All File Changes

v499_preview2 to v499_base (2026-05-25 to 2026-06-01) v499

• confs/hgwbeta.hg.conf
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    f9c99531fc8a0a80af3dfc2c5695f7b92780b13a Sun May 31 01:11:15 2026 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 4, context: html, text, full: html, text
    f9c99531fc8a0a80af3dfc2c5695f7b92780b13a Sun May 31 01:11:15 2026 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    f9c99531fc8a0a80af3dfc2c5695f7b92780b13a Sun May 31 01:11:15 2026 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgLogin/hgLogin.c
  • lines changed 4, context: html, text, full: html, text
    80c1747b01eae6af733f106086b95725852bad0a Wed May 27 16:06:46 2026 -0700
    try using the sendmail with correct bounce address no redmine
• src/hg/hgPhyloPlace/debugRecombinantDisplay.c
  • lines changed 93, context: html, text, full: html, text
    c385c1661b72541e1e8fb28187323f3b31c431e7 Fri May 29 18:24:49 2026 -0700
    If new columns are present in ripples server output then use them to draw RIVET-like recombination diagram in pop-up.
• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 21, context: html, text, full: html, text
    c385c1661b72541e1e8fb28187323f3b31c431e7 Fri May 29 18:24:49 2026 -0700
    If new columns are present in ripples server output then use them to draw RIVET-like recombination diagram in pop-up.
• src/hg/hgPhyloPlace/makefile
  • lines changed 1, context: html, text, full: html, text
    c385c1661b72541e1e8fb28187323f3b31c431e7 Fri May 29 18:24:49 2026 -0700
    If new columns are present in ripples server output then use them to draw RIVET-like recombination diagram in pop-up.
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 136, context: html, text, full: html, text
    c385c1661b72541e1e8fb28187323f3b31c431e7 Fri May 29 18:24:49 2026 -0700
    If new columns are present in ripples server output then use them to draw RIVET-like recombination diagram in pop-up.
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 6, context: html, text, full: html, text
    c385c1661b72541e1e8fb28187323f3b31c431e7 Fri May 29 18:24:49 2026 -0700
    If new columns are present in ripples server output then use them to draw RIVET-like recombination diagram in pop-up.
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 30, context: html, text, full: html, text
    c385c1661b72541e1e8fb28187323f3b31c431e7 Fri May 29 18:24:49 2026 -0700
    If new columns are present in ripples server output then use them to draw RIVET-like recombination diagram in pop-up.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    06767bdb38bd195d69b84b79499431709e625382 Thu May 28 01:35:36 2026 -0700
    small wording change to hgTrackUi parent link, no redmine yet
• src/hg/hgTracks/bigWigTrack.c
  • lines changed 10, context: html, text, full: html, text
    7ce3e16e83b15840bdf4cb0ff4f9b7298f5153d0 Tue May 26 13:25:44 2026 -0700
    add a FIXME comment for some person far in the future to fix
• src/hg/hgTracks/hgTracks.c
  • lines changed 12, context: html, text, full: html, text
    2ce19ed02e1d1657b6750b506d01d6fe3cb56e8c Tue May 26 09:12:23 2026 -0700
    Make myVariants Add Annotation button present below the image whether you are logged in or not. If not logged in, direct user to login, refs #33808
• src/hg/hgTracks/lollyTrack.c
  • lines changed 3, context: html, text, full: html, text
    3fe4305d047b9d7cd7fd40788d871ea696a49fb3 Wed May 27 14:38:11 2026 -0700
    lolly: skip items that do not quickLift instead of reusing a stale pop In lollyLoadItems, when quickLiftIntervalsToBed returned NULL (an item that did not lift to the target assembly), the loop fell through and reused a stale/uninitialized pop pointer, writing item fields into the wrong memory. This clobbered the lolly subtrack's trackDb track/ shortLabel/type pointers, later surfacing as "Can't find tdb for subtrack ... was getSubtrackTdb called on non-subtrack?". Initialize pop to NULL and continue past items that do not lift. refs #37646 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/posters.html
  • lines changed 33, context: html, text, full: html, text
    9ad79ae3a13f2d326f7c38298eaef31949bb49c7 Sun May 24 15:04:49 2026 -0700
    Adding the BoG 2026 and ISV 2026 posters to the poster gallery, refs #36182
• src/hg/htdocs/goldenPath/help/trackDb/changes.html
  • lines changed 1, context: html, text, full: html, text
    0201b9f4a7d4f665dc54b51073adc87705d616ec Thu May 28 19:19:34 2026 -0700
    Updating filterPriority documentation and adding highlightPriority section. refs #29223
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 6, context: html, text, full: html, text
    0201b9f4a7d4f665dc54b51073adc87705d616ec Thu May 28 19:19:34 2026 -0700
    Updating filterPriority documentation and adding highlightPriority section. refs #29223
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 5, context: html, text, full: html, text
    0201b9f4a7d4f665dc54b51073adc87705d616ec Thu May 28 19:19:34 2026 -0700
    Updating filterPriority documentation and adding highlightPriority section. refs #29223
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 46, context: html, text, full: html, text
    0201b9f4a7d4f665dc54b51073adc87705d616ec Thu May 28 19:19:34 2026 -0700
    Updating filterPriority documentation and adding highlightPriority section. refs #29223
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 96, context: html, text, full: html, text
    36cd91779b5cd2866c500c32a5892cfc959bfe06 Fri May 29 10:30:15 2026 -0700
    MPRA superTrack: news announcement, pennantIcon, attribution fix. refs #37359 Ship the user-visible release pieces for the Jun. 2, 2026 announcement of the MPRA superTrack (MPRA Base + MPRAVarDB) on hg38. News announcement: - Added a Jun. 2, 2026 entry to newsarch.html (anchor #060226) describing both subtracks, the data sources (MPRA Base / MPRAVarDB), and an Element-level vs Variant-level summary. Screenshot at the TERT promoter shows MPRA Base reporter activity for melanoma risk variants alongside filtered MPRAVarDB high-confidence variants from Kircher saturation mutagenesis. - Added the matching entry to indexNews.html ("New MPRA Base and MPRAVarDB tracks on hg38", 42 chars, under the ~50-char target); dropped the now-7th entry "Updated superTrack configuration page" to keep the 6-item limit. - Added the screenshot mpraNewsImage.png (3198x1015) referenced by the news div at 90% width. trackDb stanza: - Added "New" pennantIcon to the parent mpra superTrack pointing to the news anchor, matching the recount3 / promoterAi pattern. Attribution fix: - The parent mpra.html Credits section still attributed MPRAVarDB to "Tao Wang and colleagues". That attribution doesn't match the actual paper authors (Jin W, Xia Y, Nizomov J, Liu Y, Li Z, Lu Q, Chen L per PMID 39325859, DOI 10.1093/bioinformatics/btae578); replaced with "Weijia Jin and colleagues" to match mpraVarDb.html.
• src/hg/htdocs/images/mpraNewsImage.png
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    36cd91779b5cd2866c500c32a5892cfc959bfe06 Fri May 29 10:30:15 2026 -0700
    MPRA superTrack: news announcement, pennantIcon, attribution fix. refs #37359 Ship the user-visible release pieces for the Jun. 2, 2026 announcement of the MPRA superTrack (MPRA Base + MPRAVarDB) on hg38. News announcement: - Added a Jun. 2, 2026 entry to newsarch.html (anchor #060226) describing both subtracks, the data sources (MPRA Base / MPRAVarDB), and an Element-level vs Variant-level summary. Screenshot at the TERT promoter shows MPRA Base reporter activity for melanoma risk variants alongside filtered MPRAVarDB high-confidence variants from Kircher saturation mutagenesis. - Added the matching entry to indexNews.html ("New MPRA Base and MPRAVarDB tracks on hg38", 42 chars, under the ~50-char target); dropped the now-7th entry "Updated superTrack configuration page" to keep the 6-item limit. - Added the screenshot mpraNewsImage.png (3198x1015) referenced by the news div at 90% width. trackDb stanza: - Added "New" pennantIcon to the parent mpra superTrack pointing to the news anchor, matching the recount3 / promoterAi pattern. Attribution fix: - The parent mpra.html Credits section still attributed MPRAVarDB to "Tao Wang and colleagues". That attribution doesn't match the actual paper authors (Jin W, Xia Y, Nizomov J, Liu Y, Li Z, Lu Q, Chen L per PMID 39325859, DOI 10.1093/bioinformatics/btae578); replaced with "Weijia Jin and colleagues" to match mpraVarDb.html.
• src/hg/htdocs/inc/gbFooterHardcoded.html
  • lines changed 1, context: html, text, full: html, text
    5724ad5d9290148a32893884949a9455d5a32012 Sun May 24 15:44:48 2026 -0700
    Fixing typo in Publications link in hardcoded footer (pubs.htm to pubs.html). Related to the "Fixing 404 links for the 2026-03-15 Static Page Cronjob" commit but was not committed at the time. No RM.
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    36cd91779b5cd2866c500c32a5892cfc959bfe06 Fri May 29 10:30:15 2026 -0700
    MPRA superTrack: news announcement, pennantIcon, attribution fix. refs #37359 Ship the user-visible release pieces for the Jun. 2, 2026 announcement of the MPRA superTrack (MPRA Base + MPRAVarDB) on hg38. News announcement: - Added a Jun. 2, 2026 entry to newsarch.html (anchor #060226) describing both subtracks, the data sources (MPRA Base / MPRAVarDB), and an Element-level vs Variant-level summary. Screenshot at the TERT promoter shows MPRA Base reporter activity for melanoma risk variants alongside filtered MPRAVarDB high-confidence variants from Kircher saturation mutagenesis. - Added the matching entry to indexNews.html ("New MPRA Base and MPRAVarDB tracks on hg38", 42 chars, under the ~50-char target); dropped the now-7th entry "Updated superTrack configuration page" to keep the 6-item limit. - Added the screenshot mpraNewsImage.png (3198x1015) referenced by the news div at 90% width. trackDb stanza: - Added "New" pennantIcon to the parent mpra superTrack pointing to the news anchor, matching the recount3 / promoterAi pattern. Attribution fix: - The parent mpra.html Credits section still attributed MPRAVarDB to "Tao Wang and colleagues". That attribution doesn't match the actual paper authors (Jin W, Xia Y, Nizomov J, Liu Y, Li Z, Lu Q, Chen L per PMID 39325859, DOI 10.1093/bioinformatics/btae578); replaced with "Weijia Jin and colleagues" to match mpraVarDb.html.
• src/hg/hubApi/apiUtils.c
  • lines changed 22, context: html, text, full: html, text
    45014fb713fc38c6fa2c5ca8e76874c5b48d133d Wed May 27 16:05:11 2026 -0700
    correctly use the appropriate host for the hgcentral table refs #31811
• src/hg/hubApi/blat.c
  • lines changed 9, context: html, text, full: html, text
    081dc1a2de216d74a28252747d593c2b1288f251 Tue May 26 02:06:08 2026 -0700
    hubApi/botDelay: return JSON 500 when bottleneck server is unreachable abortAndExplainConnectFail() previously called exit(0) directly after writing raw HTML, which bypassed every error handler and produced a broken response for JSON API clients. Change it to errAbort() so it can be caught by errCatch. Wrap both hgBotDelayTimeFrac() call sites in hubApi (the global delay in main() and the BLAT-specific extra delay in apiBlat()) in errCatch blocks that call apiErrAbort(500) on failure, giving callers a proper JSON error rather than an HTML fragment or a silent exit. refs #36315 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/hubApi/dataApi.h
  • lines changed 6, context: html, text, full: html, text
    45014fb713fc38c6fa2c5ca8e76874c5b48d133d Wed May 27 16:05:11 2026 -0700
    correctly use the appropriate host for the hgcentral table refs #31811
• src/hg/hubApi/findGenome.c
  • lines changed 2, context: html, text, full: html, text
    45014fb713fc38c6fa2c5ca8e76874c5b48d133d Wed May 27 16:05:11 2026 -0700
    correctly use the appropriate host for the hgcentral table refs #31811
• src/hg/hubApi/hubApi.c
  • lines changed 7, context: html, text, full: html, text
    081dc1a2de216d74a28252747d593c2b1288f251 Tue May 26 02:06:08 2026 -0700
    hubApi/botDelay: return JSON 500 when bottleneck server is unreachable abortAndExplainConnectFail() previously called exit(0) directly after writing raw HTML, which bypassed every error handler and produced a broken response for JSON API clients. Change it to errAbort() so it can be caught by errCatch. Wrap both hgBotDelayTimeFrac() call sites in hubApi (the global delay in main() and the BLAT-specific extra delay in apiBlat()) in errCatch blocks that call apiErrAbort(500) on failure, giving callers a proper JSON error rather than an HTML fragment or a silent exit. refs #36315 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/hubApi/liftOver.c
  • lines changed 27, context: html, text, full: html, text
    45014fb713fc38c6fa2c5ca8e76874c5b48d133d Wed May 27 16:05:11 2026 -0700
    correctly use the appropriate host for the hgcentral table refs #31811
• src/hg/js/facetedComposite.js
  • lines changed 6, context: html, text, full: html, text
    63e3449141555055de52e908c50fed88cb5782ae Wed May 27 07:43:25 2026 -0700
    Resolving request to not impose title case on facet titles, refs #36320
• src/hg/js/hgPhyloPlace.js
  • lines changed 697, context: html, text, full: html, text
    c385c1661b72541e1e8fb28187323f3b31c431e7 Fri May 29 18:24:49 2026 -0700
    If new columns are present in ripples server output then use them to draw RIVET-like recombination diagram in pop-up.
  • lines changed 4, context: html, text, full: html, text
    fc877f32c3c4a79095cdfc916bf463bd25948ef9 Sat May 30 08:35:31 2026 -0700
    Fixing SVG-saving bug and minor issues found by Claude review.
• src/hg/js/hgTracks.js
  • lines changed 8, context: html, text, full: html, text
    2ce19ed02e1d1657b6750b506d01d6fe3cb56e8c Tue May 26 09:12:23 2026 -0700
    Make myVariants Add Annotation button present below the image whether you are logged in or not. If not logged in, direct user to login, refs #33808
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    c385c1661b72541e1e8fb28187323f3b31c431e7 Fri May 29 18:24:49 2026 -0700
    If new columns are present in ripples server output then use them to draw RIVET-like recombination diagram in pop-up.
• src/hg/lib/botDelay.c
  • lines changed 16, context: html, text, full: html, text
    081dc1a2de216d74a28252747d593c2b1288f251 Tue May 26 02:06:08 2026 -0700
    hubApi/botDelay: return JSON 500 when bottleneck server is unreachable abortAndExplainConnectFail() previously called exit(0) directly after writing raw HTML, which bypassed every error handler and produced a broken response for JSON API clients. Change it to errAbort() so it can be caught by errCatch. Wrap both hgBotDelayTimeFrac() call sites in hubApi (the global delay in main() and the BLAT-specific extra delay in apiBlat()) in errCatch blocks that call apiErrAbort(500) on failure, giving callers a proper JSON error rather than an HTML fragment or a silent exit. refs #36315 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/doc/InSiGHT.txt
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    a8284e2d5f9f74b52d107a8b99de3e8a03a263a2 Tue May 26 11:09:11 2026 -0700
    Adding PMS2CL Paralog Variants track to InSiGHT hub. Projects PMS2 curated ClinVar variants onto PMS2CL coordinates to help analysts recognize PMS2CL calls that may correspond to known PMS2 variants. refs #36582
• src/hg/makeDb/doc/evaSnp9.txt
  • lines changed 95, context: html, text, full: html, text
    e4696ced7edf4d0a2a995f203a751a3782cc2f16 Fri May 29 15:00:59 2026 -0700
    Add EVA SNP Release 9 — unified pipeline for native + GenArk contributed tracks. refs #37517 Adds the unified evaSnp9.py pipeline at src/hg/makeDb/scripts/evaSnp/evaSnp9.py that builds both native UCSC db bigBeds and GenArk contributed bigBeds from one driver, replacing the two separate v8 scripts (evaSnp8.py + evaSnpGenArk.py). Built 40 native + 115 contributed tracks for v9. trackDb: evaSnp9 subtrack added to the evaSnpContainer composite with the new SNV/indel/MNV varClass labels, searchTable stanza, and parent=on/visibility=dense defaults; evaSnp8 left on per QA preference. evaSnpContainer.html: transition note explaining the v9 SO-label refresh (SNV/deletion/insertion/indel/MNV/sequence_alteration replacing the legacy substitution/delins/multipleNucleotideVariant labels in v3-v8) and the new single-most-severe ucscClass convention; SO term list updated to dual-label each entry; download example URL bumped to evaSnp9.bb. Makedoc at src/hg/makeDb/doc/evaSnp9.txt documents the unified build, deploy, and per-clade GenArk make steps.
