/CTCF (Indiv.) Epigenetics composite pages on both assemblies with 5-bullet Description and explicit per-assay color legend in Display Conventions. - Added encode4RegLayeredDisplay.shared.html and replaced the inline Display Conventions block in 10 multiWig HTMLs with an SSI include.
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegDnase.html
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    b4808fac05f88a0170f2642a1670d571ceca4b7e Mon May 4 10:08:39 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - Added Andrews 2023 reference (PMID 37104580) to wgEncodeReg4.html supertrack page. - Added 16 missing organ rows to 5 hg38 multiWig organ availability tables (Dnase +nose; Atac +bone marrow, skin; H3K4me3 +bone, epithelium, mouth; H3K27ac +bone, epithelium, eye, mouth; Ctcf +bone, bone marrow, embryo, epithelium, mouth, penis). - Added colored Organ/Tissue cell to organ tables across 12 multiWig HTMLs (5 hg38 + 5 mm10 standard + 2 Txn) using RGB from .ra color settings. - Restructured Txn organ tables to a 4-column Organ/Source/Plus/Minus layout, removing the "all X" row prefix encoding. - Rewrote the "two versions" Description block across 12 multiWig HTMLs with parallel 3-bullet conditional logic and ENCODE-standard biosample terminology. - Updated DNase/ATAC/Histone/CTCF (Indiv.) Epigenetics composite pages on both assemblies with 5-bullet Description and explicit per-assay color legend in Display Conventions. - Added encode4RegLayeredDisplay.shared.html and replaced the inline Display Conventions block in 10 multiWig HTMLs with an SSI include.
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.html
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    b4808fac05f88a0170f2642a1670d571ceca4b7e Mon May 4 10:08:39 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - Added Andrews 2023 reference (PMID 37104580) to wgEncodeReg4.html supertrack page. - Added 16 missing organ rows to 5 hg38 multiWig organ availability tables (Dnase +nose; Atac +bone marrow, skin; H3K4me3 +bone, epithelium, mouth; H3K27ac +bone, epithelium, eye, mouth; Ctcf +bone, bone marrow, embryo, epithelium, mouth, penis). - Added colored Organ/Tissue cell to organ tables across 12 multiWig HTMLs (5 hg38 + 5 mm10 standard + 2 Txn) using RGB from .ra color settings. - Restructured Txn organ tables to a 4-column Organ/Source/Plus/Minus layout, removing the "all X" row prefix encoding. - Rewrote the "two versions" Description block across 12 multiWig HTMLs with parallel 3-bullet conditional logic and ENCODE-standard biosample terminology. - Updated DNase/ATAC/Histone/CTCF (Indiv.) Epigenetics composite pages on both assemblies with 5-bullet Description and explicit per-assay color legend in Display Conventions. - Added encode4RegLayeredDisplay.shared.html and replaced the inline Display Conventions block in 10 multiWig HTMLs with an SSI include.
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    dfa92621f4a734ac53cf35d13c6b9e2cda4b9c32 Mon May 4 10:56:43 2026 -0700
    Fix H3K27ac color hex and swapped checkmark columns in ENCODE4 Regulation HTML tables. refs #34923 Two QA fixes following Gerardo's description-page pass in b4808fac05f: - H3K27ac signal-color hex on Epigenetics description pages: #FFCD00 was the cCRE classification yellow; the assay color used by the composite (per /gbdb/{hg38,mm10}/encode4/regulation/epi_colors.json, after the contrast darkening in 46b52b437f5) is #B59100. Updated wgEncodeReg4Epigenetics.html and encode4RegEpigenetics.html. - "Available Organs and Tissues" tables on the 5 hg38 multiWig description pages had the Tissue and Primary Cell / All Biosamples columns swapped for organs that exist only as wgEncodeReg4XxxAll<Organ> in the .ra (introduced with the tp/ave fix in 0b65049e315). Inverse case: DNase lymphoid tissue showed both columns checked but only the tissue-only subtrack exists. Total 81 row corrections across DNase, ATAC, H3K4me3, H3K27ac, and CTCF. mm10 unaffected (no All-prefix subtracks).
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkCtcf.html
  • lines changed 54, context: html, text, full: html, text
    b4808fac05f88a0170f2642a1670d571ceca4b7e Mon May 4 10:08:39 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - Added Andrews 2023 reference (PMID 37104580) to wgEncodeReg4.html supertrack page. - Added 16 missing organ rows to 5 hg38 multiWig organ availability tables (Dnase +nose; Atac +bone marrow, skin; H3K4me3 +bone, epithelium, mouth; H3K27ac +bone, epithelium, eye, mouth; Ctcf +bone, bone marrow, embryo, epithelium, mouth, penis). - Added colored Organ/Tissue cell to organ tables across 12 multiWig HTMLs (5 hg38 + 5 mm10 standard + 2 Txn) using RGB from .ra color settings. - Restructured Txn organ tables to a 4-column Organ/Source/Plus/Minus layout, removing the "all X" row prefix encoding. - Rewrote the "two versions" Description block across 12 multiWig HTMLs with parallel 3-bullet conditional logic and ENCODE-standard biosample terminology. - Updated DNase/ATAC/Histone/CTCF (Indiv.) Epigenetics composite pages on both assemblies with 5-bullet Description and explicit per-assay color legend in Display Conventions. - Added encode4RegLayeredDisplay.shared.html and replaced the inline Display Conventions block in 10 multiWig HTMLs with an SSI include.
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k27ac.html
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    b4808fac05f88a0170f2642a1670d571ceca4b7e Mon May 4 10:08:39 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - Added Andrews 2023 reference (PMID 37104580) to wgEncodeReg4.html supertrack page. - Added 16 missing organ rows to 5 hg38 multiWig organ availability tables (Dnase +nose; Atac +bone marrow, skin; H3K4me3 +bone, epithelium, mouth; H3K27ac +bone, epithelium, eye, mouth; Ctcf +bone, bone marrow, embryo, epithelium, mouth, penis). - Added colored Organ/Tissue cell to organ tables across 12 multiWig HTMLs (5 hg38 + 5 mm10 standard + 2 Txn) using RGB from .ra color settings. - Restructured Txn organ tables to a 4-column Organ/Source/Plus/Minus layout, removing the "all X" row prefix encoding. - Rewrote the "two versions" Description block across 12 multiWig HTMLs with parallel 3-bullet conditional logic and ENCODE-standard biosample terminology. - Updated DNase/ATAC/Histone/CTCF (Indiv.) Epigenetics composite pages on both assemblies with 5-bullet Description and explicit per-assay color legend in Display Conventions. - Added encode4RegLayeredDisplay.shared.html and replaced the inline Display Conventions block in 10 multiWig HTMLs with an SSI include.
