Commits for max

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

41fdf8f63b9a1bd2c3a6c3010c0fc0b08bd41495 Tue Apr 28 05:45:32 2026 -0700

• fixing dataversion statement on clinvar, refs #37467
  • src/hg/makeDb/trackDb/human/clinvar.ra - lines changed 1, context: html, text, full: html, text

372ecfec7898a915f75103a1ea64a63f69eda5da Tue Apr 28 06:26:37 2026 -0700

• choriCloneEnds: drop misleading RZPD/DanioKey aliases, link to specific BACPAC library pages The RZPD prefixes (RZPD-1073/DanioKey, RZPD-73/DanioKey Pilot) are local labels from a defunct German genome resource center and aren't used elsewhere; remove from longLabels and the description bullet list. Replace the generic BACPAC home link with direct links to the three relevant library pages (CH73, CH211, CH1073), since the overall libraries.php page is cluttered with discontinued libraries. refs #35059
  • src/hg/makeDb/trackDb/zebrafish/danRer11/choriCloneEnds.html - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer11/choriCloneEnds.ra - lines changed 2, context: html, text, full: html, text

7dae59171ebf9d462438202cc85ae434e8080fe8 Tue Apr 28 06:30:43 2026 -0700

• NMD Escape MANE: dedicated .as for cleaner labelFields dropdown. refs #33737 The MANE bigBed now ships with its own autoSql, so the labelFields dropdown in the track config shows "Gene Symbol", "Gencode Accession (ENST)" and "RefSeq Accession (NM_/NR_)" - the descriptions QA asked for. The shared nmdEscCollapsed.as keeps its generic wording for the Gencode and RefSeq subtracks, where the "transcripts" column holds different accession families and a single hard-coded label would not fit both.
  • src/hg/makeDb/doc/hg38/nmd.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/scripts/nmd/nmdEscManeCollapsed.as - lines changed 16, context: html, text, full: html, text

7ad95a5c42dfbca5fcccf33d5410daf5512af04a Tue Apr 28 12:30:48 2026 -0700

• lrSv: note likely sample overlap across collections (e.g. 1KG in HPRC/CoLoRSdb). refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • src/hg/makeDb/trackDb/human/lrSv.html - lines changed 5, context: html, text, full: html, text

ced625fd01d4a62ad02ed6be998a4d17058524e1 Wed Apr 29 01:08:47 2026 -0700

• update docs for the new MPC score and a warning on hg19. refs #37478
  • src/hg/makeDb/trackDb/human/hg19/gnomadMpc.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/gnomadMpc.html - lines changed 23, context: html, text, full: html, text

33d86ed28182f6dc7903ac522f4d94bf9906274d Wed Apr 29 01:44:21 2026 -0700

• add submit button to superTrack filters, refs #36258
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 9, context: html, text, full: html, text

37a5b97198453bd06cb03d2092cae239f368e84c Wed Apr 29 05:49:14 2026 -0700

• varFreqs: add tishkoff180 subtrack (Fan et al. 2023, 180 indigenous African WGS, hg19 lift) Sites-only SNP VCF with aggregate AC/AF/AN from 180 individuals (15 each from 12 populations across Ethiopia, Tanzania, Cameroon, Botswana), sequenced at >30x on HiSeq X Ten. hg19 calls supplied by the Tishkoff lab (UPenn) and lifted to hg38 with CrossMap. Redistribution is not permitted, so tableBrowser is disabled. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>, refs #36642
  • src/hg/makeDb/doc/hg38/varFreqs.txt - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/tishkoff180.html - lines changed 93, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 16, context: html, text, full: html, text

294e9bf7a3169d3dd8c176fb896cbd0c5066ea22 Thu Apr 30 02:10:35 2026 -0700

• docs updates, refs #35059
  • src/hg/makeDb/trackDb/human/cloneEndSuper.html - lines changed 14, context: html, text, full: html, text

cea47d47e8b2d70f5655d5947669e15d59c079d6 Thu Apr 30 02:59:15 2026 -0700

• committing dbVar nr track, keeping it only on dev, may be useful one day when looking at a CNV and for comparing against the new normal dbVar track
  • src/hg/makeDb/trackDb/human/trackDb.dbVar.ra - lines changed 40, context: html, text, full: html, text

a54f86a21a62394f88021eefccba67f18a4a27e6 Thu Apr 30 05:45:35 2026 -0700

• Adding new "DRACH motif sites" track under rnaMod superTrack on hg38: every occurrence of the m6A consensus motif (DRACH) in MANE Select v1.5 transcripts, projected onto the genome via pslMap. New scripts under makeDb/scripts/rnaMod, makeDoc under makeDb/doc/hg38/rnaMod.txt. Refreshed the parent rnaMod.html. Track is alpha-only (rnaMod.ra is already alpha-included), refs #36613 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • src/hg/makeDb/doc/hg38/rnaMod.txt - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/scripts/rnaMod/drach.as - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/scripts/rnaMod/drachBedToBigBed.py - lines changed 149, context: html, text, full: html, text
  • src/hg/makeDb/scripts/rnaMod/drachFromFasta.py - lines changed 77, context: html, text, full: html, text
  • src/hg/makeDb/scripts/rnaMod/makeDrach.sh - lines changed 91, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/rnaMod.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/rnaMod.ra - lines changed 18, context: html, text, full: html, text