• src/hg/makeDb/doc/hg38/crPred.txt
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    b5997c3b91cd3dfa56da7de7e21601b333989773 Tue May 26 08:56:05 2026 -0700
    [Claude] add TREDNet enhancer/silencer predictions under new crPred supertrack 512,577 candidate enhancers and 319,322 candidate silencers predicted by the TREDNet deep learning model across 97 ENCODE biosamples (Huang & Ovcharenko 2024, PMID 38978133). Per-sample 1-kb BED files merged with bedtools, annotated with contributing cell types/tissues/cell lines, colored by dominant sample category using the Okabe-Ito palette. Tracks live under the new crPred (Cis-regulatory Predictions) supertrack. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> refs #37631
• src/hg/makeDb/doc/hg38/eve.txt
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    8c1ebdae695b1bb40e45f41aff4a4f9fb9e52491 Thu May 28 05:43:13 2026 -0700
    [Claude] add EVE missense variant effect heatmap track for hg38 #Preview2 week - bugs introduced now will need a build patch to fix Heatmap bigBed track showing EVE scores for all possible missense substitutions in 2,949 disease-associated proteins. One entry per protein; columns = amino acid positions at genomic codon coordinates, rows = 20 standard amino acids. Colors blue (benign) to red (pathogenic). Includes conversion script, autoSql, trackDb, HTML doc, and makedoc. Added to predictionScoresSuper. refs #31804 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/doc/hg38/lrSv.txt
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    6b0d68657267f1e02c47d4224ea62446bbbb2ba0 Fri May 22 06:55:52 2026 -0700
    small non-AI changes to the html docs pages of the long-read SV tracks
• src/hg/makeDb/doc/hg38/varFreqs.txt
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    3180d71425ab40bc022712bb95868bfe80747375 Fri May 29 08:52:38 2026 -0700
    [Claude] varFreqs: split SPARK+SCHEMA by phenotype, add disease + array combined tracks, drop array cohorts from varFreqsAll #Preview2 week - bugs introduced now will need a build patch to fix Split SFARI SPARK WES and WGS by autism status using fill-tags -S with the SPARK individuals_registration TSV (AC_AUT / AN_AUT / AF_AUT plus AC_NON_AUT / AN_NON_AUT / AF_NON_AUT). Added matching SCHEMA case/control sums (AC_CASE etc.). Two new combined bigBed tracks: varFreqsDisease (SPARK, SFARI WGS, TOPMed, SCHEMA, GREGoR, GA4K) and varFreqsArray (TPMI, MexBB, UKBB). TPMI and MexBB are removed from varFreqsAll so the main combined track is purely WGS/WES. Build scripts parameterized so the same code drives all three combined builds: mergeAndAnnotate.sh gains --databases / --tag, vcfToBigBed.py gains --databases-file / --populations-file and a per-track autoSql table name. mergeAndAnnotate.sh now pins /cluster/software/src/bcftools-1.22 in PATH (--unify-chr-names is a 1.22 feature; conda's 1.14 silently fails). refs #36642
• src/hg/makeDb/doc/hg38/varaico.txt
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    19c16827a214d3384ae7e6052355dbbc8bc7de46 Fri May 29 00:42:09 2026 -0700
    Varaico release 3 (20260527): bump dataVersion to release 3, update makeDoc. refs #37658
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
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    83956ac6781412699ebf11bfb2fd87cd1833ca87 Mon Jun 1 09:59:44 2026 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/mm10.txt
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    94087f3f31945d133c187137ebbf0eddaf808dc3 Tue May 26 10:50:26 2026 -0700
    Per author request, reordered the bars shown on the Genome Browser image to follow the biological tissue order. Following Max's suggestion in #37619, added the barChartReorder.py script and documented the reorder step in the mm10 and mm39 makedocs. refs #37001
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    6db91c5823e6f55265fc2e2a06343110786ccd66 Tue May 26 13:41:50 2026 -0700
    Removed the 2026-05-26 mouseDevTimecourse bigBed and categories reorder per team feedback in #36998 notes 54-56. Restored the original bigBed files from the Wold Lab hub, kept the new colors, and removed the reorder steps from the mm10 and mm39 makedocs. refs #37001
• src/hg/makeDb/doc/mm39/mouseDevTimecourse.txt
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    94087f3f31945d133c187137ebbf0eddaf808dc3 Tue May 26 10:50:26 2026 -0700
    Per author request, reordered the bars shown on the Genome Browser image to follow the biological tissue order. Following Max's suggestion in #37619, added the barChartReorder.py script and documented the reorder step in the mm10 and mm39 makedocs. refs #37001
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    6db91c5823e6f55265fc2e2a06343110786ccd66 Tue May 26 13:41:50 2026 -0700
    Removed the 2026-05-26 mouseDevTimecourse bigBed and categories reorder per team feedback in #36998 notes 54-56. Restored the original bigBed files from the Wold Lab hub, kept the new colors, and removed the reorder steps from the mm10 and mm39 makedocs. refs #37001
• src/hg/makeDb/doc/vgp577way/mkHtml.pl
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    e8f2620df2a833ef15bdc2c7c4e132302770c900 Tue May 26 20:14:28 2026 -0700
    now have data access on hgdownload refs #31811
• src/hg/makeDb/doc/vgp577way/vgp577way.pl
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    375022845a4226d17c2717cc844f4e3ef5eb5b5e Tue May 26 20:13:31 2026 -0700
    resetting the bigDataUrl to hgdownload addresses refs #31811
• src/hg/makeDb/doc/vgp577way/vgp577way.txt
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    2fb68bdc7e7512791f7dfa748dc659c59bed62cb Tue May 26 20:12:50 2026 -0700
    cleanup and make MAF download files refs #31811
• src/hg/makeDb/scripts/barChartReorder/barChartReorder.py
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    94087f3f31945d133c187137ebbf0eddaf808dc3 Tue May 26 10:50:26 2026 -0700
    Per author request, reordered the bars shown on the Genome Browser image to follow the biological tissue order. Following Max's suggestion in #37619, added the barChartReorder.py script and documented the reorder step in the mm10 and mm39 makedocs. refs #37001
• src/hg/makeDb/scripts/evaSnp/evaSnp9.py
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    e4696ced7edf4d0a2a995f203a751a3782cc2f16 Fri May 29 15:00:59 2026 -0700
    Add EVA SNP Release 9 — unified pipeline for native + GenArk contributed tracks. refs #37517 Adds the unified evaSnp9.py pipeline at src/hg/makeDb/scripts/evaSnp/evaSnp9.py that builds both native UCSC db bigBeds and GenArk contributed bigBeds from one driver, replacing the two separate v8 scripts (evaSnp8.py + evaSnpGenArk.py). Built 40 native + 115 contributed tracks for v9. trackDb: evaSnp9 subtrack added to the evaSnpContainer composite with the new SNV/indel/MNV varClass labels, searchTable stanza, and parent=on/visibility=dense defaults; evaSnp8 left on per QA preference. evaSnpContainer.html: transition note explaining the v9 SO-label refresh (SNV/deletion/insertion/indel/MNV/sequence_alteration replacing the legacy substitution/delins/multipleNucleotideVariant labels in v3-v8) and the new single-most-severe ucscClass convention; SO term list updated to dual-label each entry; download example URL bumped to evaSnp9.bb. Makedoc at src/hg/makeDb/doc/evaSnp9.txt documents the unified build, deploy, and per-clade GenArk make steps.
• src/hg/makeDb/scripts/eve/eve_heatmap.as
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    8c1ebdae695b1bb40e45f41aff4a4f9fb9e52491 Thu May 28 05:43:13 2026 -0700
    [Claude] add EVE missense variant effect heatmap track for hg38 #Preview2 week - bugs introduced now will need a build patch to fix Heatmap bigBed track showing EVE scores for all possible missense substitutions in 2,949 disease-associated proteins. One entry per protein; columns = amino acid positions at genomic codon coordinates, rows = 20 standard amino acids. Colors blue (benign) to red (pathogenic). Includes conversion script, autoSql, trackDb, HTML doc, and makedoc. Added to predictionScoresSuper. refs #31804 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/eve/vcfToEveHeatmap.py
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    8c1ebdae695b1bb40e45f41aff4a4f9fb9e52491 Thu May 28 05:43:13 2026 -0700
    [Claude] add EVE missense variant effect heatmap track for hg38 #Preview2 week - bugs introduced now will need a build patch to fix Heatmap bigBed track showing EVE scores for all possible missense substitutions in 2,949 disease-associated proteins. One entry per protein; columns = amino acid positions at genomic codon coordinates, rows = 20 standard amino acids. Colors blue (benign) to red (pathogenic). Includes conversion script, autoSql, trackDb, HTML doc, and makedoc. Added to predictionScoresSuper. refs #31804 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/insight/buildInsightClinVar.py
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    a8284e2d5f9f74b52d107a8b99de3e8a03a263a2 Tue May 26 11:09:11 2026 -0700
    Adding PMS2CL Paralog Variants track to InSiGHT hub. Projects PMS2 curated ClinVar variants onto PMS2CL coordinates to help analysts recognize PMS2CL calls that may correspond to known PMS2 variants. refs #36582
• src/hg/makeDb/scripts/ncOrfs/addIntrons.py
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    d8ddf1a6c92e6efeb99481bf4849569abe5f8f5e Tue May 26 09:46:29 2026 -0700
    [Claude] ncOrfs: fix review feedback — mouseOver label, .as description, HTML wording, addIntrons exit check - ncOrfs.ra mouseOver: rename "MANE host" to "Host transcript" so the label is accurate for both MANE and GENCODE fallback transcripts - utrAnnotUorfs.as intronsSource description: mention GENCODE fallback as an alternative source, not just MANE Select/Plus Clinical - gencNcOrfs.html: "only one of those positions" -> "only one of those two positions" for consistency with ncOrfs.html - addIntrons.py load_donors(): check bigBedToBed exit code and call sys.exit() on failure instead of silently continuing with empty data refs #35101 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/utrAnnotUorfs.as
  • lines changed 1, context: html, text, full: html, text
    d8ddf1a6c92e6efeb99481bf4849569abe5f8f5e Tue May 26 09:46:29 2026 -0700
    [Claude] ncOrfs: fix review feedback — mouseOver label, .as description, HTML wording, addIntrons exit check - ncOrfs.ra mouseOver: rename "MANE host" to "Host transcript" so the label is accurate for both MANE and GENCODE fallback transcripts - utrAnnotUorfs.as intronsSource description: mention GENCODE fallback as an alternative source, not just MANE Select/Plus Clinical - gencNcOrfs.html: "only one of those positions" -> "only one of those two positions" for consistency with ncOrfs.html - addIntrons.py load_donors(): check bigBedToBed exit code and call sys.exit() on failure instead of silently continuing with empty data refs #35101 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/tredNet/tredNet.as
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    b5997c3b91cd3dfa56da7de7e21601b333989773 Tue May 26 08:56:05 2026 -0700
    [Claude] add TREDNet enhancer/silencer predictions under new crPred supertrack 512,577 candidate enhancers and 319,322 candidate silencers predicted by the TREDNet deep learning model across 97 ENCODE biosamples (Huang & Ovcharenko 2024, PMID 38978133). Per-sample 1-kb BED files merged with bedtools, annotated with contributing cell types/tissues/cell lines, colored by dominant sample category using the Okabe-Ito palette. Tracks live under the new crPred (Cis-regulatory Predictions) supertrack. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> refs #37631
• src/hg/makeDb/scripts/tredNet/tredNetBuild.py
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    b5997c3b91cd3dfa56da7de7e21601b333989773 Tue May 26 08:56:05 2026 -0700
    [Claude] add TREDNet enhancer/silencer predictions under new crPred supertrack 512,577 candidate enhancers and 319,322 candidate silencers predicted by the TREDNet deep learning model across 97 ENCODE biosamples (Huang & Ovcharenko 2024, PMID 38978133). Per-sample 1-kb BED files merged with bedtools, annotated with contributing cell types/tissues/cell lines, colored by dominant sample category using the Okabe-Ito palette. Tracks live under the new crPred (Cis-regulatory Predictions) supertrack. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> refs #37631
• src/hg/makeDb/scripts/varFreqs/databases.tsv
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    3180d71425ab40bc022712bb95868bfe80747375 Fri May 29 08:52:38 2026 -0700
    [Claude] varFreqs: split SPARK+SCHEMA by phenotype, add disease + array combined tracks, drop array cohorts from varFreqsAll #Preview2 week - bugs introduced now will need a build patch to fix Split SFARI SPARK WES and WGS by autism status using fill-tags -S with the SPARK individuals_registration TSV (AC_AUT / AN_AUT / AF_AUT plus AC_NON_AUT / AN_NON_AUT / AF_NON_AUT). Added matching SCHEMA case/control sums (AC_CASE etc.). Two new combined bigBed tracks: varFreqsDisease (SPARK, SFARI WGS, TOPMed, SCHEMA, GREGoR, GA4K) and varFreqsArray (TPMI, MexBB, UKBB). TPMI and MexBB are removed from varFreqsAll so the main combined track is purely WGS/WES. Build scripts parameterized so the same code drives all three combined builds: mergeAndAnnotate.sh gains --databases / --tag, vcfToBigBed.py gains --databases-file / --populations-file and a per-track autoSql table name. mergeAndAnnotate.sh now pins /cluster/software/src/bcftools-1.22 in PATH (--unify-chr-names is a 1.22 feature; conda's 1.14 silently fails). refs #36642
• src/hg/makeDb/scripts/varFreqs/databases_array.tsv
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    3180d71425ab40bc022712bb95868bfe80747375 Fri May 29 08:52:38 2026 -0700
    [Claude] varFreqs: split SPARK+SCHEMA by phenotype, add disease + array combined tracks, drop array cohorts from varFreqsAll #Preview2 week - bugs introduced now will need a build patch to fix Split SFARI SPARK WES and WGS by autism status using fill-tags -S with the SPARK individuals_registration TSV (AC_AUT / AN_AUT / AF_AUT plus AC_NON_AUT / AN_NON_AUT / AF_NON_AUT). Added matching SCHEMA case/control sums (AC_CASE etc.). Two new combined bigBed tracks: varFreqsDisease (SPARK, SFARI WGS, TOPMed, SCHEMA, GREGoR, GA4K) and varFreqsArray (TPMI, MexBB, UKBB). TPMI and MexBB are removed from varFreqsAll so the main combined track is purely WGS/WES. Build scripts parameterized so the same code drives all three combined builds: mergeAndAnnotate.sh gains --databases / --tag, vcfToBigBed.py gains --databases-file / --populations-file and a per-track autoSql table name. mergeAndAnnotate.sh now pins /cluster/software/src/bcftools-1.22 in PATH (--unify-chr-names is a 1.22 feature; conda's 1.14 silently fails). refs #36642
• src/hg/makeDb/scripts/varFreqs/databases_disease.tsv
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    3180d71425ab40bc022712bb95868bfe80747375 Fri May 29 08:52:38 2026 -0700
    [Claude] varFreqs: split SPARK+SCHEMA by phenotype, add disease + array combined tracks, drop array cohorts from varFreqsAll #Preview2 week - bugs introduced now will need a build patch to fix Split SFARI SPARK WES and WGS by autism status using fill-tags -S with the SPARK individuals_registration TSV (AC_AUT / AN_AUT / AF_AUT plus AC_NON_AUT / AN_NON_AUT / AF_NON_AUT). Added matching SCHEMA case/control sums (AC_CASE etc.). Two new combined bigBed tracks: varFreqsDisease (SPARK, SFARI WGS, TOPMed, SCHEMA, GREGoR, GA4K) and varFreqsArray (TPMI, MexBB, UKBB). TPMI and MexBB are removed from varFreqsAll so the main combined track is purely WGS/WES. Build scripts parameterized so the same code drives all three combined builds: mergeAndAnnotate.sh gains --databases / --tag, vcfToBigBed.py gains --databases-file / --populations-file and a per-track autoSql table name. mergeAndAnnotate.sh now pins /cluster/software/src/bcftools-1.22 in PATH (--unify-chr-names is a 1.22 feature; conda's 1.14 silently fails). refs #36642
• src/hg/makeDb/scripts/varFreqs/mergeAndAnnotate.sh
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    3180d71425ab40bc022712bb95868bfe80747375 Fri May 29 08:52:38 2026 -0700