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k4me3.html
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    b4808fac05f88a0170f2642a1670d571ceca4b7e Mon May 4 10:08:39 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - Added Andrews 2023 reference (PMID 37104580) to wgEncodeReg4.html supertrack page. - Added 16 missing organ rows to 5 hg38 multiWig organ availability tables (Dnase +nose; Atac +bone marrow, skin; H3K4me3 +bone, epithelium, mouth; H3K27ac +bone, epithelium, eye, mouth; Ctcf +bone, bone marrow, embryo, epithelium, mouth, penis). - Added colored Organ/Tissue cell to organ tables across 12 multiWig HTMLs (5 hg38 + 5 mm10 standard + 2 Txn) using RGB from .ra color settings. - Restructured Txn organ tables to a 4-column Organ/Source/Plus/Minus layout, removing the "all X" row prefix encoding. - Rewrote the "two versions" Description block across 12 multiWig HTMLs with parallel 3-bullet conditional logic and ENCODE-standard biosample terminology. - Updated DNase/ATAC/Histone/CTCF (Indiv.) Epigenetics composite pages on both assemblies with 5-bullet Description and explicit per-assay color legend in Display Conventions. - Added encode4RegLayeredDisplay.shared.html and replaced the inline Display Conventions block in 10 multiWig HTMLs with an SSI include.
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegTxn.html
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    b4808fac05f88a0170f2642a1670d571ceca4b7e Mon May 4 10:08:39 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - Added Andrews 2023 reference (PMID 37104580) to wgEncodeReg4.html supertrack page. - Added 16 missing organ rows to 5 hg38 multiWig organ availability tables (Dnase +nose; Atac +bone marrow, skin; H3K4me3 +bone, epithelium, mouth; H3K27ac +bone, epithelium, eye, mouth; Ctcf +bone, bone marrow, embryo, epithelium, mouth, penis). - Added colored Organ/Tissue cell to organ tables across 12 multiWig HTMLs (5 hg38 + 5 mm10 standard + 2 Txn) using RGB from .ra color settings. - Restructured Txn organ tables to a 4-column Organ/Source/Plus/Minus layout, removing the "all X" row prefix encoding. - Rewrote the "two versions" Description block across 12 multiWig HTMLs with parallel 3-bullet conditional logic and ENCODE-standard biosample terminology. - Updated DNase/ATAC/Histone/CTCF (Indiv.) Epigenetics composite pages on both assemblies with 5-bullet Description and explicit per-assay color legend in Display Conventions. - Added encode4RegLayeredDisplay.shared.html and replaced the inline Display Conventions block in 10 multiWig HTMLs with an SSI include.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    d05d605337490a39f80d14cb80a69afe5bcad48d Wed Apr 29 17:17:47 2026 -0700
    Releasing the mm10 ENCODE4 cCREs tracks. Removed the alpha,beta tag from encode.cCREs.override.ra and removed the encodeCcreCombined.old.ra include, refs #37131
• src/hg/makeDb/trackDb/publicGenArk.txt
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    7a190b8ac6d95f66205385123542fc0c64a1469b Tue Apr 28 21:59:31 2026 -0700
    adding evaSnp8 contrib track refs #36957
• src/hg/makeDb/trackDb/relatedTracks.ra
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    e105b65928dcedbb510481ae55b1d5ff7bef5a90 Wed Apr 29 11:45:12 2026 -0700
    Adding related tracks between clinGenComp, dosageSensitivity, and cnvDevDelay for hg38 and hg19. No RM.
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    b7c9630cddfbbbf5d858d4d0bb27caf572593089 Wed Apr 29 16:47:22 2026 -0700
    Adding a relatedTracks setting for the BAC tracks for danRer11, refs #35059
• src/hg/makeDb/trackDb/zebrafish/danRer11/bacEndPairsLift.html
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    0f3d178cd9ea79da9e5bb42576ec57a441c41809 Wed Apr 29 14:51:31 2026 -0700
    bacEndPairsLift.html: modernize HTML, add Data Access section, fix Children's. refs #35059 Lowercase all tags and quote target="_blank" attributes per qa-html standards. Add a standard Data Access section pointing at Table Browser, Data Integrator, REST API, and the hgdownload bigBed file. Fix "Childrens Hospital" -> "Children's Hospital". Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/zebrafish/danRer11/choriCloneEnds.html
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    372ecfec7898a915f75103a1ea64a63f69eda5da Tue Apr 28 06:26:37 2026 -0700
    choriCloneEnds: drop misleading RZPD/DanioKey aliases, link to specific BACPAC library pages The RZPD prefixes (RZPD-1073/DanioKey, RZPD-73/DanioKey Pilot) are local labels from a defunct German genome resource center and aren't used elsewhere; remove from longLabels and the description bullet list. Replace the generic BACPAC home link with direct links to the three relevant library pages (CH73, CH211, CH1073), since the overall libraries.php page is cluttered with discontinued libraries. refs #35059
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    bfc0ac4ea2f3cc169bac73afc6511c07dd802a20 Wed Apr 29 14:41:53 2026 -0700
    Resolve OUP article-lookup links to canonical URLs in BAC track refs. refs #35059 bacRearray32k.html: Krzywinski 2004 NAR -> /nar/article/32/12/3651/2375827 choriCloneEnds.html: Schneider 2013 NAR -> /nar/article/41/D1/D1070/1065498 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    62814c7ee2bdfc27396d071877245867d216f5ef Wed Apr 29 14:43:58 2026 -0700
    choriCloneEnds.html: replace nbsp entities with regular spaces in bigBedToBed example. refs #35059 The example previously used &nbsp; between command-line flags, which renders fine visually but copies as literal U+00A0 bytes that break the shell command on paste. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    db75ac2f74d3149efdb945d1efe966b27ec0def8 Thu Apr 30 15:39:17 2026 -0700
    Adding a note about Pieter de Jong's contribution to the BAC tracks, refs #35059
• src/hg/makeDb/trackDb/zebrafish/danRer11/choriCloneEnds.ra
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    372ecfec7898a915f75103a1ea64a63f69eda5da Tue Apr 28 06:26:37 2026 -0700
    choriCloneEnds: drop misleading RZPD/DanioKey aliases, link to specific BACPAC library pages The RZPD prefixes (RZPD-1073/DanioKey, RZPD-73/DanioKey Pilot) are local labels from a defunct German genome resource center and aren't used elsewhere; remove from longLabels and the description bullet list. Replace the generic BACPAC home link with direct links to the three relevant library pages (CH73, CH211, CH1073), since the overall libraries.php page is cluttered with discontinued libraries. refs #35059
• src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra
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    e7d9f3a014feecf76330d77a797d5ea6eaf93a0f Thu Apr 30 16:10:41 2026 -0700
    Staging the BAC tracks on the RR, refs #35059
• src/hg/mouseStuff/chainToMaf/chainToMaf.c
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    433d9b4fce034247a83b60de96fea913fa4631d9 Thu Apr 30 08:40:54 2026 -0700
    added chainToMaf command
• src/hg/mouseStuff/chainToMaf/makefile
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    433d9b4fce034247a83b60de96fea913fa4631d9 Thu Apr 30 08:40:54 2026 -0700
    added chainToMaf command
