File Changes for lrnassar

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

• 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/hgTracks/hgTracks.c
  • 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.
• 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 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:".
• 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/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/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/mpravardb/mpravardbToBed.py
  • lines changed 22, context: html, text, full: html, text
    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/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).
  • 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/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).
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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/tp53PVS1.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/tp53PVS1Splice.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).
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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/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).
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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/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).
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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/trackDb/human/dbVarCommon.html
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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/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/hg38/mpra.html
  • lines changed 7, 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 34, context: html, text, full: html, text
    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
  • lines changed 2, 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 4, 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/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.
  • lines changed 1, context: html, text, full: html, text
    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
  • 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.
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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/wgEncodeReg4Atac.html
  • 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 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 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 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 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 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/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
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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/promoterAi.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/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.
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.html
  • 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/relatedTracks.ra
  • lines changed 15, context: html, text, full: html, text
    e105b65928dcedbb510481ae55b1d5ff7bef5a90 Wed Apr 29 11:45:12 2026 -0700
    Adding related tracks between clinGenComp, dosageSensitivity, and cnvDevDelay for hg38 and hg19. No RM.
• src/hg/utils/otto/dbVar/checkDbVar.sh
  • lines changed 125, 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/utils/otto/dbVar/checkNstd175.sh
  • lines changed 6, 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/utils/otto/dbVar/dbVarWrapper.sh
  • 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/utils/otto/dbVar/makefile
  • lines changed 4, 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/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.
  • lines changed 1, context: html, text, full: html, text
    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.
• src/utils/redmineCli
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    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.