    [Claude] varFreqs: split SPARK+SCHEMA by phenotype, add disease + array combined tracks, drop array cohorts from varFreqsAll #Preview2 week - bugs introduced now will need a build patch to fix Split SFARI SPARK WES and WGS by autism status using fill-tags -S with the SPARK individuals_registration TSV (AC_AUT / AN_AUT / AF_AUT plus AC_NON_AUT / AN_NON_AUT / AF_NON_AUT). Added matching SCHEMA case/control sums (AC_CASE etc.). Two new combined bigBed tracks: varFreqsDisease (SPARK, SFARI WGS, TOPMed, SCHEMA, GREGoR, GA4K) and varFreqsArray (TPMI, MexBB, UKBB). TPMI and MexBB are removed from varFreqsAll so the main combined track is purely WGS/WES. Build scripts parameterized so the same code drives all three combined builds: mergeAndAnnotate.sh gains --databases / --tag, vcfToBigBed.py gains --databases-file / --populations-file and a per-track autoSql table name. mergeAndAnnotate.sh now pins /cluster/software/src/bcftools-1.22 in PATH (--unify-chr-names is a 1.22 feature; conda's 1.14 silently fails). refs #36642
• src/hg/makeDb/scripts/varFreqs/populations.tsv
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    3180d71425ab40bc022712bb95868bfe80747375 Fri May 29 08:52:38 2026 -0700
    [Claude] varFreqs: split SPARK+SCHEMA by phenotype, add disease + array combined tracks, drop array cohorts from varFreqsAll #Preview2 week - bugs introduced now will need a build patch to fix Split SFARI SPARK WES and WGS by autism status using fill-tags -S with the SPARK individuals_registration TSV (AC_AUT / AN_AUT / AF_AUT plus AC_NON_AUT / AN_NON_AUT / AF_NON_AUT). Added matching SCHEMA case/control sums (AC_CASE etc.). Two new combined bigBed tracks: varFreqsDisease (SPARK, SFARI WGS, TOPMed, SCHEMA, GREGoR, GA4K) and varFreqsArray (TPMI, MexBB, UKBB). TPMI and MexBB are removed from varFreqsAll so the main combined track is purely WGS/WES. Build scripts parameterized so the same code drives all three combined builds: mergeAndAnnotate.sh gains --databases / --tag, vcfToBigBed.py gains --databases-file / --populations-file and a per-track autoSql table name. mergeAndAnnotate.sh now pins /cluster/software/src/bcftools-1.22 in PATH (--unify-chr-names is a 1.22 feature; conda's 1.14 silently fails). refs #36642
• src/hg/makeDb/scripts/varFreqs/schema_addAcAnAf.py
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    3180d71425ab40bc022712bb95868bfe80747375 Fri May 29 08:52:38 2026 -0700
    [Claude] varFreqs: split SPARK+SCHEMA by phenotype, add disease + array combined tracks, drop array cohorts from varFreqsAll #Preview2 week - bugs introduced now will need a build patch to fix Split SFARI SPARK WES and WGS by autism status using fill-tags -S with the SPARK individuals_registration TSV (AC_AUT / AN_AUT / AF_AUT plus AC_NON_AUT / AN_NON_AUT / AF_NON_AUT). Added matching SCHEMA case/control sums (AC_CASE etc.). Two new combined bigBed tracks: varFreqsDisease (SPARK, SFARI WGS, TOPMed, SCHEMA, GREGoR, GA4K) and varFreqsArray (TPMI, MexBB, UKBB). TPMI and MexBB are removed from varFreqsAll so the main combined track is purely WGS/WES. Build scripts parameterized so the same code drives all three combined builds: mergeAndAnnotate.sh gains --databases / --tag, vcfToBigBed.py gains --databases-file / --populations-file and a per-track autoSql table name. mergeAndAnnotate.sh now pins /cluster/software/src/bcftools-1.22 in PATH (--unify-chr-names is a 1.22 feature; conda's 1.14 silently fails). refs #36642
• src/hg/makeDb/scripts/varFreqs/sparkMergeVcfAddCounts.sh
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    3180d71425ab40bc022712bb95868bfe80747375 Fri May 29 08:52:38 2026 -0700
    [Claude] varFreqs: split SPARK+SCHEMA by phenotype, add disease + array combined tracks, drop array cohorts from varFreqsAll #Preview2 week - bugs introduced now will need a build patch to fix Split SFARI SPARK WES and WGS by autism status using fill-tags -S with the SPARK individuals_registration TSV (AC_AUT / AN_AUT / AF_AUT plus AC_NON_AUT / AN_NON_AUT / AF_NON_AUT). Added matching SCHEMA case/control sums (AC_CASE etc.). Two new combined bigBed tracks: varFreqsDisease (SPARK, SFARI WGS, TOPMed, SCHEMA, GREGoR, GA4K) and varFreqsArray (TPMI, MexBB, UKBB). TPMI and MexBB are removed from varFreqsAll so the main combined track is purely WGS/WES. Build scripts parameterized so the same code drives all three combined builds: mergeAndAnnotate.sh gains --databases / --tag, vcfToBigBed.py gains --databases-file / --populations-file and a per-track autoSql table name. mergeAndAnnotate.sh now pins /cluster/software/src/bcftools-1.22 in PATH (--unify-chr-names is a 1.22 feature; conda's 1.14 silently fails). refs #36642
• src/hg/makeDb/scripts/varFreqs/vcfToBigBed.py
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    3180d71425ab40bc022712bb95868bfe80747375 Fri May 29 08:52:38 2026 -0700
    [Claude] varFreqs: split SPARK+SCHEMA by phenotype, add disease + array combined tracks, drop array cohorts from varFreqsAll #Preview2 week - bugs introduced now will need a build patch to fix Split SFARI SPARK WES and WGS by autism status using fill-tags -S with the SPARK individuals_registration TSV (AC_AUT / AN_AUT / AF_AUT plus AC_NON_AUT / AN_NON_AUT / AF_NON_AUT). Added matching SCHEMA case/control sums (AC_CASE etc.). Two new combined bigBed tracks: varFreqsDisease (SPARK, SFARI WGS, TOPMed, SCHEMA, GREGoR, GA4K) and varFreqsArray (TPMI, MexBB, UKBB). TPMI and MexBB are removed from varFreqsAll so the main combined track is purely WGS/WES. Build scripts parameterized so the same code drives all three combined builds: mergeAndAnnotate.sh gains --databases / --tag, vcfToBigBed.py gains --databases-file / --populations-file and a per-track autoSql table name. mergeAndAnnotate.sh now pins /cluster/software/src/bcftools-1.22 in PATH (--unify-chr-names is a 1.22 feature; conda's 1.14 silently fails). refs #36642
• src/hg/makeDb/trackDb/encode4RegLayeredDisplay.shared.html
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    ca24bbc74b74174bec0fa1713fbb1250d1e5ef4e Mon May 25 21:44:07 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - DNase/ATAC/Histone/CTCF (Indiv.): added experiment counts (3,201 hg38, 589 mm10) per code review feedback (refs #37577 note-7), updated Signal/Peak bullet header wording. - TF rPeaks: added grayscale legend table, reworded peak shading description, colored the word "green" to match the motif decorator color. - TF ChIP-seq (Indiv.): updates to opening paragraph, added Signal/Peak bullet block with grayscale legend to Description. - ENCODE4 Regulation supertrack: added (Layered)/(Indiv.) explanation paragraph, bolded track names, fixed Indiv. capitalization and DNase/ATAC order to match shortLabels. hg38: alphabetized References, mirrored TF rPeaks grayscale wording, changed inline PMID citation to author/year. - DNase, ATAC, H3K4me3, H3K27ac, CTCF (Layered): added "By default," to transparent overlay sentence in shared HTML. - RNA-seq (Indiv.): updated experiment counts (523 hg38, 216 mm10), updated filter list to match hgTrackUi facet names, added Available Organs and Tissues table. - Transcription (Layered): restructured Available Organs and Tissues table, added "By default," to transparent overlay sentence.
• src/hg/makeDb/trackDb/evaSnp.ra
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    e4696ced7edf4d0a2a995f203a751a3782cc2f16 Fri May 29 15:00:59 2026 -0700
    Add EVA SNP Release 9 — unified pipeline for native + GenArk contributed tracks. refs #37517 Adds the unified evaSnp9.py pipeline at src/hg/makeDb/scripts/evaSnp/evaSnp9.py that builds both native UCSC db bigBeds and GenArk contributed bigBeds from one driver, replacing the two separate v8 scripts (evaSnp8.py + evaSnpGenArk.py). Built 40 native + 115 contributed tracks for v9. trackDb: evaSnp9 subtrack added to the evaSnpContainer composite with the new SNV/indel/MNV varClass labels, searchTable stanza, and parent=on/visibility=dense defaults; evaSnp8 left on per QA preference. evaSnpContainer.html: transition note explaining the v9 SO-label refresh (SNV/deletion/insertion/indel/MNV/sequence_alteration replacing the legacy substitution/delins/multipleNucleotideVariant labels in v3-v8) and the new single-most-severe ucscClass convention; SO term list updated to dual-label each entry; download example URL bumped to evaSnp9.bb. Makedoc at src/hg/makeDb/doc/evaSnp9.txt documents the unified build, deploy, and per-clade GenArk make steps.
• src/hg/makeDb/trackDb/evaSnpContainer.html
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    e4696ced7edf4d0a2a995f203a751a3782cc2f16 Fri May 29 15:00:59 2026 -0700
    Add EVA SNP Release 9 — unified pipeline for native + GenArk contributed tracks. refs #37517 Adds the unified evaSnp9.py pipeline at src/hg/makeDb/scripts/evaSnp/evaSnp9.py that builds both native UCSC db bigBeds and GenArk contributed bigBeds from one driver, replacing the two separate v8 scripts (evaSnp8.py + evaSnpGenArk.py). Built 40 native + 115 contributed tracks for v9. trackDb: evaSnp9 subtrack added to the evaSnpContainer composite with the new SNV/indel/MNV varClass labels, searchTable stanza, and parent=on/visibility=dense defaults; evaSnp8 left on per QA preference. evaSnpContainer.html: transition note explaining the v9 SO-label refresh (SNV/deletion/insertion/indel/MNV/sequence_alteration replacing the legacy substitution/delins/multipleNucleotideVariant labels in v3-v8) and the new single-most-severe ucscClass convention; SO term list updated to dual-label each entry; download example URL bumped to evaSnp9.bb. Makedoc at src/hg/makeDb/doc/evaSnp9.txt documents the unified build, deploy, and per-clade GenArk make steps.
• src/hg/makeDb/trackDb/human/aprSv.html
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    6b0d68657267f1e02c47d4224ea62446bbbb2ba0 Fri May 22 06:55:52 2026 -0700
    small non-AI changes to the html docs pages of the long-read SV tracks
• src/hg/makeDb/trackDb/human/clinPred.html
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    bafa5b1fa3546c23f9091e08304355490ded9ead Tue May 26 11:34:39 2026 -0700
    Address CR feedback on v498 description pages. refs #37533 varFreqs.html: fix contact-us sentence punctuation/grammar, replace "ships" with "provides"/"includes" in two spots, and rewrite the "trackUI labels" sentence to refer to the track configuration page and the combined-track bigBed (per Gerardo's question about what trackUI labels meant). clinPred.html: replace em-dashes around "those that do not change the encoded amino acid" with commas. predictionScoresSuper.html: reorder references alphabetically by first author.
• src/hg/makeDb/trackDb/human/colorsDbSv.html
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    6b0d68657267f1e02c47d4224ea62446bbbb2ba0 Fri May 22 06:55:52 2026 -0700
    small non-AI changes to the html docs pages of the long-read SV tracks
• src/hg/makeDb/trackDb/human/cpc1Sv.html
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    6b0d68657267f1e02c47d4224ea62446bbbb2ba0 Fri May 22 06:55:52 2026 -0700
    small non-AI changes to the html docs pages of the long-read SV tracks
• src/hg/makeDb/trackDb/human/dbVarNr.html
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    6b0d68657267f1e02c47d4224ea62446bbbb2ba0 Fri May 22 06:55:52 2026 -0700
    small non-AI changes to the html docs pages of the long-read SV tracks
• src/hg/makeDb/trackDb/human/eve.html
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    8c1ebdae695b1bb40e45f41aff4a4f9fb9e52491 Thu May 28 05:43:13 2026 -0700
    [Claude] add EVE missense variant effect heatmap track for hg38 #Preview2 week - bugs introduced now will need a build patch to fix Heatmap bigBed track showing EVE scores for all possible missense substitutions in 2,949 disease-associated proteins. One entry per protein; columns = amino acid positions at genomic codon coordinates, rows = 20 standard amino acids. Colors blue (benign) to red (pathogenic). Includes conversion script, autoSql, trackDb, HTML doc, and makedoc. Added to predictionScoresSuper. refs #31804 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/eve.ra
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    8c1ebdae695b1bb40e45f41aff4a4f9fb9e52491 Thu May 28 05:43:13 2026 -0700
    [Claude] add EVE missense variant effect heatmap track for hg38 #Preview2 week - bugs introduced now will need a build patch to fix Heatmap bigBed track showing EVE scores for all possible missense substitutions in 2,949 disease-associated proteins. One entry per protein; columns = amino acid positions at genomic codon coordinates, rows = 20 standard amino acids. Colors blue (benign) to red (pathogenic). Includes conversion script, autoSql, trackDb, HTML doc, and makedoc. Added to predictionScoresSuper. refs #31804 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/crPred.html
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    b5997c3b91cd3dfa56da7de7e21601b333989773 Tue May 26 08:56:05 2026 -0700
    [Claude] add TREDNet enhancer/silencer predictions under new crPred supertrack 512,577 candidate enhancers and 319,322 candidate silencers predicted by the TREDNet deep learning model across 97 ENCODE biosamples (Huang & Ovcharenko 2024, PMID 38978133). Per-sample 1-kb BED files merged with bedtools, annotated with contributing cell types/tissues/cell lines, colored by dominant sample category using the Okabe-Ito palette. Tracks live under the new crPred (Cis-regulatory Predictions) supertrack. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> refs #37631
• src/hg/makeDb/trackDb/human/hg38/crPred.ra
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    b5997c3b91cd3dfa56da7de7e21601b333989773 Tue May 26 08:56:05 2026 -0700
    [Claude] add TREDNet enhancer/silencer predictions under new crPred supertrack 512,577 candidate enhancers and 319,322 candidate silencers predicted by the TREDNet deep learning model across 97 ENCODE biosamples (Huang & Ovcharenko 2024, PMID 38978133). Per-sample 1-kb BED files merged with bedtools, annotated with contributing cell types/tissues/cell lines, colored by dominant sample category using the Okabe-Ito palette. Tracks live under the new crPred (Cis-regulatory Predictions) supertrack. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> refs #37631
• src/hg/makeDb/trackDb/human/hg38/gencNcOrfs.html
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    d8ddf1a6c92e6efeb99481bf4849569abe5f8f5e Tue May 26 09:46:29 2026 -0700
    [Claude] ncOrfs: fix review feedback — mouseOver label, .as description, HTML wording, addIntrons exit check - ncOrfs.ra mouseOver: rename "MANE host" to "Host transcript" so the label is accurate for both MANE and GENCODE fallback transcripts - utrAnnotUorfs.as intronsSource description: mention GENCODE fallback as an alternative source, not just MANE Select/Plus Clinical - gencNcOrfs.html: "only one of those positions" -> "only one of those two positions" for consistency with ncOrfs.html - addIntrons.py load_donors(): check bigBedToBed exit code and call sys.exit() on failure instead of silently continuing with empty data refs #35101 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/mpra.html
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    36cd91779b5cd2866c500c32a5892cfc959bfe06 Fri May 29 10:30:15 2026 -0700
    MPRA superTrack: news announcement, pennantIcon, attribution fix. refs #37359 Ship the user-visible release pieces for the Jun. 2, 2026 announcement of the MPRA superTrack (MPRA Base + MPRAVarDB) on hg38. News announcement: - Added a Jun. 2, 2026 entry to newsarch.html (anchor #060226) describing both subtracks, the data sources (MPRA Base / MPRAVarDB), and an Element-level vs Variant-level summary. Screenshot at the TERT promoter shows MPRA Base reporter activity for melanoma risk variants alongside filtered MPRAVarDB high-confidence variants from Kircher saturation mutagenesis. - Added the matching entry to indexNews.html ("New MPRA Base and MPRAVarDB tracks on hg38", 42 chars, under the ~50-char target); dropped the now-7th entry "Updated superTrack configuration page" to keep the 6-item limit. - Added the screenshot mpraNewsImage.png (3198x1015) referenced by the news div at 90% width. trackDb stanza: - Added "New" pennantIcon to the parent mpra superTrack pointing to the news anchor, matching the recount3 / promoterAi pattern. Attribution fix: - The parent mpra.html Credits section still attributed MPRAVarDB to "Tao Wang and colleagues". That attribution doesn't match the actual paper authors (Jin W, Xia Y, Nizomov J, Liu Y, Li Z, Lu Q, Chen L per PMID 39325859, DOI 10.1093/bioinformatics/btae578); replaced with "Weijia Jin and colleagues" to match mpraVarDb.html.