• src/hg/mouseStuff/chainToMaf/tests/expected/localNoPrefix.maf
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    433d9b4fce034247a83b60de96fea913fa4631d9 Thu Apr 30 08:40:54 2026 -0700
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• src/hg/mouseStuff/chainToMaf/tests/expected/localPrefix.maf
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    433d9b4fce034247a83b60de96fea913fa4631d9 Thu Apr 30 08:40:54 2026 -0700
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• src/hg/mouseStuff/chainToMaf/tests/expected/rescorePrefix.maf
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    433d9b4fce034247a83b60de96fea913fa4631d9 Thu Apr 30 08:40:54 2026 -0700
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• src/hg/mouseStuff/chainToMaf/tests/expected/urlPrefix.maf
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    433d9b4fce034247a83b60de96fea913fa4631d9 Thu Apr 30 08:40:54 2026 -0700
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• src/hg/mouseStuff/chainToMaf/tests/input/hg38.mm10.test.chain
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    433d9b4fce034247a83b60de96fea913fa4631d9 Thu Apr 30 08:40:54 2026 -0700
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• src/hg/mouseStuff/chainToMaf/tests/makefile
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    433d9b4fce034247a83b60de96fea913fa4631d9 Thu Apr 30 08:40:54 2026 -0700
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• src/hg/mouseStuff/makefile
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    433d9b4fce034247a83b60de96fea913fa4631d9 Thu Apr 30 08:40:54 2026 -0700
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    bd52273cf2a3053227cd2d0131938d8caf571d39 Fri May 1 22:35:39 2026 -0700
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• src/hg/utils/automation/AsmHub.pm
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    717d052c4047454ff8bece9b57a5d7f54c4f0154 Fri May 1 13:23:12 2026 -0700
    one more explicit path name for cron safety refs #31811
• src/hg/utils/automation/addQuickLift.py
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    974a36818d9920f331467faf1668e602c2c0e1fe Fri May 1 13:39:41 2026 -0700
    add correct path to hgsql refs #31811
• src/hg/utils/automation/asmHubAllGaps.pl
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    bdc5df573ffaa879405a4e13f10c205fed01c4d1 Fri May 1 12:55:06 2026 -0700
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• src/hg/utils/automation/asmHubAugustusGene.pl
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    bdc5df573ffaa879405a4e13f10c205fed01c4d1 Fri May 1 12:55:06 2026 -0700
    explicit /cluster/bin/ path names for kent binaries to allow these scripts to function in cron jobs refs #31811
• src/hg/utils/automation/asmHubChainNetTrackDb.sh
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    dbf1f3970c63ee81e66dca929395aa575a536a26 Thu Apr 30 11:52:20 2026 -0700
    eliminate duplicate code section and protect all net tracks with file exist test refs #31811
• src/hg/utils/automation/asmHubCpG.pl
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    bdc5df573ffaa879405a4e13f10c205fed01c4d1 Fri May 1 12:55:06 2026 -0700
    explicit /cluster/bin/ path names for kent binaries to allow these scripts to function in cron jobs refs #31811
• src/hg/utils/automation/asmHubEnsGene.pl
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    bdc5df573ffaa879405a4e13f10c205fed01c4d1 Fri May 1 12:55:06 2026 -0700
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• src/hg/utils/automation/asmHubGc5Percent.pl
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    24891487d4c04f503b44631ea97773e8a2071b56 Fri May 1 12:39:24 2026 -0700
    explicit path names to allow these scripts to work on cron jobs refs #31811
• src/hg/utils/automation/asmHubNcbiGene.pl
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    bdc5df573ffaa879405a4e13f10c205fed01c4d1 Fri May 1 12:55:06 2026 -0700
    explicit /cluster/bin/ path names for kent binaries to allow these scripts to function in cron jobs refs #31811
• src/hg/utils/automation/asmHubNcbiRefSeq.pl
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    bdc5df573ffaa879405a4e13f10c205fed01c4d1 Fri May 1 12:55:06 2026 -0700
    explicit /cluster/bin/ path names for kent binaries to allow these scripts to function in cron jobs refs #31811
• src/hg/utils/automation/asmHubRepeatMasker.sh
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    e1625b2bf30df1d1f9385bc79fc2cbd45a05d511 Fri May 1 12:41:32 2026 -0700
    explicit path names to allow these scripts to work on cron jobs refs #31811
• src/hg/utils/automation/asmHubSimpleRepeat.pl
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    bdc5df573ffaa879405a4e13f10c205fed01c4d1 Fri May 1 12:55:06 2026 -0700
    explicit /cluster/bin/ path names for kent binaries to allow these scripts to function in cron jobs refs #31811
• src/hg/utils/automation/asmHubTanDups.pl
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    bdc5df573ffaa879405a4e13f10c205fed01c4d1 Fri May 1 12:55:06 2026 -0700
    explicit /cluster/bin/ path names for kent binaries to allow these scripts to function in cron jobs refs #31811
• src/hg/utils/automation/asmHubTrackDb.sh
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    24891487d4c04f503b44631ea97773e8a2071b56 Fri May 1 12:39:24 2026 -0700
    explicit path names to allow these scripts to work on cron jobs refs #31811
• src/hg/utils/automation/asmHubWindowMasker.pl
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    bdc5df573ffaa879405a4e13f10c205fed01c4d1 Fri May 1 12:55:06 2026 -0700
    explicit /cluster/bin/ path names for kent binaries to allow these scripts to function in cron jobs refs #31811
• src/hg/utils/automation/asmHubXenoRefGene.pl
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    bdc5df573ffaa879405a4e13f10c205fed01c4d1 Fri May 1 12:55:06 2026 -0700
    explicit /cluster/bin/ path names for kent binaries to allow these scripts to function in cron jobs refs #31811
• src/hg/utils/automation/doTandemDup.pl
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    49a0c84e41b604f646f25a3aa09fbb9a8e1177fa Tue Apr 28 11:28:49 2026 -0700
    try cluster running at 48Gb to avoid stoppage
• src/hg/utils/automation/kegAlignLastz.sh
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    d89c66b838902fda9dc142405b160305abc0d103 Wed Apr 29 16:18:52 2026 -0700
    this now only starts the alignment, the after alignment business has moved to other cron jobs refs #31811
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    210c39cf46050fb9024471e07422aba588183dc8 Thu Apr 30 10:07:53 2026 -0700
    claude says to not use the -b bash setting refs #31811
• src/hg/utils/otto/clinvar/clinVarToBed
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    b1b12153630874f63ec80e6f0d000504921a4719 Tue Apr 28 18:13:17 2026 -0700
    clinVarToBed: strip trailing backslash before tab in submission_summary so MySQL LOAD DATA doesn't eat the field separator, refs #37477 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    c4713fb5e2fe484ad7ca9821888225f2234a6599 Tue Apr 28 21:03:47 2026 -0700
    delete bogus character