63653eb7f4fcccfedec87fe115ed0a954012c3ad Thu Apr 30 05:46:04 2026 -0700

• Adding new "m6A-Atlas v2 sites" track under rnaMod superTrack on hg38: 427760 high-confidence base-resolution m6A sites compiled by m6A-Atlas v2 (Liang 2024) from 12 detection technologies across 24 cell lines / tissues. Filters on region, technique, cell line, biotype, #techniques, #cell lines. Track lives in its own m6aAtlas.ra file, included alpha-only via trackDb.ra, refs #36613 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • src/hg/makeDb/doc/hg38/rnaMod.txt - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/scripts/rnaMod/m6aAtlas.as - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/scripts/rnaMod/m6aAtlasToBed.py - lines changed 155, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/m6aAtlas.html - lines changed 122, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/m6aAtlas.ra - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/rnaMod.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

9fbdfa3416ffde377072fafd2de44059155c3b44 Thu Apr 30 06:57:35 2026 -0700

• lrSv: add lrSvAll merged track combining all long-read SV subtracks Variants are merged on exact (chrom, start, end, svType, svLen, insLen). Per-database AC columns are stored as strings; "unknown" is used where the source dataset has only placeholder AC values (deCODE, SVatalog 101, 1KG ONT 100). Kim PD Brain is split into affected (PD+ILBD) and healthy (HC) AC columns. Gustafson contributes sampleCount instead of AC. Output: 2,694,871 unique SVs from 3,706,100 input rows across 15 subtracks (27% dedup). The merged track sits as the first subtrack of the lrSv supertrack with filters on sources, svType, svLen, insLen, maxAF/minAF, AC, and sourceCount. The trackDb stanza is generated by the build script directly into human/lrSvAll.ra and pulled in via 'include lrSvAll.ra' from lrSv.ra, so labels in databases.tsv stay the single source of truth. lrSv.html: add a "Disease cases" column to the dataset summary, strip parenthesized internal track names from the section headers, and shorten exact SV counts to ~Nk / ~N.NM in the prose. refs #36642
  • src/hg/makeDb/scripts/lrSv/databases.tsv - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py - lines changed 643, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSv.html - lines changed 68, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSv.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSvAll.ra - lines changed 41, context: html, text, full: html, text

28b0357b2f17050e591d3d21e3fe2511e2ad0b55 Mon May 4 05:50:49 2026 -0700

• hgTrackUi: address #37426 QA feedback - Drop the unconditional bottom Submit button (introduced in 33d86ed) — it duplicated the existing top Submit on composites like refSeqComposite. Gate it on tdbIsSuperTrack so only superTracks get the bottom Submit (the case the original commit was meant to address). - Render the "Reset to defaults" link on superTrack pages too. Wire up the cart-clear path: superTrack children live in tdb->children (slRef), not tdb->subtracks, so cartRemoveAllForTdbAndChildren wouldn't reach them — walk children explicitly. - Filters heading: "Filters " → "Filters:" (matches the "Apply visibility:" / "Show or hide ...:" style elsewhere on the page). - Reword the Filters info tooltip per Gerardo's QA suggestion. refs #37426
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 24, context: html, text, full: html, text

24fece8377dedf184e8e872325ff2af175076552 Mon May 4 05:51:05 2026 -0700

• hui: fix duplicated filter UI on bigGenePred; tighten supertrack filter changes Two issues, both surfaced reviewing #37426: 1. bigGenePred tracks (e.g. openprot) rendered every filterBy/highlightBy <select> twice with the same id. dropdownchecklist.js binds the first instance only, leaving the second copy display:none — users saw filter labels under the second copy with no input fields under them. The duplication was pre-existing (since 7d9e5c172d1b reorganized genePredCfgUi/scoreCfgUi): genePredCfgUi rendered filterBy inline, then for bigGenePred called scoreCfgUi which rendered filterBy again. Skip the inline rendering for bigGenePred and let scoreCfgUi own it; plain genePred (which doesn't reach scoreCfgUi here) is unchanged. 2. Tighten the supertrack filter changes from 66ea6cb4eaf: - cfgBeginBoxAndTitle: revert the title==NULL "emit nothing" branch. The supertrack flow exits scoreCfgUi before reaching this anyway, so the change was only affecting other title==NULL callers like interactUi.c — pure unintended side effect. - numericFiltersShowAll: revert the title==NULL <BR> suppression for the same reason. The supertrack <h3> heading already provides enough separation. - buildFilterBy: tighten the errAbort relaxation. The previous condition (as != NULL && getLabelSetting == NULL) let a typo'd filterValues.<field> on a regular subtrack silently render a useless filter whenever a matching filterLabel.<field> was present. Restrict the relaxation to as==NULL (the supertrack / noData case). Add a warn() before errAbort so hub makers reading the page see an actionable hint, not just an opaque abort. refs #37426
  • src/hg/lib/hui.c - lines changed 31, context: html, text, full: html, text