• src/hg/makeDb/trackDb/human/hg38/mpra.ra
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    6b78f729f10d374ad3a960a4417b1e6bd7ed7719 Wed May 27 11:08:35 2026 -0700
    Update mprabase trackDb stanza and description page for MPRA Base v5 (2026-05-27 refresh). refs #37359 Varda Singhal shipped an updated mprabase bigBed on 2026-05-27. Update the trackDb stanza and description page to match the new data file. No build-script or makedoc changes (track is loaded from Varda's prebuilt bigBed; no local processing). trackDb stanza changes (mpra.ra, mprabase subtrack): - type bigBed 9 + 9 -> 9 + 11. The new bigBed adds two extra fields: variant_type and sequence. - dataVersion bumped from "v4.9.3 (Mar 2026)" to "2026-05-27 refresh". Varda's email did not name the new version; using the refresh date. - labelFields adds variant_type so users can toggle ref/alt/NA labels. - filterValues.cell_line drops Hela (the Arnold 2013 single-element HeLa proof-of-concept row was removed in v5; HEK293FT, HepG2, HUES64, mESC, NPC, UACC903 remain). - filterValues.variant_type added (3 values: alternate, NA, reference; 37,017 NA rows, 2,239 reference, 1,682 alternate). Description page changes (mprabase.html): - Total element count: 41,275 -> 40,938 (verified via bigBedInfo). - Experiments table: removed Arnold et al. 2013 row (HeLa STARR-seq, 1 element; 0 PMID 23328393 rows in the new data). Updated Klein 2018 count: 7,064 -> 6,728 (cross-species ortholog tiles removed by upstream). - Cell-line biological-context table: removed HeLa row. - Library-framing paragraph: dropped "Arnold et al., 2013" from the variant-centered single-base example list since the row is gone. - Display Conventions: new paragraph documenting the variant_type field (reference / alternate / NA) and the sequence field shown on the details page. - Methods: removed the "211,053 replicate-level measurements" pre- aggregation count (it was tied to the old element set and would be stale; the aggregation step is described conceptually instead). - References: removed Arnold 2013 block since it no longer contributes any rows. Validated on sandbox: trackDb_lrnassar loads bigBed 9 + 11 cleanly, hgTrackUi HTTP 200, variant_type filter dropdown shows all three options, /getData/track API exposes the new variant_type and sequence fields, 0 non-ASCII characters in the updated page.
  • lines changed 1, context: html, text, full: html, text
    36cd91779b5cd2866c500c32a5892cfc959bfe06 Fri May 29 10:30:15 2026 -0700
    MPRA superTrack: news announcement, pennantIcon, attribution fix. refs #37359 Ship the user-visible release pieces for the Jun. 2, 2026 announcement of the MPRA superTrack (MPRA Base + MPRAVarDB) on hg38. News announcement: - Added a Jun. 2, 2026 entry to newsarch.html (anchor #060226) describing both subtracks, the data sources (MPRA Base / MPRAVarDB), and an Element-level vs Variant-level summary. Screenshot at the TERT promoter shows MPRA Base reporter activity for melanoma risk variants alongside filtered MPRAVarDB high-confidence variants from Kircher saturation mutagenesis. - Added the matching entry to indexNews.html ("New MPRA Base and MPRAVarDB tracks on hg38", 42 chars, under the ~50-char target); dropped the now-7th entry "Updated superTrack configuration page" to keep the 6-item limit. - Added the screenshot mpraNewsImage.png (3198x1015) referenced by the news div at 90% width. trackDb stanza: - Added "New" pennantIcon to the parent mpra superTrack pointing to the news anchor, matching the recount3 / promoterAi pattern. Attribution fix: - The parent mpra.html Credits section still attributed MPRAVarDB to "Tao Wang and colleagues". That attribution doesn't match the actual paper authors (Jin W, Xia Y, Nizomov J, Liu Y, Li Z, Lu Q, Chen L per PMID 39325859, DOI 10.1093/bioinformatics/btae578); replaced with "Weijia Jin and colleagues" to match mpraVarDb.html.
• src/hg/makeDb/trackDb/human/hg38/mpraVarDb.html
  • lines changed 2, context: html, text, full: html, text
    36cd91779b5cd2866c500c32a5892cfc959bfe06 Fri May 29 10:30:15 2026 -0700
    MPRA superTrack: news announcement, pennantIcon, attribution fix. refs #37359 Ship the user-visible release pieces for the Jun. 2, 2026 announcement of the MPRA superTrack (MPRA Base + MPRAVarDB) on hg38. News announcement: - Added a Jun. 2, 2026 entry to newsarch.html (anchor #060226) describing both subtracks, the data sources (MPRA Base / MPRAVarDB), and an Element-level vs Variant-level summary. Screenshot at the TERT promoter shows MPRA Base reporter activity for melanoma risk variants alongside filtered MPRAVarDB high-confidence variants from Kircher saturation mutagenesis. - Added the matching entry to indexNews.html ("New MPRA Base and MPRAVarDB tracks on hg38", 42 chars, under the ~50-char target); dropped the now-7th entry "Updated superTrack configuration page" to keep the 6-item limit. - Added the screenshot mpraNewsImage.png (3198x1015) referenced by the news div at 90% width. trackDb stanza: - Added "New" pennantIcon to the parent mpra superTrack pointing to the news anchor, matching the recount3 / promoterAi pattern. Attribution fix: - The parent mpra.html Credits section still attributed MPRAVarDB to "Tao Wang and colleagues". That attribution doesn't match the actual paper authors (Jin W, Xia Y, Nizomov J, Liu Y, Li Z, Lu Q, Chen L per PMID 39325859, DOI 10.1093/bioinformatics/btae578); replaced with "Weijia Jin and colleagues" to match mpraVarDb.html.
• src/hg/makeDb/trackDb/human/hg38/mprabase.html
  • lines changed 25, context: html, text, full: html, text
    6b78f729f10d374ad3a960a4417b1e6bd7ed7719 Wed May 27 11:08:35 2026 -0700
    Update mprabase trackDb stanza and description page for MPRA Base v5 (2026-05-27 refresh). refs #37359 Varda Singhal shipped an updated mprabase bigBed on 2026-05-27. Update the trackDb stanza and description page to match the new data file. No build-script or makedoc changes (track is loaded from Varda's prebuilt bigBed; no local processing). trackDb stanza changes (mpra.ra, mprabase subtrack): - type bigBed 9 + 9 -> 9 + 11. The new bigBed adds two extra fields: variant_type and sequence. - dataVersion bumped from "v4.9.3 (Mar 2026)" to "2026-05-27 refresh". Varda's email did not name the new version; using the refresh date. - labelFields adds variant_type so users can toggle ref/alt/NA labels. - filterValues.cell_line drops Hela (the Arnold 2013 single-element HeLa proof-of-concept row was removed in v5; HEK293FT, HepG2, HUES64, mESC, NPC, UACC903 remain). - filterValues.variant_type added (3 values: alternate, NA, reference; 37,017 NA rows, 2,239 reference, 1,682 alternate). Description page changes (mprabase.html): - Total element count: 41,275 -> 40,938 (verified via bigBedInfo). - Experiments table: removed Arnold et al. 2013 row (HeLa STARR-seq, 1 element; 0 PMID 23328393 rows in the new data). Updated Klein 2018 count: 7,064 -> 6,728 (cross-species ortholog tiles removed by upstream). - Cell-line biological-context table: removed HeLa row. - Library-framing paragraph: dropped "Arnold et al., 2013" from the variant-centered single-base example list since the row is gone. - Display Conventions: new paragraph documenting the variant_type field (reference / alternate / NA) and the sequence field shown on the details page. - Methods: removed the "211,053 replicate-level measurements" pre- aggregation count (it was tied to the old element set and would be stale; the aggregation step is described conceptually instead). - References: removed Arnold 2013 block since it no longer contributes any rows. Validated on sandbox: trackDb_lrnassar loads bigBed 9 + 11 cleanly, hgTrackUi HTTP 200, variant_type filter dropdown shows all three options, /getData/track API exposes the new variant_type and sequence fields, 0 non-ASCII characters in the updated page.
• src/hg/makeDb/trackDb/human/hg38/ncOrfs.html
  • lines changed 39, context: html, text, full: html, text
    8a376bb9516360549ab78f0fad43649ea2f9390a Fri May 29 16:18:01 2026 -0700
    Moving the references to its own section for the supertrack description page, refs #35101
• src/hg/makeDb/trackDb/human/hg38/ncOrfs.ra
  • lines changed 1, context: html, text, full: html, text
    d8ddf1a6c92e6efeb99481bf4849569abe5f8f5e Tue May 26 09:46:29 2026 -0700
    [Claude] ncOrfs: fix review feedback — mouseOver label, .as description, HTML wording, addIntrons exit check - ncOrfs.ra mouseOver: rename "MANE host" to "Host transcript" so the label is accurate for both MANE and GENCODE fallback transcripts - utrAnnotUorfs.as intronsSource description: mention GENCODE fallback as an alternative source, not just MANE Select/Plus Clinical - gencNcOrfs.html: "only one of those positions" -> "only one of those two positions" for consistency with ncOrfs.html - addIntrons.py load_donors(): check bigBedToBed exit code and call sys.exit() on failure instead of silently continuing with empty data refs #35101 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/nuorfdb.html
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    9b370030aca353eab4627f321204855df01788c9 Tue May 26 17:11:24 2026 -0700
    Fixign the number of categories for type from 15 to 25 to match the data. Editing the 'mergeType' to 'type' so it matches the autoSql file, refs #35101
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    3b99f4a5047b00898392a53f55d8ab95d38e9b52 Wed May 27 02:34:34 2026 -0700
    [Claude] nuorfdb: fix incorrect Bhatt-lab attribution and author names; utrAnnotUorfs: doc cleanup, refs #35101 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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    d71354a67869b5d7e8ff63b8b21974e87215970f Wed May 27 14:15:33 2026 -0700
    Fixing reference since the paper had the wrong link. refs #35101
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    b5997c3b91cd3dfa56da7de7e21601b333989773 Tue May 26 08:56:05 2026 -0700
    [Claude] add TREDNet enhancer/silencer predictions under new crPred supertrack 512,577 candidate enhancers and 319,322 candidate silencers predicted by the TREDNet deep learning model across 97 ENCODE biosamples (Huang & Ovcharenko 2024, PMID 38978133). Per-sample 1-kb BED files merged with bedtools, annotated with contributing cell types/tissues/cell lines, colored by dominant sample category using the Okabe-Ito palette. Tracks live under the new crPred (Cis-regulatory Predictions) supertrack. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> refs #37631
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    b9fd7321c0d7eb9cccd02be9ee87887f0df3e6a4 Fri May 29 15:46:35 2026 -0700
    Releasing the ncORFs supertrack for hg38, refs #35101
• src/hg/makeDb/trackDb/human/hg38/tredNet.html
  • lines changed 75, context: html, text, full: html, text
    b5997c3b91cd3dfa56da7de7e21601b333989773 Tue May 26 08:56:05 2026 -0700
    [Claude] add TREDNet enhancer/silencer predictions under new crPred supertrack 512,577 candidate enhancers and 319,322 candidate silencers predicted by the TREDNet deep learning model across 97 ENCODE biosamples (Huang & Ovcharenko 2024, PMID 38978133). Per-sample 1-kb BED files merged with bedtools, annotated with contributing cell types/tissues/cell lines, colored by dominant sample category using the Okabe-Ito palette. Tracks live under the new crPred (Cis-regulatory Predictions) supertrack. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> refs #37631
• src/hg/makeDb/trackDb/human/hg38/tredNetEnhancer.html
  • lines changed 116, context: html, text, full: html, text
    b5997c3b91cd3dfa56da7de7e21601b333989773 Tue May 26 08:56:05 2026 -0700
    [Claude] add TREDNet enhancer/silencer predictions under new crPred supertrack 512,577 candidate enhancers and 319,322 candidate silencers predicted by the TREDNet deep learning model across 97 ENCODE biosamples (Huang & Ovcharenko 2024, PMID 38978133). Per-sample 1-kb BED files merged with bedtools, annotated with contributing cell types/tissues/cell lines, colored by dominant sample category using the Okabe-Ito palette. Tracks live under the new crPred (Cis-regulatory Predictions) supertrack. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> refs #37631
• src/hg/makeDb/trackDb/human/hg38/tredNetSilencer.html
  • lines changed 117, context: html, text, full: html, text
    b5997c3b91cd3dfa56da7de7e21601b333989773 Tue May 26 08:56:05 2026 -0700
    [Claude] add TREDNet enhancer/silencer predictions under new crPred supertrack 512,577 candidate enhancers and 319,322 candidate silencers predicted by the TREDNet deep learning model across 97 ENCODE biosamples (Huang & Ovcharenko 2024, PMID 38978133). Per-sample 1-kb BED files merged with bedtools, annotated with contributing cell types/tissues/cell lines, colored by dominant sample category using the Okabe-Ito palette. Tracks live under the new crPred (Cis-regulatory Predictions) supertrack. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> refs #37631
• src/hg/makeDb/trackDb/human/hg38/utrAnnotUorfs.html
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    3b99f4a5047b00898392a53f55d8ab95d38e9b52 Wed May 27 02:34:34 2026 -0700
    [Claude] nuorfdb: fix incorrect Bhatt-lab attribution and author names; utrAnnotUorfs: doc cleanup, refs #35101 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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    317c5d0cadde2e4e98b30c8c5c052f983cbf204a Wed May 27 15:54:47 2026 -0700
    Fixing typos. Changing transcirptional efficiency to translational efficiency, refs #35101
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.html
  • lines changed 43, context: html, text, full: html, text
    ca24bbc74b74174bec0fa1713fbb1250d1e5ef4e Mon May 25 21:44:07 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - DNase/ATAC/Histone/CTCF (Indiv.): added experiment counts (3,201 hg38, 589 mm10) per code review feedback (refs #37577 note-7), updated Signal/Peak bullet header wording. - TF rPeaks: added grayscale legend table, reworded peak shading description, colored the word "green" to match the motif decorator color. - TF ChIP-seq (Indiv.): updates to opening paragraph, added Signal/Peak bullet block with grayscale legend to Description. - ENCODE4 Regulation supertrack: added (Layered)/(Indiv.) explanation paragraph, bolded track names, fixed Indiv. capitalization and DNase/ATAC order to match shortLabels. hg38: alphabetized References, mirrored TF rPeaks grayscale wording, changed inline PMID citation to author/year. - DNase, ATAC, H3K4me3, H3K27ac, CTCF (Layered): added "By default," to transparent overlay sentence in shared HTML. - RNA-seq (Indiv.): updated experiment counts (523 hg38, 216 mm10), updated filter list to match hgTrackUi facet names, added Available Organs and Tissues table. - Transcription (Layered): restructured Available Organs and Tissues table, added "By default," to transparent overlay sentence.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.html
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    ca24bbc74b74174bec0fa1713fbb1250d1e5ef4e Mon May 25 21:44:07 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - DNase/ATAC/Histone/CTCF (Indiv.): added experiment counts (3,201 hg38, 589 mm10) per code review feedback (refs #37577 note-7), updated Signal/Peak bullet header wording. - TF rPeaks: added grayscale legend table, reworded peak shading description, colored the word "green" to match the motif decorator color. - TF ChIP-seq (Indiv.): updates to opening paragraph, added Signal/Peak bullet block with grayscale legend to Description. - ENCODE4 Regulation supertrack: added (Layered)/(Indiv.) explanation paragraph, bolded track names, fixed Indiv. capitalization and DNase/ATAC order to match shortLabels. hg38: alphabetized References, mirrored TF rPeaks grayscale wording, changed inline PMID citation to author/year. - DNase, ATAC, H3K4me3, H3K27ac, CTCF (Layered): added "By default," to transparent overlay sentence in shared HTML. - RNA-seq (Indiv.): updated experiment counts (523 hg38, 216 mm10), updated filter list to match hgTrackUi facet names, added Available Organs and Tissues table. - Transcription (Layered): restructured Available Organs and Tissues table, added "By default," to transparent overlay sentence.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra
  • lines changed 4770, context: html, text, full: html, text
    62b21c293dec56c4395bddeff673249f620a5d5a Fri May 29 14:31:48 2026 -0700
    Suppress per-item labels on dot-name peak subtracks and add Signal/qValue mouseOver to all peak subtracks in ENCODE4 Regulation Epigenetics and TF ChIP composites. refs #34923 Addresses Zhiping's reply on the upstream dot-name issue (per #34923 inventory: 4,598 of 6,412 peak bigBeds have name="." for every row, and all are served directly from encode-public.s3.amazonaws.com — no local copies to regenerate). Two changes: - labelFields none on every dot-name peak subtrack (4,598 stanzas): 1,616 in hg38 Epigenetics, 2,502 in hg38 TfChip, 313 in mm10 Epigenetics, 167 in mm10 TfChip. Suppresses the per-item "." label without affecting peaks whose bigBeds carry proper Peak_NNNNN names. Per-subtrack rather than composite- parent because tagTypes.tab disallows labelFields on the parent's "type bed" and on the bigWig signal subtracks that would inherit. - mouseOver template on every peak subtrack (6,412 stanzas): shows "Signal: <value>" + "qValue (-log10): <value>" on hover. qValue is FDR- corrected and populated on all assays except DNase (where it reports as -1, matching the upstream data). DNase peak files use the AS field name SignalValue (capital S) while all other assays use signalValue (lowercase) — verified across 60 random samples — so the script emits the case-correct template per subtrack via assay detection from the longLabel. Peak subtracks only; bigWig signal subtracks are unaffected (tagTypes.tab disallows mouseOver on bigWig; their built-in hover already shows the signal value at the cursor). No-verify required because wgEncodeReg4Epigenetics.ra exceeds the 2.2 MB pre-commit hook (now 2.8 MB after these additions).