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    dfac508f415202b72edde722acc394bf3a626f43 Wed Apr 29 07:11:56 2026 -0700
    clinVarToBed: restore r-prefix on backslash-stripping perl cmd Without the raw-string prefix, Python interprets \\ as a single backslash and \t as a tab before the command reaches the shell, so perl saw s/\(?=<TAB>|$)//g instead of s/\\(?=\t|$)//g and the fix from b1b1215 was a no-op. refs #37477
• src/hg/utils/otto/dbVar/checkDbVar.sh
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    b85c12cf9af0ee1a954b8cced961bcbd909b7979 Wed Apr 29 12:04:36 2026 -0700
    Expand dbVar tracks to expose all six nstd186 source studies and add new Somatic and Other composites. refs #37406 Restructure the dbVar supertrack: - Renamed from "dbVar Common Struct Var" to "dbVar Struct Var". - dbVar Common SV: added subtracks for Lee, Abel, and Byrska-Bishop (the three nstd186 source studies that were missing from our Curated Common track), and for the American/East Asian/South Asian/Other populations. - dbVar Conflict SV: description page refreshed; subtrack longLabel clarified. - dbVar Somatic SV (new): single subtrack pulling somatic_sv.bb from the dbVar hub. Default hidden. - dbVar Other SV (new): residual bucket for dbVar SVs not classified as common, somatic, or clinical, split into Healthy and Phenotype subtracks. Default hidden. NCBI sometimes calls this "presumed normal"; the description page notes the equivalence. mergeSpannedItems on for the dense subtracks (normal_healthy ~5.6M items, normal_phenotype ~410K, somatic_sv ~67K). - ClinVar SVs are not duplicated; description pages cross-link to the existing ClinVar track instead. Description pages: rewrite dbVarCommon.html and dbVarCurated.html, refresh dbVarConflict.html, add dbVarSomatic.html and dbVarOther.html. Retire the unused dbVar_common.html. Methods links now point at NCBI's dbVar Overview rather than the FTP directory listing. searchTable termRegex widened to ^[den]ssv[0-9]+ so dssv* accessions in normal_healthy resolve. Otto: stage downloads to release/\${db}.new/, validate per file (size floor and 10% itemCount delta vs the current live copy), then atomically swap via directory rename with a one-cycle .prev rollback. On validation failure, leave .new/ in place for human inspection and exit non-zero so the wrapper emails. On no-op runs the wrapper now stays silent. checkNstd175.sh's "update done" message moved inside the update branch so silence is honoured. New-file detection (via a knownFiles.txt manifest) emails when NCBI adds a file we don't yet expose. knownFiles.txt itself lives only at the deployment path under /hive/data/outside/otto/dbVar/, not in the tree.
• src/hg/utils/otto/dbVar/checkNstd175.sh
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    b85c12cf9af0ee1a954b8cced961bcbd909b7979 Wed Apr 29 12:04:36 2026 -0700
    Expand dbVar tracks to expose all six nstd186 source studies and add new Somatic and Other composites. refs #37406 Restructure the dbVar supertrack: - Renamed from "dbVar Common Struct Var" to "dbVar Struct Var". - dbVar Common SV: added subtracks for Lee, Abel, and Byrska-Bishop (the three nstd186 source studies that were missing from our Curated Common track), and for the American/East Asian/South Asian/Other populations. - dbVar Conflict SV: description page refreshed; subtrack longLabel clarified. - dbVar Somatic SV (new): single subtrack pulling somatic_sv.bb from the dbVar hub. Default hidden. - dbVar Other SV (new): residual bucket for dbVar SVs not classified as common, somatic, or clinical, split into Healthy and Phenotype subtracks. Default hidden. NCBI sometimes calls this "presumed normal"; the description page notes the equivalence. mergeSpannedItems on for the dense subtracks (normal_healthy ~5.6M items, normal_phenotype ~410K, somatic_sv ~67K). - ClinVar SVs are not duplicated; description pages cross-link to the existing ClinVar track instead. Description pages: rewrite dbVarCommon.html and dbVarCurated.html, refresh dbVarConflict.html, add dbVarSomatic.html and dbVarOther.html. Retire the unused dbVar_common.html. Methods links now point at NCBI's dbVar Overview rather than the FTP directory listing. searchTable termRegex widened to ^[den]ssv[0-9]+ so dssv* accessions in normal_healthy resolve. Otto: stage downloads to release/\${db}.new/, validate per file (size floor and 10% itemCount delta vs the current live copy), then atomically swap via directory rename with a one-cycle .prev rollback. On validation failure, leave .new/ in place for human inspection and exit non-zero so the wrapper emails. On no-op runs the wrapper now stays silent. checkNstd175.sh's "update done" message moved inside the update branch so silence is honoured. New-file detection (via a knownFiles.txt manifest) emails when NCBI adds a file we don't yet expose. knownFiles.txt itself lives only at the deployment path under /hive/data/outside/otto/dbVar/, not in the tree.
• src/hg/utils/otto/dbVar/dbVarWrapper.sh
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    b85c12cf9af0ee1a954b8cced961bcbd909b7979 Wed Apr 29 12:04:36 2026 -0700
    Expand dbVar tracks to expose all six nstd186 source studies and add new Somatic and Other composites. refs #37406 Restructure the dbVar supertrack: - Renamed from "dbVar Common Struct Var" to "dbVar Struct Var". - dbVar Common SV: added subtracks for Lee, Abel, and Byrska-Bishop (the three nstd186 source studies that were missing from our Curated Common track), and for the American/East Asian/South Asian/Other populations. - dbVar Conflict SV: description page refreshed; subtrack longLabel clarified. - dbVar Somatic SV (new): single subtrack pulling somatic_sv.bb from the dbVar hub. Default hidden. - dbVar Other SV (new): residual bucket for dbVar SVs not classified as common, somatic, or clinical, split into Healthy and Phenotype subtracks. Default hidden. NCBI sometimes calls this "presumed normal"; the description page notes the equivalence. mergeSpannedItems on for the dense subtracks (normal_healthy ~5.6M items, normal_phenotype ~410K, somatic_sv ~67K). - ClinVar SVs are not duplicated; description pages cross-link to the existing ClinVar track instead. Description pages: rewrite dbVarCommon.html and dbVarCurated.html, refresh dbVarConflict.html, add dbVarSomatic.html and dbVarOther.html. Retire the unused dbVar_common.html. Methods links now point at NCBI's dbVar Overview rather than the FTP directory listing. searchTable termRegex widened to ^[den]ssv[0-9]+ so dssv* accessions in normal_healthy resolve. Otto: stage downloads to release/\${db}.new/, validate per file (size floor and 10% itemCount delta vs the current live copy), then atomically swap via directory rename with a one-cycle .prev rollback. On validation failure, leave .new/ in place for human inspection and exit non-zero so the wrapper emails. On no-op runs the wrapper now stays silent. checkNstd175.sh's "update done" message moved inside the update branch so silence is honoured. New-file detection (via a knownFiles.txt manifest) emails when NCBI adds a file we don't yet expose. knownFiles.txt itself lives only at the deployment path under /hive/data/outside/otto/dbVar/, not in the tree.