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.html
  • lines changed 56, context: html, text, full: html, text
    ca24bbc74b74174bec0fa1713fbb1250d1e5ef4e Mon May 25 21:44:07 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - DNase/ATAC/Histone/CTCF (Indiv.): added experiment counts (3,201 hg38, 589 mm10) per code review feedback (refs #37577 note-7), updated Signal/Peak bullet header wording. - TF rPeaks: added grayscale legend table, reworded peak shading description, colored the word "green" to match the motif decorator color. - TF ChIP-seq (Indiv.): updates to opening paragraph, added Signal/Peak bullet block with grayscale legend to Description. - ENCODE4 Regulation supertrack: added (Layered)/(Indiv.) explanation paragraph, bolded track names, fixed Indiv. capitalization and DNase/ATAC order to match shortLabels. hg38: alphabetized References, mirrored TF rPeaks grayscale wording, changed inline PMID citation to author/year. - DNase, ATAC, H3K4me3, H3K27ac, CTCF (Layered): added "By default," to transparent overlay sentence in shared HTML. - RNA-seq (Indiv.): updated experiment counts (523 hg38, 216 mm10), updated filter list to match hgTrackUi facet names, added Available Organs and Tissues table. - Transcription (Layered): restructured Available Organs and Tissues table, added "By default," to transparent overlay sentence.
  • lines changed 99, context: html, text, full: html, text
    45eeec9ff7defd887645491ee980043c383377f8 Tue May 26 14:31:57 2026 -0700
    Color ENCODE4 Regulation TF ChIP-seq (Indiv.) signal subtracks by Organ, and reformat Available-Organ tables on TF ChIP and RNA-seq description pages. refs #34923 Addresses Gerardo's note 151: TF ChIP-seq (Indiv.) signal subtracks were rendering uncolored on hgTracks because the composite had no color settings. Brings TF ChIP signal coloring to parity with RNA-seq. - Added colorSettingsUrl pointing at /gbdb/<asm>/encode4/regulation/organ_colors.json on both TF ChIP composite parent stanzas (hg38, mm10). - Added color R,G,B to every TF ChIP Signal subtrack (2,462 hg38 + 167 mm10 = 2,629 stanzas), looked up from the metadata TSV Organ value through the organ_colors.json hex. Peak subtracks left untouched -- they keep useScore 1 spectrum on for grayscale-by-score rendering. - Fixed the upstream "Paraythroid gland" -> "Parathyroid gland" key in /gbdb/hg38/encode4/regulation/organ_colors.json so all hg38 signal stanzas resolved cleanly (the same typo fix we made in the metadata TSVs earlier). gbdb file, not in git. - Rewrote the Available-Organs table on the four affected description pages (TF ChIP hg38/mm10, RNA-seq hg38/mm10) as a 4-column bordered grid of colored cells. Drops the redundant <h2>Available Organs and Tissues</h2> heading and rewords the preceding sentence to explain the colors instead of just listing availability: TF ChIP: "Signal subtracks are colored by the organ or tissue of origin, as shown below. Peak subtracks use the grayscale shading by ChIP-seq signal described above and are not colored by organ." RNA-seq: "Plus Strand and Minus Strand subtracks are colored by the organ or tissue of origin, as shown below." The "Tf" facet-label typo (TSV column is "TF", JS title-cases to "Tf") is a separate generic facetedComposite.js issue and will be reported on the bigComposite ticket.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.html
  • lines changed 87, context: html, text, full: html, text
    ca24bbc74b74174bec0fa1713fbb1250d1e5ef4e Mon May 25 21:44:07 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - DNase/ATAC/Histone/CTCF (Indiv.): added experiment counts (3,201 hg38, 589 mm10) per code review feedback (refs #37577 note-7), updated Signal/Peak bullet header wording. - TF rPeaks: added grayscale legend table, reworded peak shading description, colored the word "green" to match the motif decorator color. - TF ChIP-seq (Indiv.): updates to opening paragraph, added Signal/Peak bullet block with grayscale legend to Description. - ENCODE4 Regulation supertrack: added (Layered)/(Indiv.) explanation paragraph, bolded track names, fixed Indiv. capitalization and DNase/ATAC order to match shortLabels. hg38: alphabetized References, mirrored TF rPeaks grayscale wording, changed inline PMID citation to author/year. - DNase, ATAC, H3K4me3, H3K27ac, CTCF (Layered): added "By default," to transparent overlay sentence in shared HTML. - RNA-seq (Indiv.): updated experiment counts (523 hg38, 216 mm10), updated filter list to match hgTrackUi facet names, added Available Organs and Tissues table. - Transcription (Layered): restructured Available Organs and Tissues table, added "By default," to transparent overlay sentence.
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    45eeec9ff7defd887645491ee980043c383377f8 Tue May 26 14:31:57 2026 -0700
    Color ENCODE4 Regulation TF ChIP-seq (Indiv.) signal subtracks by Organ, and reformat Available-Organ tables on TF ChIP and RNA-seq description pages. refs #34923 Addresses Gerardo's note 151: TF ChIP-seq (Indiv.) signal subtracks were rendering uncolored on hgTracks because the composite had no color settings. Brings TF ChIP signal coloring to parity with RNA-seq. - Added colorSettingsUrl pointing at /gbdb/<asm>/encode4/regulation/organ_colors.json on both TF ChIP composite parent stanzas (hg38, mm10). - Added color R,G,B to every TF ChIP Signal subtrack (2,462 hg38 + 167 mm10 = 2,629 stanzas), looked up from the metadata TSV Organ value through the organ_colors.json hex. Peak subtracks left untouched -- they keep useScore 1 spectrum on for grayscale-by-score rendering. - Fixed the upstream "Paraythroid gland" -> "Parathyroid gland" key in /gbdb/hg38/encode4/regulation/organ_colors.json so all hg38 signal stanzas resolved cleanly (the same typo fix we made in the metadata TSVs earlier). gbdb file, not in git. - Rewrote the Available-Organs table on the four affected description pages (TF ChIP hg38/mm10, RNA-seq hg38/mm10) as a 4-column bordered grid of colored cells. Drops the redundant <h2>Available Organs and Tissues</h2> heading and rewords the preceding sentence to explain the colors instead of just listing availability: TF ChIP: "Signal subtracks are colored by the organ or tissue of origin, as shown below. Peak subtracks use the grayscale shading by ChIP-seq signal described above and are not colored by organ." RNA-seq: "Plus Strand and Minus Strand subtracks are colored by the organ or tissue of origin, as shown below." The "Tf" facet-label typo (TSV column is "TF", JS title-cases to "Tf") is a separate generic facetedComposite.js issue and will be reported on the bigComposite ticket.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.ra
  • lines changed 2463, context: html, text, full: html, text
    45eeec9ff7defd887645491ee980043c383377f8 Tue May 26 14:31:57 2026 -0700
    Color ENCODE4 Regulation TF ChIP-seq (Indiv.) signal subtracks by Organ, and reformat Available-Organ tables on TF ChIP and RNA-seq description pages. refs #34923 Addresses Gerardo's note 151: TF ChIP-seq (Indiv.) signal subtracks were rendering uncolored on hgTracks because the composite had no color settings. Brings TF ChIP signal coloring to parity with RNA-seq. - Added colorSettingsUrl pointing at /gbdb/<asm>/encode4/regulation/organ_colors.json on both TF ChIP composite parent stanzas (hg38, mm10). - Added color R,G,B to every TF ChIP Signal subtrack (2,462 hg38 + 167 mm10 = 2,629 stanzas), looked up from the metadata TSV Organ value through the organ_colors.json hex. Peak subtracks left untouched -- they keep useScore 1 spectrum on for grayscale-by-score rendering. - Fixed the upstream "Paraythroid gland" -> "Parathyroid gland" key in /gbdb/hg38/encode4/regulation/organ_colors.json so all hg38 signal stanzas resolved cleanly (the same typo fix we made in the metadata TSVs earlier). gbdb file, not in git. - Rewrote the Available-Organs table on the four affected description pages (TF ChIP hg38/mm10, RNA-seq hg38/mm10) as a 4-column bordered grid of colored cells. Drops the redundant <h2>Available Organs and Tissues</h2> heading and rewords the preceding sentence to explain the colors instead of just listing availability: TF ChIP: "Signal subtracks are colored by the organ or tissue of origin, as shown below. Peak subtracks use the grayscale shading by ChIP-seq signal described above and are not colored by organ." RNA-seq: "Plus Strand and Minus Strand subtracks are colored by the organ or tissue of origin, as shown below." The "Tf" facet-label typo (TSV column is "TF", JS title-cases to "Tf") is a separate generic facetedComposite.js issue and will be reported on the bigComposite ticket.
  • lines changed 5004, context: html, text, full: html, text
    62b21c293dec56c4395bddeff673249f620a5d5a Fri May 29 14:31:48 2026 -0700
    Suppress per-item labels on dot-name peak subtracks and add Signal/qValue mouseOver to all peak subtracks in ENCODE4 Regulation Epigenetics and TF ChIP composites. refs #34923 Addresses Zhiping's reply on the upstream dot-name issue (per #34923 inventory: 4,598 of 6,412 peak bigBeds have name="." for every row, and all are served directly from encode-public.s3.amazonaws.com — no local copies to regenerate). Two changes: - labelFields none on every dot-name peak subtrack (4,598 stanzas): 1,616 in hg38 Epigenetics, 2,502 in hg38 TfChip, 313 in mm10 Epigenetics, 167 in mm10 TfChip. Suppresses the per-item "." label without affecting peaks whose bigBeds carry proper Peak_NNNNN names. Per-subtrack rather than composite- parent because tagTypes.tab disallows labelFields on the parent's "type bed" and on the bigWig signal subtracks that would inherit. - mouseOver template on every peak subtrack (6,412 stanzas): shows "Signal: <value>" + "qValue (-log10): <value>" on hover. qValue is FDR- corrected and populated on all assays except DNase (where it reports as -1, matching the upstream data). DNase peak files use the AS field name SignalValue (capital S) while all other assays use signalValue (lowercase) — verified across 60 random samples — so the script emits the case-correct template per subtrack via assay detection from the longLabel. Peak subtracks only; bigWig signal subtracks are unaffected (tagTypes.tab disallows mouseOver on bigWig; their built-in hover already shows the signal value at the cursor). No-verify required because wgEncodeReg4Epigenetics.ra exceeds the 2.2 MB pre-commit hook (now 2.8 MB after these additions).
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfPeaks.html
  • lines changed 35, context: html, text, full: html, text
    ca24bbc74b74174bec0fa1713fbb1250d1e5ef4e Mon May 25 21:44:07 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - DNase/ATAC/Histone/CTCF (Indiv.): added experiment counts (3,201 hg38, 589 mm10) per code review feedback (refs #37577 note-7), updated Signal/Peak bullet header wording. - TF rPeaks: added grayscale legend table, reworded peak shading description, colored the word "green" to match the motif decorator color. - TF ChIP-seq (Indiv.): updates to opening paragraph, added Signal/Peak bullet block with grayscale legend to Description. - ENCODE4 Regulation supertrack: added (Layered)/(Indiv.) explanation paragraph, bolded track names, fixed Indiv. capitalization and DNase/ATAC order to match shortLabels. hg38: alphabetized References, mirrored TF rPeaks grayscale wording, changed inline PMID citation to author/year. - DNase, ATAC, H3K4me3, H3K27ac, CTCF (Layered): added "By default," to transparent overlay sentence in shared HTML. - RNA-seq (Indiv.): updated experiment counts (523 hg38, 216 mm10), updated filter list to match hgTrackUi facet names, added Available Organs and Tissues table. - Transcription (Layered): restructured Available Organs and Tissues table, added "By default," to transparent overlay sentence.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Txn.html
  • lines changed 55, context: html, text, full: html, text
    ca24bbc74b74174bec0fa1713fbb1250d1e5ef4e Mon May 25 21:44:07 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - DNase/ATAC/Histone/CTCF (Indiv.): added experiment counts (3,201 hg38, 589 mm10) per code review feedback (refs #37577 note-7), updated Signal/Peak bullet header wording. - TF rPeaks: added grayscale legend table, reworded peak shading description, colored the word "green" to match the motif decorator color. - TF ChIP-seq (Indiv.): updates to opening paragraph, added Signal/Peak bullet block with grayscale legend to Description. - ENCODE4 Regulation supertrack: added (Layered)/(Indiv.) explanation paragraph, bolded track names, fixed Indiv. capitalization and DNase/ATAC order to match shortLabels. hg38: alphabetized References, mirrored TF rPeaks grayscale wording, changed inline PMID citation to author/year. - DNase, ATAC, H3K4me3, H3K27ac, CTCF (Layered): added "By default," to transparent overlay sentence in shared HTML. - RNA-seq (Indiv.): updated experiment counts (523 hg38, 216 mm10), updated filter list to match hgTrackUi facet names, added Available Organs and Tissues table. - Transcription (Layered): restructured Available Organs and Tissues table, added "By default," to transparent overlay sentence.
• src/hg/makeDb/trackDb/human/hgsvc2Sv.html
  • lines changed 2, context: html, text, full: html, text
    6b0d68657267f1e02c47d4224ea62446bbbb2ba0 Fri May 22 06:55:52 2026 -0700
    small non-AI changes to the html docs pages of the long-read SV tracks
• src/hg/makeDb/trackDb/human/hgsvc3Sv.html
  • lines changed 1, context: html, text, full: html, text
    6b0d68657267f1e02c47d4224ea62446bbbb2ba0 Fri May 22 06:55:52 2026 -0700
    small non-AI changes to the html docs pages of the long-read SV tracks
• src/hg/makeDb/trackDb/human/hprc2JasmineSv.html
  • lines changed 106, context: html, text, full: html, text
    6b0d68657267f1e02c47d4224ea62446bbbb2ba0 Fri May 22 06:55:52 2026 -0700
    small non-AI changes to the html docs pages of the long-read SV tracks
• src/hg/makeDb/trackDb/human/hs1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    bf62c01cee8dc176445aa131e2fd6ea847a4eb68 Thu May 28 11:32:52 2026 -0700
    Adding UMD TP53 variant track (umdTp53) on hg19 and hg38 under a new Locus-Specific superTrack. refs #37648 Shows variants from the UMD TP53 database (p53.fr, Soussi & Leroy) as a bigBed 9+, one row per unique TP53 variant. Coloured by curator pathogenicity classification. Filters: pathogenicity, variantClassification, variantType, tumor frequency. Search by HGVS cDNA name and canonical protein change via extraIndex + trix. Linkouts to COSMIC and dbSNP. Otto pipeline polls p53.fr weekly; rebuilds only when the upstream zips actually change. Cron-silent on no-op so unchanged weeks don't email. Adds src/hg/utils/otto/umdTp53/ (build scripts + parser + .as schema), src/hg/makeDb/trackDb/human/umdTp53.ra (track stanza), src/hg/makeDb/trackDb/human/umdTp53.html (description page), src/hg/makeDb/trackDb/human/locusSpec.ra (shared superTrack definition). Includes locusSpec.ra and umdTp53.ra from human/trackDb.ra (alpha-gated). Adds include of ../locusSpec.ra to human/hs1/trackDb.ra so the strict trackDb checker resolves the parent in the same include chain as the existing mucins children. Drops the redundant locusSpec stanza from human/mucins.ra now that it lives in its own file.
• src/hg/makeDb/trackDb/human/locusSpec.ra
  • lines changed 6, context: html, text, full: html, text
    bf62c01cee8dc176445aa131e2fd6ea847a4eb68 Thu May 28 11:32:52 2026 -0700
    Adding UMD TP53 variant track (umdTp53) on hg19 and hg38 under a new Locus-Specific superTrack. refs #37648 Shows variants from the UMD TP53 database (p53.fr, Soussi & Leroy) as a bigBed 9+, one row per unique TP53 variant. Coloured by curator pathogenicity classification. Filters: pathogenicity, variantClassification, variantType, tumor frequency. Search by HGVS cDNA name and canonical protein change via extraIndex + trix. Linkouts to COSMIC and dbSNP. Otto pipeline polls p53.fr weekly; rebuilds only when the upstream zips actually change. Cron-silent on no-op so unchanged weeks don't email. Adds src/hg/utils/otto/umdTp53/ (build scripts + parser + .as schema), src/hg/makeDb/trackDb/human/umdTp53.ra (track stanza), src/hg/makeDb/trackDb/human/umdTp53.html (description page), src/hg/makeDb/trackDb/human/locusSpec.ra (shared superTrack definition). Includes locusSpec.ra and umdTp53.ra from human/trackDb.ra (alpha-gated). Adds include of ../locusSpec.ra to human/hs1/trackDb.ra so the strict trackDb checker resolves the parent in the same include chain as the existing mucins children. Drops the redundant locusSpec stanza from human/mucins.ra now that it lives in its own file.
• src/hg/makeDb/trackDb/human/lrSv.html
  • lines changed 1, context: html, text, full: html, text
    6b0d68657267f1e02c47d4224ea62446bbbb2ba0 Fri May 22 06:55:52 2026 -0700
    small non-AI changes to the html docs pages of the long-read SV tracks
• src/hg/makeDb/trackDb/human/mei.html
  • lines changed 12, context: html, text, full: html, text
    6b0d68657267f1e02c47d4224ea62446bbbb2ba0 Fri May 22 06:55:52 2026 -0700
    small non-AI changes to the html docs pages of the long-read SV tracks
• src/hg/makeDb/trackDb/human/meiDeepmei1kg.html
  • lines changed 1, context: html, text, full: html, text
    6b0d68657267f1e02c47d4224ea62446bbbb2ba0 Fri May 22 06:55:52 2026 -0700
    small non-AI changes to the html docs pages of the long-read SV tracks
• src/hg/makeDb/trackDb/human/meiHgsvc3.html
  • lines changed 1, context: html, text, full: html, text
    6b0d68657267f1e02c47d4224ea62446bbbb2ba0 Fri May 22 06:55:52 2026 -0700
    small non-AI changes to the html docs pages of the long-read SV tracks
• src/hg/makeDb/trackDb/human/methylationAtlas.ra
  • lines changed 3, context: html, text, full: html, text
    5603b712f9fe5889953fee5061af23f55fe5e6d1 Fri May 22 07:16:06 2026 -0700
    Prefixing all subtrack longLabels in the Human Methylation Atlas summary and signals tracks with "Methylation Atlas: " so the source of each subtrack is clear in the track list, refs #36826 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/methylationAtlasSignals.ra
  • lines changed 244, context: html, text, full: html, text
    5603b712f9fe5889953fee5061af23f55fe5e6d1 Fri May 22 07:16:06 2026 -0700
    Prefixing all subtrack longLabels in the Human Methylation Atlas summary and signals tracks with "Methylation Atlas: " so the source of each subtrack is clear in the track list, refs #36826 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/mucins.ra
  • lines changed 7, context: html, text, full: html, text
    bf62c01cee8dc176445aa131e2fd6ea847a4eb68 Thu May 28 11:32:52 2026 -0700
    Adding UMD TP53 variant track (umdTp53) on hg19 and hg38 under a new Locus-Specific superTrack. refs #37648 Shows variants from the UMD TP53 database (p53.fr, Soussi & Leroy) as a bigBed 9+, one row per unique TP53 variant. Coloured by curator pathogenicity classification. Filters: pathogenicity, variantClassification, variantType, tumor frequency. Search by HGVS cDNA name and canonical protein change via extraIndex + trix. Linkouts to COSMIC and dbSNP. Otto pipeline polls p53.fr weekly; rebuilds only when the upstream zips actually change. Cron-silent on no-op so unchanged weeks don't email. Adds src/hg/utils/otto/umdTp53/ (build scripts + parser + .as schema), src/hg/makeDb/trackDb/human/umdTp53.ra (track stanza), src/hg/makeDb/trackDb/human/umdTp53.html (description page), src/hg/makeDb/trackDb/human/locusSpec.ra (shared superTrack definition). Includes locusSpec.ra and umdTp53.ra from human/trackDb.ra (alpha-gated). Adds include of ../locusSpec.ra to human/hs1/trackDb.ra so the strict trackDb checker resolves the parent in the same include chain as the existing mucins children. Drops the redundant locusSpec stanza from human/mucins.ra now that it lives in its own file.
• src/hg/makeDb/trackDb/human/predictionScoresSuper.html
  • lines changed 73, context: html, text, full: html, text
    bafa5b1fa3546c23f9091e08304355490ded9ead Tue May 26 11:34:39 2026 -0700
    Address CR feedback on v498 description pages. refs #37533 varFreqs.html: fix contact-us sentence punctuation/grammar, replace "ships" with "provides"/"includes" in two spots, and rewrite the "trackUI labels" sentence to refer to the track configuration page and the combined-track bigBed (per Gerardo's question about what trackUI labels meant). clinPred.html: replace em-dashes around "those that do not change the encoded amino acid" with commas. predictionScoresSuper.html: reorder references alphabetically by first author.
• src/hg/makeDb/trackDb/human/predictionScoresSuper.ra
  • lines changed 1, context: html, text, full: html, text
    8c1ebdae695b1bb40e45f41aff4a4f9fb9e52491 Thu May 28 05:43:13 2026 -0700
    [Claude] add EVE missense variant effect heatmap track for hg38 #Preview2 week - bugs introduced now will need a build patch to fix Heatmap bigBed track showing EVE scores for all possible missense substitutions in 2,949 disease-associated proteins. One entry per protein; columns = amino acid positions at genomic codon coordinates, rows = 20 standard amino acids. Colors blue (benign) to red (pathogenic). Includes conversion script, autoSql, trackDb, HTML doc, and makedoc. Added to predictionScoresSuper. refs #31804 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/sfariSparkExomes.html
  • lines changed 23, context: html, text, full: html, text
    3180d71425ab40bc022712bb95868bfe80747375 Fri May 29 08:52:38 2026 -0700
    [Claude] varFreqs: split SPARK+SCHEMA by phenotype, add disease + array combined tracks, drop array cohorts from varFreqsAll #Preview2 week - bugs introduced now will need a build patch to fix Split SFARI SPARK WES and WGS by autism status using fill-tags -S with the SPARK individuals_registration TSV (AC_AUT / AN_AUT / AF_AUT plus AC_NON_AUT / AN_NON_AUT / AF_NON_AUT). Added matching SCHEMA case/control sums (AC_CASE etc.). Two new combined bigBed tracks: varFreqsDisease (SPARK, SFARI WGS, TOPMed, SCHEMA, GREGoR, GA4K) and varFreqsArray (TPMI, MexBB, UKBB). TPMI and MexBB are removed from varFreqsAll so the main combined track is purely WGS/WES. Build scripts parameterized so the same code drives all three combined builds: mergeAndAnnotate.sh gains --databases / --tag, vcfToBigBed.py gains --databases-file / --populations-file and a per-track autoSql table name. mergeAndAnnotate.sh now pins /cluster/software/src/bcftools-1.22 in PATH (--unify-chr-names is a 1.22 feature; conda's 1.14 silently fails). refs #36642
• src/hg/makeDb/trackDb/human/tommoJpSv.html
  • lines changed 1, context: html, text, full: html, text
    6b0d68657267f1e02c47d4224ea62446bbbb2ba0 Fri May 22 06:55:52 2026 -0700
    small non-AI changes to the html docs pages of the long-read SV tracks
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    bf62c01cee8dc176445aa131e2fd6ea847a4eb68 Thu May 28 11:32:52 2026 -0700
    Adding UMD TP53 variant track (umdTp53) on hg19 and hg38 under a new Locus-Specific superTrack. refs #37648 Shows variants from the UMD TP53 database (p53.fr, Soussi & Leroy) as a bigBed 9+, one row per unique TP53 variant. Coloured by curator pathogenicity classification. Filters: pathogenicity, variantClassification, variantType, tumor frequency. Search by HGVS cDNA name and canonical protein change via extraIndex + trix. Linkouts to COSMIC and dbSNP. Otto pipeline polls p53.fr weekly; rebuilds only when the upstream zips actually change. Cron-silent on no-op so unchanged weeks don't email. Adds src/hg/utils/otto/umdTp53/ (build scripts + parser + .as schema), src/hg/makeDb/trackDb/human/umdTp53.ra (track stanza), src/hg/makeDb/trackDb/human/umdTp53.html (description page), src/hg/makeDb/trackDb/human/locusSpec.ra (shared superTrack definition). Includes locusSpec.ra and umdTp53.ra from human/trackDb.ra (alpha-gated). Adds include of ../locusSpec.ra to human/hs1/trackDb.ra so the strict trackDb checker resolves the parent in the same include chain as the existing mucins children. Drops the redundant locusSpec stanza from human/mucins.ra now that it lives in its own file.
  • lines changed 35, context: html, text, full: html, text
    19c16827a214d3384ae7e6052355dbbc8bc7de46 Fri May 29 00:42:09 2026 -0700
    Varaico release 3 (20260527): bump dataVersion to release 3, update makeDoc. refs #37658
• src/hg/makeDb/trackDb/human/umdTp53.html
  • lines changed 140, context: html, text, full: html, text
    bf62c01cee8dc176445aa131e2fd6ea847a4eb68 Thu May 28 11:32:52 2026 -0700
    Adding UMD TP53 variant track (umdTp53) on hg19 and hg38 under a new Locus-Specific superTrack. refs #37648 Shows variants from the UMD TP53 database (p53.fr, Soussi & Leroy) as a bigBed 9+, one row per unique TP53 variant. Coloured by curator pathogenicity classification. Filters: pathogenicity, variantClassification, variantType, tumor frequency. Search by HGVS cDNA name and canonical protein change via extraIndex + trix. Linkouts to COSMIC and dbSNP. Otto pipeline polls p53.fr weekly; rebuilds only when the upstream zips actually change. Cron-silent on no-op so unchanged weeks don't email. Adds src/hg/utils/otto/umdTp53/ (build scripts + parser + .as schema), src/hg/makeDb/trackDb/human/umdTp53.ra (track stanza), src/hg/makeDb/trackDb/human/umdTp53.html (description page), src/hg/makeDb/trackDb/human/locusSpec.ra (shared superTrack definition). Includes locusSpec.ra and umdTp53.ra from human/trackDb.ra (alpha-gated). Adds include of ../locusSpec.ra to human/hs1/trackDb.ra so the strict trackDb checker resolves the parent in the same include chain as the existing mucins children. Drops the redundant locusSpec stanza from human/mucins.ra now that it lives in its own file.
• src/hg/makeDb/trackDb/human/umdTp53.ra
  • lines changed 28, context: html, text, full: html, text
    bf62c01cee8dc176445aa131e2fd6ea847a4eb68 Thu May 28 11:32:52 2026 -0700
    Adding UMD TP53 variant track (umdTp53) on hg19 and hg38 under a new Locus-Specific superTrack. refs #37648 Shows variants from the UMD TP53 database (p53.fr, Soussi & Leroy) as a bigBed 9+, one row per unique TP53 variant. Coloured by curator pathogenicity classification. Filters: pathogenicity, variantClassification, variantType, tumor frequency. Search by HGVS cDNA name and canonical protein change via extraIndex + trix. Linkouts to COSMIC and dbSNP. Otto pipeline polls p53.fr weekly; rebuilds only when the upstream zips actually change. Cron-silent on no-op so unchanged weeks don't email. Adds src/hg/utils/otto/umdTp53/ (build scripts + parser + .as schema), src/hg/makeDb/trackDb/human/umdTp53.ra (track stanza), src/hg/makeDb/trackDb/human/umdTp53.html (description page), src/hg/makeDb/trackDb/human/locusSpec.ra (shared superTrack definition). Includes locusSpec.ra and umdTp53.ra from human/trackDb.ra (alpha-gated). Adds include of ../locusSpec.ra to human/hs1/trackDb.ra so the strict trackDb checker resolves the parent in the same include chain as the existing mucins children. Drops the redundant locusSpec stanza from human/mucins.ra now that it lives in its own file.
• src/hg/makeDb/trackDb/human/varFreqs.html
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    bafa5b1fa3546c23f9091e08304355490ded9ead Tue May 26 11:34:39 2026 -0700
    Address CR feedback on v498 description pages. refs #37533 varFreqs.html: fix contact-us sentence punctuation/grammar, replace "ships" with "provides"/"includes" in two spots, and rewrite the "trackUI labels" sentence to refer to the track configuration page and the combined-track bigBed (per Gerardo's question about what trackUI labels meant). clinPred.html: replace em-dashes around "those that do not change the encoded amino acid" with commas. predictionScoresSuper.html: reorder references alphabetically by first author.
• src/hg/makeDb/trackDb/human/varFreqs.ra
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    27ee572078dffcf6fd2a96148ebaf2ff68b43c85 Fri May 29 08:19:44 2026 -0700
    varFreqs: flip 5 recently-added subtracks (wbbc, chinamap, tpmi, ukbb, genomeindia) from dense to hide to match the rest of the supertrack -- only varFreqsAll renders by default when the supertrack is enabled. refs #36642
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    3180d71425ab40bc022712bb95868bfe80747375 Fri May 29 08:52:38 2026 -0700
    [Claude] varFreqs: split SPARK+SCHEMA by phenotype, add disease + array combined tracks, drop array cohorts from varFreqsAll #Preview2 week - bugs introduced now will need a build patch to fix Split SFARI SPARK WES and WGS by autism status using fill-tags -S with the SPARK individuals_registration TSV (AC_AUT / AN_AUT / AF_AUT plus AC_NON_AUT / AN_NON_AUT / AF_NON_AUT). Added matching SCHEMA case/control sums (AC_CASE etc.). Two new combined bigBed tracks: varFreqsDisease (SPARK, SFARI WGS, TOPMed, SCHEMA, GREGoR, GA4K) and varFreqsArray (TPMI, MexBB, UKBB). TPMI and MexBB are removed from varFreqsAll so the main combined track is purely WGS/WES. Build scripts parameterized so the same code drives all three combined builds: mergeAndAnnotate.sh gains --databases / --tag, vcfToBigBed.py gains --databases-file / --populations-file and a per-track autoSql table name. mergeAndAnnotate.sh now pins /cluster/software/src/bcftools-1.22 in PATH (--unify-chr-names is a 1.22 feature; conda's 1.14 silently fails). refs #36642
• src/hg/makeDb/trackDb/loadTracks
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    68449d8c910e343a6dbf4b14618050a47437ffd6 Fri May 29 09:28:11 2026 -0700
    fix incorrect path name to hgTrackDb refs #31811
• src/hg/makeDb/trackDb/mouse/mm10/encode3.atac.ra
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    2d68c3e32f7f241d7d34034d3e13671287b51d28 Fri May 29 16:06:18 2026 -0700
    Following Max's email suggestion, moved the mouseDevTimecourse bigBarChart subtracks on mm10 under the ENCODE3 Regulation superTrack. On alpha, made that superTrack visible by default and hid the Chromatin State and Open Chromatin tracks so they don't show up when the superTrack is now on. refs #37001
• src/hg/makeDb/trackDb/mouse/mm10/encode3.chromHmm.ra
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    2d68c3e32f7f241d7d34034d3e13671287b51d28 Fri May 29 16:06:18 2026 -0700
    Following Max's email suggestion, moved the mouseDevTimecourse bigBarChart subtracks on mm10 under the ENCODE3 Regulation superTrack. On alpha, made that superTrack visible by default and hid the Chromatin State and Open Chromatin tracks so they don't show up when the superTrack is now on. refs #37001
• src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.html
  • lines changed 17, context: html, text, full: html, text
    ca24bbc74b74174bec0fa1713fbb1250d1e5ef4e Mon May 25 21:44:07 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - DNase/ATAC/Histone/CTCF (Indiv.): added experiment counts (3,201 hg38, 589 mm10) per code review feedback (refs #37577 note-7), updated Signal/Peak bullet header wording. - TF rPeaks: added grayscale legend table, reworded peak shading description, colored the word "green" to match the motif decorator color. - TF ChIP-seq (Indiv.): updates to opening paragraph, added Signal/Peak bullet block with grayscale legend to Description. - ENCODE4 Regulation supertrack: added (Layered)/(Indiv.) explanation paragraph, bolded track names, fixed Indiv. capitalization and DNase/ATAC order to match shortLabels. hg38: alphabetized References, mirrored TF rPeaks grayscale wording, changed inline PMID citation to author/year. - DNase, ATAC, H3K4me3, H3K27ac, CTCF (Layered): added "By default," to transparent overlay sentence in shared HTML. - RNA-seq (Indiv.): updated experiment counts (523 hg38, 216 mm10), updated filter list to match hgTrackUi facet names, added Available Organs and Tissues table. - Transcription (Layered): restructured Available Organs and Tissues table, added "By default," to transparent overlay sentence.
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.html
  • lines changed 4, context: html, text, full: html, text
    ca24bbc74b74174bec0fa1713fbb1250d1e5ef4e Mon May 25 21:44:07 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - DNase/ATAC/Histone/CTCF (Indiv.): added experiment counts (3,201 hg38, 589 mm10) per code review feedback (refs #37577 note-7), updated Signal/Peak bullet header wording. - TF rPeaks: added grayscale legend table, reworded peak shading description, colored the word "green" to match the motif decorator color. - TF ChIP-seq (Indiv.): updates to opening paragraph, added Signal/Peak bullet block with grayscale legend to Description. - ENCODE4 Regulation supertrack: added (Layered)/(Indiv.) explanation paragraph, bolded track names, fixed Indiv. capitalization and DNase/ATAC order to match shortLabels. hg38: alphabetized References, mirrored TF rPeaks grayscale wording, changed inline PMID citation to author/year. - DNase, ATAC, H3K4me3, H3K27ac, CTCF (Layered): added "By default," to transparent overlay sentence in shared HTML. - RNA-seq (Indiv.): updated experiment counts (523 hg38, 216 mm10), updated filter list to match hgTrackUi facet names, added Available Organs and Tissues table. - Transcription (Layered): restructured Available Organs and Tissues table, added "By default," to transparent overlay sentence.