• src/hg/utils/otto/dbVar/makefile
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    b85c12cf9af0ee1a954b8cced961bcbd909b7979 Wed Apr 29 12:04:36 2026 -0700
    Expand dbVar tracks to expose all six nstd186 source studies and add new Somatic and Other composites. refs #37406 Restructure the dbVar supertrack: - Renamed from "dbVar Common Struct Var" to "dbVar Struct Var". - dbVar Common SV: added subtracks for Lee, Abel, and Byrska-Bishop (the three nstd186 source studies that were missing from our Curated Common track), and for the American/East Asian/South Asian/Other populations. - dbVar Conflict SV: description page refreshed; subtrack longLabel clarified. - dbVar Somatic SV (new): single subtrack pulling somatic_sv.bb from the dbVar hub. Default hidden. - dbVar Other SV (new): residual bucket for dbVar SVs not classified as common, somatic, or clinical, split into Healthy and Phenotype subtracks. Default hidden. NCBI sometimes calls this "presumed normal"; the description page notes the equivalence. mergeSpannedItems on for the dense subtracks (normal_healthy ~5.6M items, normal_phenotype ~410K, somatic_sv ~67K). - ClinVar SVs are not duplicated; description pages cross-link to the existing ClinVar track instead. Description pages: rewrite dbVarCommon.html and dbVarCurated.html, refresh dbVarConflict.html, add dbVarSomatic.html and dbVarOther.html. Retire the unused dbVar_common.html. Methods links now point at NCBI's dbVar Overview rather than the FTP directory listing. searchTable termRegex widened to ^[den]ssv[0-9]+ so dssv* accessions in normal_healthy resolve. Otto: stage downloads to release/\${db}.new/, validate per file (size floor and 10% itemCount delta vs the current live copy), then atomically swap via directory rename with a one-cycle .prev rollback. On validation failure, leave .new/ in place for human inspection and exit non-zero so the wrapper emails. On no-op runs the wrapper now stays silent. checkNstd175.sh's "update done" message moved inside the update branch so silence is honoured. New-file detection (via a knownFiles.txt manifest) emails when NCBI adds a file we don't yet expose. knownFiles.txt itself lives only at the deployment path under /hive/data/outside/otto/dbVar/, not in the tree.
• src/hg/utils/otto/measles/buildTree.sh
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    6bc045a7d9e23c14433beeeaecf349ff5d5785a1 Wed Apr 15 11:03:33 2026 -0700
    Use viral_usher to build daily measles tree.
• src/hg/utils/otto/otto.crontab
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    e01c7bc914e4adcf8a815d4666c270160bd45602 Tue Apr 28 13:14:39 2026 -0700
    Changing the otto job to 1am as it runs many find commands and could be causing a slowdown, no RM.
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    9965011a5b04936d45a5db8daa9b236ee7521dfa Tue Apr 28 19:18:26 2026 -0700
    Drop redundant umask 002 from otto crontab InSiGHT cron entry per CR. refs #37418 doUpdate.sh already sets umask 002 internally and otto's .bashrc sets it for interactive shells, so the cron line setting is redundant.
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    1c74bbe38be86c61ba4d1ffae3b020e4905d5a3d Wed Apr 29 09:02:56 2026 -0700
    Updating the git crontab to match the one running on /hive, no Redmine.
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    a9d4e09a91905f56c4e2c8945a8d7855985a1751 Wed Apr 29 14:43:43 2026 -0700
    Forgot a semicolon, no Redmine.
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    4e6a1fde309912e1c07c1b24e91e0ca1bea0e07c Thu Apr 30 23:19:34 2026 -0700
    readjust ottoRequest to run every 7 minutes refs #31811
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    bc1dd635cfd41140693da19ddcd578ad3f5b30d6 Fri May 1 10:03:42 2026 -0700
    Added new lineages.
• src/hg/utils/otto/userRequests/README.txt
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    2e1569df889bd13a340cf75a5c1182c798ab5955 Mon Apr 27 14:13:16 2026 -0700
    added quickLift file construction and getting to the end complete result refs #31811
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    430bb5b5b7601fa51ed1872e5c7a55def547c450 Wed Apr 29 14:27:34 2026 -0700
    refactor the workflowMonitor to get json operations into galaxyState.py and finalizing state diagram refs #31811
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    476ebb957aebb1a7f20ea71301e894c5422bd57e Wed Apr 29 21:41:01 2026 -0700
    subtle timing issue resolved and minor bugs fixed refs #31811
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    cecf287ff26c79831fb222f8da03cd14546174e0 Wed Apr 29 23:02:43 2026 -0700
    expand process description in README refs #31811
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    e8d1fff44e0f7ecd4629cfcc2ac671d6af78d8ae Thu Apr 30 12:54:54 2026 -0700
    add an ottoRequest table interactive CGI viewer and verify lift.over URL links for email are valid refs #31811
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    211c215c654c363993a9d480cbda679de0bbd7e9 Fri May 1 13:59:15 2026 -0700
    eliminating stderr information to avoid cron job noise refs #31811
• src/hg/utils/otto/userRequests/galaxyCleanup.py
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    1ad3e0a11b1650d330a3d69ae7cbea771d647bc0 Wed Apr 29 21:52:42 2026 -0700
    adding galaxy cleanup process to release history and workflow metadata refs #31811
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    211c215c654c363993a9d480cbda679de0bbd7e9 Fri May 1 13:59:15 2026 -0700
    eliminating stderr information to avoid cron job noise refs #31811
• src/hg/utils/otto/userRequests/galaxyState.py
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    430bb5b5b7601fa51ed1872e5c7a55def547c450 Wed Apr 29 14:27:34 2026 -0700
    refactor the workflowMonitor to get json operations into galaxyState.py and finalizing state diagram refs #31811
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    a5fca314f31035baabe4d29cd6ff1d40ccddef0d Thu Apr 30 23:59:37 2026 -0700
    do not need the stderr status information messages refs #31811
• src/hg/utils/otto/userRequests/galaxyStatus.py
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    70b873ace3ffca0850aa635f7fc43c71cc7b09d5 Fri May 1 14:50:19 2026 -0700
    further silent the cron outputs and add a status indicator to the watch.cgi page refs #31811
• src/hg/utils/otto/userRequests/kegAlignLastz.sh
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    8dc26c657ea6c756d3ebf6bc38b525a940294400 Thu Apr 30 10:09:22 2026 -0700
    kegAlignLastz.sh should be with the other ottoRequest scripts refs #31811
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    d7fec1a55508e24c02bb2754c42baaad1d3c8394 Thu Apr 30 10:12:42 2026 -0700
    remove all the cruft from pairLastz.sh copy, not needed here refs #31811