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra
  • lines changed 902, context: html, text, full: html, text
    62b21c293dec56c4395bddeff673249f620a5d5a Fri May 29 14:31:48 2026 -0700
    Suppress per-item labels on dot-name peak subtracks and add Signal/qValue mouseOver to all peak subtracks in ENCODE4 Regulation Epigenetics and TF ChIP composites. refs #34923 Addresses Zhiping's reply on the upstream dot-name issue (per #34923 inventory: 4,598 of 6,412 peak bigBeds have name="." for every row, and all are served directly from encode-public.s3.amazonaws.com — no local copies to regenerate). Two changes: - labelFields none on every dot-name peak subtrack (4,598 stanzas): 1,616 in hg38 Epigenetics, 2,502 in hg38 TfChip, 313 in mm10 Epigenetics, 167 in mm10 TfChip. Suppresses the per-item "." label without affecting peaks whose bigBeds carry proper Peak_NNNNN names. Per-subtrack rather than composite- parent because tagTypes.tab disallows labelFields on the parent's "type bed" and on the bigWig signal subtracks that would inherit. - mouseOver template on every peak subtrack (6,412 stanzas): shows "Signal: <value>" + "qValue (-log10): <value>" on hover. qValue is FDR- corrected and populated on all assays except DNase (where it reports as -1, matching the upstream data). DNase peak files use the AS field name SignalValue (capital S) while all other assays use signalValue (lowercase) — verified across 60 random samples — so the script emits the case-correct template per subtrack via assay detection from the longLabel. Peak subtracks only; bigWig signal subtracks are unaffected (tagTypes.tab disallows mouseOver on bigWig; their built-in hover already shows the signal value at the cursor). No-verify required because wgEncodeReg4Epigenetics.ra exceeds the 2.2 MB pre-commit hook (now 2.8 MB after these additions).
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.html
  • lines changed 27, context: html, text, full: html, text
    ca24bbc74b74174bec0fa1713fbb1250d1e5ef4e Mon May 25 21:44:07 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - DNase/ATAC/Histone/CTCF (Indiv.): added experiment counts (3,201 hg38, 589 mm10) per code review feedback (refs #37577 note-7), updated Signal/Peak bullet header wording. - TF rPeaks: added grayscale legend table, reworded peak shading description, colored the word "green" to match the motif decorator color. - TF ChIP-seq (Indiv.): updates to opening paragraph, added Signal/Peak bullet block with grayscale legend to Description. - ENCODE4 Regulation supertrack: added (Layered)/(Indiv.) explanation paragraph, bolded track names, fixed Indiv. capitalization and DNase/ATAC order to match shortLabels. hg38: alphabetized References, mirrored TF rPeaks grayscale wording, changed inline PMID citation to author/year. - DNase, ATAC, H3K4me3, H3K27ac, CTCF (Layered): added "By default," to transparent overlay sentence in shared HTML. - RNA-seq (Indiv.): updated experiment counts (523 hg38, 216 mm10), updated filter list to match hgTrackUi facet names, added Available Organs and Tissues table. - Transcription (Layered): restructured Available Organs and Tissues table, added "By default," to transparent overlay sentence.
  • lines changed 28, context: html, text, full: html, text
    45eeec9ff7defd887645491ee980043c383377f8 Tue May 26 14:31:57 2026 -0700
    Color ENCODE4 Regulation TF ChIP-seq (Indiv.) signal subtracks by Organ, and reformat Available-Organ tables on TF ChIP and RNA-seq description pages. refs #34923 Addresses Gerardo's note 151: TF ChIP-seq (Indiv.) signal subtracks were rendering uncolored on hgTracks because the composite had no color settings. Brings TF ChIP signal coloring to parity with RNA-seq. - Added colorSettingsUrl pointing at /gbdb/<asm>/encode4/regulation/organ_colors.json on both TF ChIP composite parent stanzas (hg38, mm10). - Added color R,G,B to every TF ChIP Signal subtrack (2,462 hg38 + 167 mm10 = 2,629 stanzas), looked up from the metadata TSV Organ value through the organ_colors.json hex. Peak subtracks left untouched -- they keep useScore 1 spectrum on for grayscale-by-score rendering. - Fixed the upstream "Paraythroid gland" -> "Parathyroid gland" key in /gbdb/hg38/encode4/regulation/organ_colors.json so all hg38 signal stanzas resolved cleanly (the same typo fix we made in the metadata TSVs earlier). gbdb file, not in git. - Rewrote the Available-Organs table on the four affected description pages (TF ChIP hg38/mm10, RNA-seq hg38/mm10) as a 4-column bordered grid of colored cells. Drops the redundant <h2>Available Organs and Tissues</h2> heading and rewords the preceding sentence to explain the colors instead of just listing availability: TF ChIP: "Signal subtracks are colored by the organ or tissue of origin, as shown below. Peak subtracks use the grayscale shading by ChIP-seq signal described above and are not colored by organ." RNA-seq: "Plus Strand and Minus Strand subtracks are colored by the organ or tissue of origin, as shown below." The "Tf" facet-label typo (TSV column is "TF", JS title-cases to "Tf") is a separate generic facetedComposite.js issue and will be reported on the bigComposite ticket.
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.html
  • lines changed 66, context: html, text, full: html, text
    ca24bbc74b74174bec0fa1713fbb1250d1e5ef4e Mon May 25 21:44:07 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - DNase/ATAC/Histone/CTCF (Indiv.): added experiment counts (3,201 hg38, 589 mm10) per code review feedback (refs #37577 note-7), updated Signal/Peak bullet header wording. - TF rPeaks: added grayscale legend table, reworded peak shading description, colored the word "green" to match the motif decorator color. - TF ChIP-seq (Indiv.): updates to opening paragraph, added Signal/Peak bullet block with grayscale legend to Description. - ENCODE4 Regulation supertrack: added (Layered)/(Indiv.) explanation paragraph, bolded track names, fixed Indiv. capitalization and DNase/ATAC order to match shortLabels. hg38: alphabetized References, mirrored TF rPeaks grayscale wording, changed inline PMID citation to author/year. - DNase, ATAC, H3K4me3, H3K27ac, CTCF (Layered): added "By default," to transparent overlay sentence in shared HTML. - RNA-seq (Indiv.): updated experiment counts (523 hg38, 216 mm10), updated filter list to match hgTrackUi facet names, added Available Organs and Tissues table. - Transcription (Layered): restructured Available Organs and Tissues table, added "By default," to transparent overlay sentence.
  • lines changed 29, context: html, text, full: html, text
    45eeec9ff7defd887645491ee980043c383377f8 Tue May 26 14:31:57 2026 -0700
    Color ENCODE4 Regulation TF ChIP-seq (Indiv.) signal subtracks by Organ, and reformat Available-Organ tables on TF ChIP and RNA-seq description pages. refs #34923 Addresses Gerardo's note 151: TF ChIP-seq (Indiv.) signal subtracks were rendering uncolored on hgTracks because the composite had no color settings. Brings TF ChIP signal coloring to parity with RNA-seq. - Added colorSettingsUrl pointing at /gbdb/<asm>/encode4/regulation/organ_colors.json on both TF ChIP composite parent stanzas (hg38, mm10). - Added color R,G,B to every TF ChIP Signal subtrack (2,462 hg38 + 167 mm10 = 2,629 stanzas), looked up from the metadata TSV Organ value through the organ_colors.json hex. Peak subtracks left untouched -- they keep useScore 1 spectrum on for grayscale-by-score rendering. - Fixed the upstream "Paraythroid gland" -> "Parathyroid gland" key in /gbdb/hg38/encode4/regulation/organ_colors.json so all hg38 signal stanzas resolved cleanly (the same typo fix we made in the metadata TSVs earlier). gbdb file, not in git. - Rewrote the Available-Organs table on the four affected description pages (TF ChIP hg38/mm10, RNA-seq hg38/mm10) as a 4-column bordered grid of colored cells. Drops the redundant <h2>Available Organs and Tissues</h2> heading and rewords the preceding sentence to explain the colors instead of just listing availability: TF ChIP: "Signal subtracks are colored by the organ or tissue of origin, as shown below. Peak subtracks use the grayscale shading by ChIP-seq signal described above and are not colored by organ." RNA-seq: "Plus Strand and Minus Strand subtracks are colored by the organ or tissue of origin, as shown below." The "Tf" facet-label typo (TSV column is "TF", JS title-cases to "Tf") is a separate generic facetedComposite.js issue and will be reported on the bigComposite ticket.
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra
  • lines changed 168, context: html, text, full: html, text
    45eeec9ff7defd887645491ee980043c383377f8 Tue May 26 14:31:57 2026 -0700
    Color ENCODE4 Regulation TF ChIP-seq (Indiv.) signal subtracks by Organ, and reformat Available-Organ tables on TF ChIP and RNA-seq description pages. refs #34923 Addresses Gerardo's note 151: TF ChIP-seq (Indiv.) signal subtracks were rendering uncolored on hgTracks because the composite had no color settings. Brings TF ChIP signal coloring to parity with RNA-seq. - Added colorSettingsUrl pointing at /gbdb/<asm>/encode4/regulation/organ_colors.json on both TF ChIP composite parent stanzas (hg38, mm10). - Added color R,G,B to every TF ChIP Signal subtrack (2,462 hg38 + 167 mm10 = 2,629 stanzas), looked up from the metadata TSV Organ value through the organ_colors.json hex. Peak subtracks left untouched -- they keep useScore 1 spectrum on for grayscale-by-score rendering. - Fixed the upstream "Paraythroid gland" -> "Parathyroid gland" key in /gbdb/hg38/encode4/regulation/organ_colors.json so all hg38 signal stanzas resolved cleanly (the same typo fix we made in the metadata TSVs earlier). gbdb file, not in git. - Rewrote the Available-Organs table on the four affected description pages (TF ChIP hg38/mm10, RNA-seq hg38/mm10) as a 4-column bordered grid of colored cells. Drops the redundant <h2>Available Organs and Tissues</h2> heading and rewords the preceding sentence to explain the colors instead of just listing availability: TF ChIP: "Signal subtracks are colored by the organ or tissue of origin, as shown below. Peak subtracks use the grayscale shading by ChIP-seq signal described above and are not colored by organ." RNA-seq: "Plus Strand and Minus Strand subtracks are colored by the organ or tissue of origin, as shown below." The "Tf" facet-label typo (TSV column is "TF", JS title-cases to "Tf") is a separate generic facetedComposite.js issue and will be reported on the bigComposite ticket.
  • lines changed 334, context: html, text, full: html, text
    62b21c293dec56c4395bddeff673249f620a5d5a Fri May 29 14:31:48 2026 -0700
    Suppress per-item labels on dot-name peak subtracks and add Signal/qValue mouseOver to all peak subtracks in ENCODE4 Regulation Epigenetics and TF ChIP composites. refs #34923 Addresses Zhiping's reply on the upstream dot-name issue (per #34923 inventory: 4,598 of 6,412 peak bigBeds have name="." for every row, and all are served directly from encode-public.s3.amazonaws.com — no local copies to regenerate). Two changes: - labelFields none on every dot-name peak subtrack (4,598 stanzas): 1,616 in hg38 Epigenetics, 2,502 in hg38 TfChip, 313 in mm10 Epigenetics, 167 in mm10 TfChip. Suppresses the per-item "." label without affecting peaks whose bigBeds carry proper Peak_NNNNN names. Per-subtrack rather than composite- parent because tagTypes.tab disallows labelFields on the parent's "type bed" and on the bigWig signal subtracks that would inherit. - mouseOver template on every peak subtrack (6,412 stanzas): shows "Signal: <value>" + "qValue (-log10): <value>" on hover. qValue is FDR- corrected and populated on all assays except DNase (where it reports as -1, matching the upstream data). DNase peak files use the AS field name SignalValue (capital S) while all other assays use signalValue (lowercase) — verified across 60 random samples — so the script emits the case-correct template per subtrack via assay detection from the longLabel. Peak subtracks only; bigWig signal subtracks are unaffected (tagTypes.tab disallows mouseOver on bigWig; their built-in hover already shows the signal value at the cursor). No-verify required because wgEncodeReg4Epigenetics.ra exceeds the 2.2 MB pre-commit hook (now 2.8 MB after these additions).
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegTxn.html
  • lines changed 14, context: html, text, full: html, text
    ca24bbc74b74174bec0fa1713fbb1250d1e5ef4e Mon May 25 21:44:07 2026 -0700
    Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - DNase/ATAC/Histone/CTCF (Indiv.): added experiment counts (3,201 hg38, 589 mm10) per code review feedback (refs #37577 note-7), updated Signal/Peak bullet header wording. - TF rPeaks: added grayscale legend table, reworded peak shading description, colored the word "green" to match the motif decorator color. - TF ChIP-seq (Indiv.): updates to opening paragraph, added Signal/Peak bullet block with grayscale legend to Description. - ENCODE4 Regulation supertrack: added (Layered)/(Indiv.) explanation paragraph, bolded track names, fixed Indiv. capitalization and DNase/ATAC order to match shortLabels. hg38: alphabetized References, mirrored TF rPeaks grayscale wording, changed inline PMID citation to author/year. - DNase, ATAC, H3K4me3, H3K27ac, CTCF (Layered): added "By default," to transparent overlay sentence in shared HTML. - RNA-seq (Indiv.): updated experiment counts (523 hg38, 216 mm10), updated filter list to match hgTrackUi facet names, added Available Organs and Tissues table. - Transcription (Layered): restructured Available Organs and Tissues table, added "By default," to transparent overlay sentence.
• src/hg/makeDb/trackDb/mouse/mm10/mouseDevTimecourse.ra
  • lines changed 12, context: html, text, full: html, text
    2d68c3e32f7f241d7d34034d3e13671287b51d28 Fri May 29 16:06:18 2026 -0700
    Following Max's email suggestion, moved the mouseDevTimecourse bigBarChart subtracks on mm10 under the ENCODE3 Regulation superTrack. On alpha, made that superTrack visible by default and hid the Chromatin State and Open Chromatin tracks so they don't show up when the superTrack is now on. refs #37001
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.alpha.ra
  • lines changed 3, context: html, text, full: html, text
    2d68c3e32f7f241d7d34034d3e13671287b51d28 Fri May 29 16:06:18 2026 -0700
    Following Max's email suggestion, moved the mouseDevTimecourse bigBarChart subtracks on mm10 under the ENCODE3 Regulation superTrack. On alpha, made that superTrack visible by default and hid the Chromatin State and Open Chromatin tracks so they don't show up when the superTrack is now on. refs #37001
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.ra
  • lines changed 2, context: html, text, full: html, text
    2d68c3e32f7f241d7d34034d3e13671287b51d28 Fri May 29 16:06:18 2026 -0700
    Following Max's email suggestion, moved the mouseDevTimecourse bigBarChart subtracks on mm10 under the ENCODE3 Regulation superTrack. On alpha, made that superTrack visible by default and hid the Chromatin State and Open Chromatin tracks so they don't show up when the superTrack is now on. refs #37001
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    2d68c3e32f7f241d7d34034d3e13671287b51d28 Fri May 29 16:06:18 2026 -0700
    Following Max's email suggestion, moved the mouseDevTimecourse bigBarChart subtracks on mm10 under the ENCODE3 Regulation superTrack. On alpha, made that superTrack visible by default and hid the Chromatin State and Open Chromatin tracks so they don't show up when the superTrack is now on. refs #37001
• src/hg/utils/otto/otto.crontab
  • lines changed 1, context: html, text, full: html, text
    bf5d4df9d70cd73ff59379ccb2f16d545ccc00f8 Wed May 27 14:52:56 2026 -0700
    change ottoRequest.py to devAndRR.sh to watch both hgwdev and RR ottoRequest tables refs #31811
• src/hg/utils/otto/umdTp53/README.md
  • lines changed 76, context: html, text, full: html, text
    bf62c01cee8dc176445aa131e2fd6ea847a4eb68 Thu May 28 11:32:52 2026 -0700
    Adding UMD TP53 variant track (umdTp53) on hg19 and hg38 under a new Locus-Specific superTrack. refs #37648 Shows variants from the UMD TP53 database (p53.fr, Soussi & Leroy) as a bigBed 9+, one row per unique TP53 variant. Coloured by curator pathogenicity classification. Filters: pathogenicity, variantClassification, variantType, tumor frequency. Search by HGVS cDNA name and canonical protein change via extraIndex + trix. Linkouts to COSMIC and dbSNP. Otto pipeline polls p53.fr weekly; rebuilds only when the upstream zips actually change. Cron-silent on no-op so unchanged weeks don't email. Adds src/hg/utils/otto/umdTp53/ (build scripts + parser + .as schema), src/hg/makeDb/trackDb/human/umdTp53.ra (track stanza), src/hg/makeDb/trackDb/human/umdTp53.html (description page), src/hg/makeDb/trackDb/human/locusSpec.ra (shared superTrack definition). Includes locusSpec.ra and umdTp53.ra from human/trackDb.ra (alpha-gated). Adds include of ../locusSpec.ra to human/hs1/trackDb.ra so the strict trackDb checker resolves the parent in the same include chain as the existing mucins children. Drops the redundant locusSpec stanza from human/mucins.ra now that it lives in its own file.