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    3976a8ec6b27464bd64e93916821dbcb52cd7671 Thu Apr 30 23:01:52 2026 -0700
    this actually might be working all the way through now refs #31811
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    3a85cb72b4b01663b80635ce8c7196100627d188 Thu Apr 30 23:49:28 2026 -0700
    cron jobs expose PATH issues refs #31811
• src/hg/utils/otto/userRequests/ottoRequest.py
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    a51a9e2eec975f01419e03107d70c74dfe5e0766 Tue Apr 28 14:35:28 2026 -0700
    different response messages for liftRequest vs. assembly request refs #31811
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    3976a8ec6b27464bd64e93916821dbcb52cd7671 Thu Apr 30 23:01:52 2026 -0700
    this actually might be working all the way through now refs #31811
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    211c215c654c363993a9d480cbda679de0bbd7e9 Fri May 1 13:59:15 2026 -0700
    eliminating stderr information to avoid cron job noise refs #31811
• src/hg/utils/otto/userRequests/ottoRequestAlign.sh
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    d9aaedf4614b86b3f4bd2aae4b44443019a14b45 Mon Apr 27 15:26:46 2026 -0700
    claude says it does not like the b in: set -beEu -o pipefail - so remove that and now have worked all the way to email notification to the user with all files present in appropriate locations refs #31811
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    430bb5b5b7601fa51ed1872e5c7a55def547c450 Wed Apr 29 14:27:34 2026 -0700
    refactor the workflowMonitor to get json operations into galaxyState.py and finalizing state diagram refs #31811
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    797000a8e6ef069d3e5a7b5034c0305f0ee97697 Wed Apr 29 16:20:51 2026 -0700
    enable the startup of the alignment refs #31811
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    476ebb957aebb1a7f20ea71301e894c5422bd57e Wed Apr 29 21:41:01 2026 -0700
    subtle timing issue resolved and minor bugs fixed refs #31811
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    a4870c92799d2687ff7c6602663f5ec6e5599af2 Thu Apr 30 10:16:07 2026 -0700
    kegAlignLastz.sh has moved to this scripts directory refs #31811
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    3a85cb72b4b01663b80635ce8c7196100627d188 Thu Apr 30 23:49:28 2026 -0700
    cron jobs expose PATH issues refs #31811
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    70b873ace3ffca0850aa635f7fc43c71cc7b09d5 Fri May 1 14:50:19 2026 -0700
    further silent the cron outputs and add a status indicator to the watch.cgi page refs #31811
• src/hg/utils/otto/userRequests/ottoRequestPush.py
  • lines changed 100, context: html, text, full: html, text
    41e8cd7271a59ef3d02db98d3064078444378fcb Wed Apr 29 14:24:47 2026 -0700
    beginning of the push script - to be continued refs #31811
  • lines changed 128, context: html, text, full: html, text
    5fed84fb663f977b33c69348c7990081a789b5dd Wed Apr 29 23:02:21 2026 -0700
    fixup printf in workflowMonitor.sh to make a clean successInvocationId.txt file and add business in ottoRequestPush.py to add status=6 setting to successful pushed file sets refs #31811
  • lines changed 17, context: html, text, full: html, text
    f1ab1958cec7cf4f14056692907e7518aa67273b Thu Apr 30 10:25:36 2026 -0700
    use flock to ensure only one instance of this script is ever running at one time refs #31811
  • lines changed 4, context: html, text, full: html, text
    0aa99b19411f52674c57d49c8b41c2706c78bf29 Thu Apr 30 10:44:15 2026 -0700
    add URL path names to the final email notice refs #31811
  • lines changed 13, context: html, text, full: html, text
    3976a8ec6b27464bd64e93916821dbcb52cd7671 Thu Apr 30 23:01:52 2026 -0700
    this actually might be working all the way through now refs #31811
  • lines changed 5, context: html, text, full: html, text
    4b4338b902614b327f6921ed1255415508250510 Fri May 1 13:53:01 2026 -0700
    do not need to see the stderr informational outputs refs #31811
  • lines changed 3, context: html, text, full: html, text
    211c215c654c363993a9d480cbda679de0bbd7e9 Fri May 1 13:59:15 2026 -0700
    eliminating stderr information to avoid cron job noise refs #31811
  • lines changed 3, context: html, text, full: html, text
    dca6b246ce843e81430fbcda629c2478876b16fb Fri May 1 15:45:20 2026 -0700
    silence in the back there refs #31811
• src/hg/utils/otto/userRequests/ottoRequestView.cgi
  • lines changed 214, context: html, text, full: html, text
    e8d1fff44e0f7ecd4629cfcc2ac671d6af78d8ae Thu Apr 30 12:54:54 2026 -0700
    add an ottoRequest table interactive CGI viewer and verify lift.over URL links for email are valid refs #31811
  • lines changed 4, context: html, text, full: html, text
    c62810dcb9b6b76fd427ce776219fb5eb02357dd Thu Apr 30 13:18:29 2026 -0700
    set the table to class sortable to allow column header sort function refs #31811
  • lines changed 57, context: html, text, full: html, text
    70b873ace3ffca0850aa635f7fc43c71cc7b09d5 Fri May 1 14:50:19 2026 -0700
    further silent the cron outputs and add a status indicator to the watch.cgi page refs #31811
  • lines changed 12, context: html, text, full: html, text
    aeaebac6e25be25c1205747abf248fd7092ebdb3 Sat May 2 14:53:35 2026 -0700
    add a reset button and outlinks to browsers refs #31811
• src/hg/utils/otto/userRequests/ottoRequestWatch.sh
  • lines changed 35, context: html, text, full: html, text
    2e1569df889bd13a340cf75a5c1182c798ab5955 Mon Apr 27 14:13:16 2026 -0700
    added quickLift file construction and getting to the end complete result refs #31811
  • lines changed 182, context: html, text, full: html, text
    d9aaedf4614b86b3f4bd2aae4b44443019a14b45 Mon Apr 27 15:26:46 2026 -0700
    claude says it does not like the b in: set -beEu -o pipefail - so remove that and now have worked all the way to email notification to the user with all files present in appropriate locations refs #31811
  • lines changed 35, context: html, text, full: html, text
    430bb5b5b7601fa51ed1872e5c7a55def547c450 Wed Apr 29 14:27:34 2026 -0700
    refactor the workflowMonitor to get json operations into galaxyState.py and finalizing state diagram refs #31811
  • lines changed 5, context: html, text, full: html, text
    476ebb957aebb1a7f20ea71301e894c5422bd57e Wed Apr 29 21:41:01 2026 -0700
    subtle timing issue resolved and minor bugs fixed refs #31811
  • lines changed 10, context: html, text, full: html, text
    1ad3e0a11b1650d330a3d69ae7cbea771d647bc0 Wed Apr 29 21:52:42 2026 -0700
    adding galaxy cleanup process to release history and workflow metadata refs #31811
  • lines changed 35, context: html, text, full: html, text
    0aa99b19411f52674c57d49c8b41c2706c78bf29 Thu Apr 30 10:44:15 2026 -0700
    add URL path names to the final email notice refs #31811
  • lines changed 22, context: html, text, full: html, text
    e8d1fff44e0f7ecd4629cfcc2ac671d6af78d8ae Thu Apr 30 12:54:54 2026 -0700
    add an ottoRequest table interactive CGI viewer and verify lift.over URL links for email are valid refs #31811
  • lines changed 25, context: html, text, full: html, text
    3976a8ec6b27464bd64e93916821dbcb52cd7671 Thu Apr 30 23:01:52 2026 -0700
    this actually might be working all the way through now refs #31811
  • lines changed 10, context: html, text, full: html, text
    3a85cb72b4b01663b80635ce8c7196100627d188 Thu Apr 30 23:49:28 2026 -0700
    cron jobs expose PATH issues refs #31811
  • lines changed 1, context: html, text, full: html, text
    a5fca314f31035baabe4d29cd6ff1d40ccddef0d Thu Apr 30 23:59:37 2026 -0700
    do not need the stderr status information messages refs #31811
  • lines changed 5, context: html, text, full: html, text
    211c215c654c363993a9d480cbda679de0bbd7e9 Fri May 1 13:59:15 2026 -0700
    eliminating stderr information to avoid cron job noise refs #31811
  • lines changed 43, context: html, text, full: html, text
    70b873ace3ffca0850aa635f7fc43c71cc7b09d5 Fri May 1 14:50:19 2026 -0700
    further silent the cron outputs and add a status indicator to the watch.cgi page refs #31811
  • lines changed 1, context: html, text, full: html, text
    dca6b246ce843e81430fbcda629c2478876b16fb Fri May 1 15:45:20 2026 -0700
    silence in the back there refs #31811
  • lines changed 4, context: html, text, full: html, text
    55fcac8a40acd4e41d0bcdff1c878f7214a58d6d Sun May 3 13:20:45 2026 -0700
    should be cron quiet now on no error conditions refs #31811
• src/hg/utils/otto/userRequests/workflowMonitor.sh
  • lines changed 119, context: html, text, full: html, text
    2e1569df889bd13a340cf75a5c1182c798ab5955 Mon Apr 27 14:13:16 2026 -0700
    added quickLift file construction and getting to the end complete result refs #31811
  • lines changed 2, context: html, text, full: html, text
    d9aaedf4614b86b3f4bd2aae4b44443019a14b45 Mon Apr 27 15:26:46 2026 -0700
    claude says it does not like the b in: set -beEu -o pipefail - so remove that and now have worked all the way to email notification to the user with all files present in appropriate locations refs #31811
  • lines changed 242, context: html, text, full: html, text
    430bb5b5b7601fa51ed1872e5c7a55def547c450 Wed Apr 29 14:27:34 2026 -0700
    refactor the workflowMonitor to get json operations into galaxyState.py and finalizing state diagram refs #31811
  • lines changed 3, context: html, text, full: html, text
    476ebb957aebb1a7f20ea71301e894c5422bd57e Wed Apr 29 21:41:01 2026 -0700
    subtle timing issue resolved and minor bugs fixed refs #31811
  • lines changed 1, context: html, text, full: html, text
    5fed84fb663f977b33c69348c7990081a789b5dd Wed Apr 29 23:02:21 2026 -0700
    fixup printf in workflowMonitor.sh to make a clean successInvocationId.txt file and add business in ottoRequestPush.py to add status=6 setting to successful pushed file sets refs #31811
  • lines changed 1, context: html, text, full: html, text
    3976a8ec6b27464bd64e93916821dbcb52cd7671 Thu Apr 30 23:01:52 2026 -0700
    this actually might be working all the way through now refs #31811
  • lines changed 10, context: html, text, full: html, text
    3a85cb72b4b01663b80635ce8c7196100627d188 Thu Apr 30 23:49:28 2026 -0700
    cron jobs expose PATH issues refs #31811
  • lines changed 4, context: html, text, full: html, text
    36e424927ba8b56ebb84e78ad311c4bfde7c0246 Fri May 1 10:49:53 2026 -0700
    no need for the stderr output and all kent commands use full /cluster/bin/ path names to avoid cron job problems refs #31811
  • lines changed 2, context: html, text, full: html, text
    70b873ace3ffca0850aa635f7fc43c71cc7b09d5 Fri May 1 14:50:19 2026 -0700
    further silent the cron outputs and add a status indicator to the watch.cgi page refs #31811
  • lines changed 9, context: html, text, full: html, text
    55fcac8a40acd4e41d0bcdff1c878f7214a58d6d Sun May 3 13:20:45 2026 -0700
    should be cron quiet now on no error conditions refs #31811
• src/inc/cheapcgi.h
  • lines changed 6, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/lib/cheapcgi.c
  • lines changed 13, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/lib/jsonParse.c
  • lines changed 6, context: html, text, full: html, text
    4bb9e8caea515342ba98d3871da76cd4ec69916f Fri May 1 14:10:00 2026 -0700
    Initial myVariants implementation: a form on hgTracks where users can enter item details in one of three ways: hgvs/item search, simple bed form, advanced bed form where additional non-bed fields can dynamically created. Allows changing the color of items, writing descriptions, and editing the items after creation. Show overlaps with hardcoded tracks when hgc page is open (not in the hgc dialog). Next commit has implementation of sharing these tracks with other users
• src/product/installer/docker/Dockerfile
  • lines changed 4, context: html, text, full: html, text
    9566b4b5d624c76d58568c740a99218a9089f224 Fri May 1 13:48:16 2026 -0700
    docker: persistent trackDb cache at /usr/local/apache/trash/trackDbCache The cgi default cacheTrackDbDir is /dev/shm/trackDbCache, which is a small tmpfs in containers and gets cleared on restart. Override it to a directory under apache trash so the cache is durable. refs #37475
• src/utils/qa/quickLiftBench/README.md
  • lines changed 80, context: html, text, full: html, text
    cfd2b848b9ee185619c7e677269329964d147327 Mon Apr 27 16:10:16 2026 -0700
    quickLiftBench: switch to saved-session comparisons, refs #37445 Replace the per-track URL-builder schema (db/track/hubUrl + positions list) with saved-session refs of the form `user/sessionName`. Each variant loads a saved session and renders at the session's own saved region; native and quickLifted sessions live on different assemblies, so identical chr:start-end ranges would not be biologically equivalent. Drop hgt.reset=1 from the URL: it re-applied default-track visibility, defeating hideTracks=1. Cart isolation comes from a fresh requests.Session() per case (new hgsid -> fresh cart). Headline metric is total_ms, parsed from the "Overall total time" footer span; load_ms_sum and draw_ms_sum are summed across per-track rows. Add bench1_hgwdev and bench1_rr cases pointing at the first real native/lifted session pair (Brianraney/benchQuickNative1 vs benchQuickList1). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 7, context: html, text, full: html, text
    2b658cb29039048ff6ab3dac31f10519b3349bcc Tue Apr 28 09:06:06 2026 -0700