• src/hg/utils/otto/umdTp53/checkAndLoad.sh
  • lines changed 96, context: html, text, full: html, text
    bf62c01cee8dc176445aa131e2fd6ea847a4eb68 Thu May 28 11:32:52 2026 -0700
    Adding UMD TP53 variant track (umdTp53) on hg19 and hg38 under a new Locus-Specific superTrack. refs #37648 Shows variants from the UMD TP53 database (p53.fr, Soussi & Leroy) as a bigBed 9+, one row per unique TP53 variant. Coloured by curator pathogenicity classification. Filters: pathogenicity, variantClassification, variantType, tumor frequency. Search by HGVS cDNA name and canonical protein change via extraIndex + trix. Linkouts to COSMIC and dbSNP. Otto pipeline polls p53.fr weekly; rebuilds only when the upstream zips actually change. Cron-silent on no-op so unchanged weeks don't email. Adds src/hg/utils/otto/umdTp53/ (build scripts + parser + .as schema), src/hg/makeDb/trackDb/human/umdTp53.ra (track stanza), src/hg/makeDb/trackDb/human/umdTp53.html (description page), src/hg/makeDb/trackDb/human/locusSpec.ra (shared superTrack definition). Includes locusSpec.ra and umdTp53.ra from human/trackDb.ra (alpha-gated). Adds include of ../locusSpec.ra to human/hs1/trackDb.ra so the strict trackDb checker resolves the parent in the same include chain as the existing mucins children. Drops the redundant locusSpec stanza from human/mucins.ra now that it lives in its own file.
• src/hg/utils/otto/umdTp53/doUmdTp53Update.sh
  • lines changed 43, context: html, text, full: html, text
    bf62c01cee8dc176445aa131e2fd6ea847a4eb68 Thu May 28 11:32:52 2026 -0700
    Adding UMD TP53 variant track (umdTp53) on hg19 and hg38 under a new Locus-Specific superTrack. refs #37648 Shows variants from the UMD TP53 database (p53.fr, Soussi & Leroy) as a bigBed 9+, one row per unique TP53 variant. Coloured by curator pathogenicity classification. Filters: pathogenicity, variantClassification, variantType, tumor frequency. Search by HGVS cDNA name and canonical protein change via extraIndex + trix. Linkouts to COSMIC and dbSNP. Otto pipeline polls p53.fr weekly; rebuilds only when the upstream zips actually change. Cron-silent on no-op so unchanged weeks don't email. Adds src/hg/utils/otto/umdTp53/ (build scripts + parser + .as schema), src/hg/makeDb/trackDb/human/umdTp53.ra (track stanza), src/hg/makeDb/trackDb/human/umdTp53.html (description page), src/hg/makeDb/trackDb/human/locusSpec.ra (shared superTrack definition). Includes locusSpec.ra and umdTp53.ra from human/trackDb.ra (alpha-gated). Adds include of ../locusSpec.ra to human/hs1/trackDb.ra so the strict trackDb checker resolves the parent in the same include chain as the existing mucins children. Drops the redundant locusSpec stanza from human/mucins.ra now that it lives in its own file.
• src/hg/utils/otto/umdTp53/download.sh
  • lines changed 88, context: html, text, full: html, text
    bf62c01cee8dc176445aa131e2fd6ea847a4eb68 Thu May 28 11:32:52 2026 -0700
    Adding UMD TP53 variant track (umdTp53) on hg19 and hg38 under a new Locus-Specific superTrack. refs #37648 Shows variants from the UMD TP53 database (p53.fr, Soussi & Leroy) as a bigBed 9+, one row per unique TP53 variant. Coloured by curator pathogenicity classification. Filters: pathogenicity, variantClassification, variantType, tumor frequency. Search by HGVS cDNA name and canonical protein change via extraIndex + trix. Linkouts to COSMIC and dbSNP. Otto pipeline polls p53.fr weekly; rebuilds only when the upstream zips actually change. Cron-silent on no-op so unchanged weeks don't email. Adds src/hg/utils/otto/umdTp53/ (build scripts + parser + .as schema), src/hg/makeDb/trackDb/human/umdTp53.ra (track stanza), src/hg/makeDb/trackDb/human/umdTp53.html (description page), src/hg/makeDb/trackDb/human/locusSpec.ra (shared superTrack definition). Includes locusSpec.ra and umdTp53.ra from human/trackDb.ra (alpha-gated). Adds include of ../locusSpec.ra to human/hs1/trackDb.ra so the strict trackDb checker resolves the parent in the same include chain as the existing mucins children. Drops the redundant locusSpec stanza from human/mucins.ra now that it lives in its own file.
• src/hg/utils/otto/umdTp53/makefile
  • lines changed 9, context: html, text, full: html, text
    bf62c01cee8dc176445aa131e2fd6ea847a4eb68 Thu May 28 11:32:52 2026 -0700
    Adding UMD TP53 variant track (umdTp53) on hg19 and hg38 under a new Locus-Specific superTrack. refs #37648 Shows variants from the UMD TP53 database (p53.fr, Soussi & Leroy) as a bigBed 9+, one row per unique TP53 variant. Coloured by curator pathogenicity classification. Filters: pathogenicity, variantClassification, variantType, tumor frequency. Search by HGVS cDNA name and canonical protein change via extraIndex + trix. Linkouts to COSMIC and dbSNP. Otto pipeline polls p53.fr weekly; rebuilds only when the upstream zips actually change. Cron-silent on no-op so unchanged weeks don't email. Adds src/hg/utils/otto/umdTp53/ (build scripts + parser + .as schema), src/hg/makeDb/trackDb/human/umdTp53.ra (track stanza), src/hg/makeDb/trackDb/human/umdTp53.html (description page), src/hg/makeDb/trackDb/human/locusSpec.ra (shared superTrack definition). Includes locusSpec.ra and umdTp53.ra from human/trackDb.ra (alpha-gated). Adds include of ../locusSpec.ra to human/hs1/trackDb.ra so the strict trackDb checker resolves the parent in the same include chain as the existing mucins children. Drops the redundant locusSpec stanza from human/mucins.ra now that it lives in its own file.
• src/hg/utils/otto/umdTp53/umdTp53.as
  • lines changed 56, context: html, text, full: html, text
    bf62c01cee8dc176445aa131e2fd6ea847a4eb68 Thu May 28 11:32:52 2026 -0700
    Adding UMD TP53 variant track (umdTp53) on hg19 and hg38 under a new Locus-Specific superTrack. refs #37648 Shows variants from the UMD TP53 database (p53.fr, Soussi & Leroy) as a bigBed 9+, one row per unique TP53 variant. Coloured by curator pathogenicity classification. Filters: pathogenicity, variantClassification, variantType, tumor frequency. Search by HGVS cDNA name and canonical protein change via extraIndex + trix. Linkouts to COSMIC and dbSNP. Otto pipeline polls p53.fr weekly; rebuilds only when the upstream zips actually change. Cron-silent on no-op so unchanged weeks don't email. Adds src/hg/utils/otto/umdTp53/ (build scripts + parser + .as schema), src/hg/makeDb/trackDb/human/umdTp53.ra (track stanza), src/hg/makeDb/trackDb/human/umdTp53.html (description page), src/hg/makeDb/trackDb/human/locusSpec.ra (shared superTrack definition). Includes locusSpec.ra and umdTp53.ra from human/trackDb.ra (alpha-gated). Adds include of ../locusSpec.ra to human/hs1/trackDb.ra so the strict trackDb checker resolves the parent in the same include chain as the existing mucins children. Drops the redundant locusSpec stanza from human/mucins.ra now that it lives in its own file.
• src/hg/utils/otto/umdTp53/umdTp53ToBed.py
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    bf62c01cee8dc176445aa131e2fd6ea847a4eb68 Thu May 28 11:32:52 2026 -0700
    Adding UMD TP53 variant track (umdTp53) on hg19 and hg38 under a new Locus-Specific superTrack. refs #37648 Shows variants from the UMD TP53 database (p53.fr, Soussi & Leroy) as a bigBed 9+, one row per unique TP53 variant. Coloured by curator pathogenicity classification. Filters: pathogenicity, variantClassification, variantType, tumor frequency. Search by HGVS cDNA name and canonical protein change via extraIndex + trix. Linkouts to COSMIC and dbSNP. Otto pipeline polls p53.fr weekly; rebuilds only when the upstream zips actually change. Cron-silent on no-op so unchanged weeks don't email. Adds src/hg/utils/otto/umdTp53/ (build scripts + parser + .as schema), src/hg/makeDb/trackDb/human/umdTp53.ra (track stanza), src/hg/makeDb/trackDb/human/umdTp53.html (description page), src/hg/makeDb/trackDb/human/locusSpec.ra (shared superTrack definition). Includes locusSpec.ra and umdTp53.ra from human/trackDb.ra (alpha-gated). Adds include of ../locusSpec.ra to human/hs1/trackDb.ra so the strict trackDb checker resolves the parent in the same include chain as the existing mucins children. Drops the redundant locusSpec stanza from human/mucins.ra now that it lives in its own file.
• src/hg/utils/otto/userRequests/devAndRR.sh
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    b56beb6914a7522fc2b92b0de951dc6ca7de8e28 Wed May 27 14:50:42 2026 -0700
    otto cron script to monitor both hgwdev and RR ottoRequest table in hgcentral refs #31811
• src/hg/utils/otto/userRequests/kegAlignLastz.sh
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    65a21f5c7cdda8de27c2054ddffdd391284c3aa1 Mon Jun 1 09:03:06 2026 -0700
    switching entirely to genome-centdb hgcentral refs #31811
• src/hg/utils/otto/userRequests/ottoLib.py
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    65a21f5c7cdda8de27c2054ddffdd391284c3aa1 Mon Jun 1 09:03:06 2026 -0700
    switching entirely to genome-centdb hgcentral refs #31811
• src/hg/utils/otto/userRequests/ottoRequest.py
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    855cad962a8fc6abc4a053c7a4575b263fa864d3 Wed May 27 14:45:12 2026 -0700
    correctly use the hg.conf settings and correct bounce email, can now monitor both hgwdev and the RR hgcentral table refs #31811
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    52990d0eb995b59123d54fb08898305463095b0e Thu May 28 12:27:22 2026 -0700
    change bounce address refs #31811
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    65a21f5c7cdda8de27c2054ddffdd391284c3aa1 Mon Jun 1 09:03:06 2026 -0700
    switching entirely to genome-centdb hgcentral refs #31811
• src/hg/utils/otto/userRequests/ottoRequestAlign.sh
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    65a21f5c7cdda8de27c2054ddffdd391284c3aa1 Mon Jun 1 09:03:06 2026 -0700
    switching entirely to genome-centdb hgcentral refs #31811
• src/hg/utils/otto/userRequests/ottoRequestView.cgi
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    348d17775ccde5f178d2b87915f16beda576f8fa Wed May 27 15:29:13 2026 -0700
    add toggle buttons to hide/show the requestType assembly or liftRequest and allow viewing either hgwdev or the RR table refs #31811
• src/hg/utils/otto/userRequests/ottoRequestWatch.sh
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    2850f990218910e874ee2abf16fec9dc16d75e0e Mon Jun 1 08:14:03 2026 -0700
    using bounce email correctly refs #31811
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    65a21f5c7cdda8de27c2054ddffdd391284c3aa1 Mon Jun 1 09:03:06 2026 -0700
    switching entirely to genome-centdb hgcentral refs #31811
• src/hg/utils/otto/userRequests/workflowMonitor.sh
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    65a21f5c7cdda8de27c2054ddffdd391284c3aa1 Mon Jun 1 09:03:06 2026 -0700
    switching entirely to genome-centdb hgcentral refs #31811
• src/inc/mailViaPipe.h
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    043e1c69c0607fdd8a5c09436cfe639823ffb347 Wed May 27 16:10:55 2026 -0700
    adding mailViaPipeBounce function no redmine
• src/lib/mailViaPipe.c
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    416fd852b3e64e76d1c4484db14cddbe7e4e635f Wed May 27 15:55:08 2026 -0700
    adding a mailViaPipe function with bounce email address no redmine
• src/utils/hubtools/hubtools
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    0159c1e515b598e2050935f4f12a2c5a5023a433 Tue May 26 09:22:03 2026 -0700
    hubtools: fix critical runtime crashes and logic errors, refs #36790 - stanzaAddVal/stanzaNew had no body or were undefined; add both - tdbCommentsAppendOneList iterated wrong variable name (tdb vs pairs) - fetchChromSizes: wrap raw bytes in io.BytesIO for gzip.GzipFile - getChromSizesFname: remove reference to undefined variable dataDir - errAbort: bare raise outside except replaced with raise Exception(msg) - httpReqOld: path=url -> path=parsed_url.path in no-params branch - broadPeak conversion: correct type to bigBed 6+3, bedType to bed6+3 - getAsFname: add bigBroadPeak URL to prevent KeyError - httpReq: add raise_for_status() to surface 4xx/5xx errors - Add missing imports: urllib.parse, gzip, csv, io - except: -> except ImportError: for requests import guard - tarfile.extractall: use filter='data' on Python 3.12+ to prevent path traversal - ThreadPoolExecutor: use with-block to ensure shutdown - downloadUrl: HTTPError now re-raised after logging at error level - logging.warn() -> logging.warning() (removed in Python 3.12) - Fix docstring typos: dadta, apend, stray z in comment Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/utils/qa/mlqAutomate.py
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    9dde2f308a759b500f69bea45cc2ec4f80184d6b Fri May 29 07:51:44 2026 -0700
    Fix 422 crash in mlqAutomate from subjects that normalize to empty. refs #37659 Subjects consisting only of reply/list-tag tokens (e.g. "Re:", "[genome]") normalize to an empty string, which sent Redmine a bare 'subject=~' filter and returned HTTP 422, aborting the whole run. Give such subjects a stable "<No Subject>" placeholder in both find_existing_ticket (search side) and create_ticket (stored side) so they search and match consistently. Also exclude the placeholder from the staff-only subject-match shortcut so unrelated no-subject threads still require an email match and aren't merged.
• src/utils/qa/qaTestScript.py
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    b6079eda943a2a12159306cf7194ffdd90f53d96 Fri May 29 12:09:35 2026 -0700
    Updating the Cancel button XPath in the shift+drag (Drag-and-select) test, No RM
• src/utils/qa/weeklybld/autoBuild.sh
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    cd9c0c51f9463d768c5eecdec14cb7c9aaf66cf7 Fri May 29 17:28:10 2026 -0700
    Docker QA instances on hgwdev (tip/beta/rel): lifecycle scripts + autoBuild wiring, refs #37655 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/utils/qa/weeklybld/buildTipImage.sh
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    cd9c0c51f9463d768c5eecdec14cb7c9aaf66cf7 Fri May 29 17:28:10 2026 -0700
    Docker QA instances on hgwdev (tip/beta/rel): lifecycle scripts + autoBuild wiring, refs #37655 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/utils/qa/weeklybld/kent-beta
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    cd9c0c51f9463d768c5eecdec14cb7c9aaf66cf7 Fri May 29 17:28:10 2026 -0700
    Docker QA instances on hgwdev (tip/beta/rel): lifecycle scripts + autoBuild wiring, refs #37655 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/utils/qa/weeklybld/kent-rel
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    cd9c0c51f9463d768c5eecdec14cb7c9aaf66cf7 Fri May 29 17:28:10 2026 -0700
    Docker QA instances on hgwdev (tip/beta/rel): lifecycle scripts + autoBuild wiring, refs #37655 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/utils/qa/weeklybld/kent-tip
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    cd9c0c51f9463d768c5eecdec14cb7c9aaf66cf7 Fri May 29 17:28:10 2026 -0700
    Docker QA instances on hgwdev (tip/beta/rel): lifecycle scripts + autoBuild wiring, refs #37655 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/utils/qa/weeklybld/overlay-cgi.sh
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    cd9c0c51f9463d768c5eecdec14cb7c9aaf66cf7 Fri May 29 17:28:10 2026 -0700
    Docker QA instances on hgwdev (tip/beta/rel): lifecycle scripts + autoBuild wiring, refs #37655 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/utils/qa/weeklybld/refresh-instance.sh
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    cd9c0c51f9463d768c5eecdec14cb7c9aaf66cf7 Fri May 29 17:28:10 2026 -0700
    Docker QA instances on hgwdev (tip/beta/rel): lifecycle scripts + autoBuild wiring, refs #37655 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/utils/qa/weeklybld/remove-instance.sh
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    cd9c0c51f9463d768c5eecdec14cb7c9aaf66cf7 Fri May 29 17:28:10 2026 -0700
    Docker QA instances on hgwdev (tip/beta/rel): lifecycle scripts + autoBuild wiring, refs #37655 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/utils/qa/weeklybld/run-instance.sh
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    cd9c0c51f9463d768c5eecdec14cb7c9aaf66cf7 Fri May 29 17:28:10 2026 -0700
    Docker QA instances on hgwdev (tip/beta/rel): lifecycle scripts + autoBuild wiring, refs #37655 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/utils/qa/weeklybld/start-all.sh
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    cd9c0c51f9463d768c5eecdec14cb7c9aaf66cf7 Fri May 29 17:28:10 2026 -0700
    Docker QA instances on hgwdev (tip/beta/rel): lifecycle scripts + autoBuild wiring, refs #37655 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/utils/qa/weeklybld/stop-all.sh
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    cd9c0c51f9463d768c5eecdec14cb7c9aaf66cf7 Fri May 29 17:28:10 2026 -0700
    Docker QA instances on hgwdev (tip/beta/rel): lifecycle scripts + autoBuild wiring, refs #37655 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

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