    quickLiftBench: add --phases for per-phase timing breakdown, refs #37445 Add --phases flag that writes phases.tsv alongside results.tsv and summary.tsv. Long-form rows of every <span class='timing'> marker emitted by hgTracks (chromAliasSetup, trackDbLoad, parallel data fetch, image generation, cart write, etc.), one row per (case, variant, iteration, phase). A per-(case, variant, phase) median+p90 summary is appended. Useful for localizing where total_ms gaps come from. The first run on bench1_hgwdev surfaced the missing parallel-fetch span on the lifted variant (filed as #37470). Drop the now-unused parse_overall_total helper; total_ms is read directly from parse_phase_timings using the OVERALL_TIMING_LABEL key. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 33, context: html, text, full: html, text
    23790efe33021ccd1691bf5f4262c1396a1f6e9d Fri May 1 12:49:13 2026 -0700
    quickLiftBench: phase_asserts mechanism + parallel-fetch regression case phase_asserts is a per-case schema in cases.yaml that declares regex matches against the per-iteration timing spans, with optional required/min_median_ms/max_median_ms bounds. When a case declares phase_asserts, the runner captures phase data automatically and runs the asserts after iterations complete; any failure prints to stderr and exits non-zero. The new regress_quickLift_parallel case uses this to assert that the "Waiting for parallel..." span fires for the lifted multi-track session Brianraney/benchQuickPara with a median between 500 and 15000 ms -- discriminating the working sandbox build from a pre-fix hgwdev where only non-quickLift tracks parallelize at ~50 ms. refs #37488, #37470
• src/utils/qa/quickLiftBench/cases.yaml
  • lines changed 83, context: html, text, full: html, text
    cfd2b848b9ee185619c7e677269329964d147327 Mon Apr 27 16:10:16 2026 -0700
    quickLiftBench: switch to saved-session comparisons, refs #37445 Replace the per-track URL-builder schema (db/track/hubUrl + positions list) with saved-session refs of the form `user/sessionName`. Each variant loads a saved session and renders at the session's own saved region; native and quickLifted sessions live on different assemblies, so identical chr:start-end ranges would not be biologically equivalent. Drop hgt.reset=1 from the URL: it re-applied default-track visibility, defeating hideTracks=1. Cart isolation comes from a fresh requests.Session() per case (new hgsid -> fresh cart). Headline metric is total_ms, parsed from the "Overall total time" footer span; load_ms_sum and draw_ms_sum are summed across per-track rows. Add bench1_hgwdev and bench1_rr cases pointing at the first real native/lifted session pair (Brianraney/benchQuickNative1 vs benchQuickList1). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 25, context: html, text, full: html, text
    23790efe33021ccd1691bf5f4262c1396a1f6e9d Fri May 1 12:49:13 2026 -0700
    quickLiftBench: phase_asserts mechanism + parallel-fetch regression case phase_asserts is a per-case schema in cases.yaml that declares regex matches against the per-iteration timing spans, with optional required/min_median_ms/max_median_ms bounds. When a case declares phase_asserts, the runner captures phase data automatically and runs the asserts after iterations complete; any failure prints to stderr and exits non-zero. The new regress_quickLift_parallel case uses this to assert that the "Waiting for parallel..." span fires for the lifted multi-track session Brianraney/benchQuickPara with a median between 500 and 15000 ms -- discriminating the working sandbox build from a pre-fix hgwdev where only non-quickLift tracks parallelize at ~50 ms. refs #37488, #37470
• src/utils/qa/quickLiftBench/quickLiftBench.py
  • lines changed 201, context: html, text, full: html, text
    cfd2b848b9ee185619c7e677269329964d147327 Mon Apr 27 16:10:16 2026 -0700
    quickLiftBench: switch to saved-session comparisons, refs #37445 Replace the per-track URL-builder schema (db/track/hubUrl + positions list) with saved-session refs of the form `user/sessionName`. Each variant loads a saved session and renders at the session's own saved region; native and quickLifted sessions live on different assemblies, so identical chr:start-end ranges would not be biologically equivalent. Drop hgt.reset=1 from the URL: it re-applied default-track visibility, defeating hideTracks=1. Cart isolation comes from a fresh requests.Session() per case (new hgsid -> fresh cart). Headline metric is total_ms, parsed from the "Overall total time" footer span; load_ms_sum and draw_ms_sum are summed across per-track rows. Add bench1_hgwdev and bench1_rr cases pointing at the first real native/lifted session pair (Brianraney/benchQuickNative1 vs benchQuickList1). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 73, context: html, text, full: html, text
    2b658cb29039048ff6ab3dac31f10519b3349bcc Tue Apr 28 09:06:06 2026 -0700
    quickLiftBench: add --phases for per-phase timing breakdown, refs #37445 Add --phases flag that writes phases.tsv alongside results.tsv and summary.tsv. Long-form rows of every <span class='timing'> marker emitted by hgTracks (chromAliasSetup, trackDbLoad, parallel data fetch, image generation, cart write, etc.), one row per (case, variant, iteration, phase). A per-(case, variant, phase) median+p90 summary is appended. Useful for localizing where total_ms gaps come from. The first run on bench1_hgwdev surfaced the missing parallel-fetch span on the lifted variant (filed as #37470). Drop the now-unused parse_overall_total helper; total_ms is read directly from parse_phase_timings using the OVERALL_TIMING_LABEL key. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 121, context: html, text, full: html, text
    23790efe33021ccd1691bf5f4262c1396a1f6e9d Fri May 1 12:49:13 2026 -0700
    quickLiftBench: phase_asserts mechanism + parallel-fetch regression case phase_asserts is a per-case schema in cases.yaml that declares regex matches against the per-iteration timing spans, with optional required/min_median_ms/max_median_ms bounds. When a case declares phase_asserts, the runner captures phase data automatically and runs the asserts after iterations complete; any failure prints to stderr and exits non-zero. The new regress_quickLift_parallel case uses this to assert that the "Waiting for parallel..." span fires for the lifted multi-track session Brianraney/benchQuickPara with a median between 500 and 15000 ms -- discriminating the working sandbox build from a pre-fix hgwdev where only non-quickLift tracks parallelize at ~50 ms. refs #37488, #37470
• src/utils/redmineCli
  • lines changed 30, context: html, text, full: html, text
    3fb134a6ffe6d0b369926292362dd266b6da1247 Tue Apr 28 19:18:35 2026 -0700
    redmineCli: validate --released-to-rr checkbox values per CR. refs #37418 Add _validate_bool helper accepting 0/1/true/false/yes/no/on/off and normalizing to "0"/"1". Apply to --released-to-rr (CF 47, a Redmine checkbox) and to the --custom-field ID=VALUE escape hatch when ID matches a known typed field, so validation cannot be bypassed.

• lines changed: 34906
• files changed: 360