Commits for lrnassar

v500_base to v501_preview (2026-06-29 to 2026-07-06) v501

5d23e68307f894bdcd024c138adc588591eceaaa Mon Jun 29 12:11:44 2026 -0700

• Polish TAD description pages and bold the track mouseOvers. refs #21599 Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution summary table (track / feature / calling method / resolution), placed at the end of the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra) to the Methods section; sentence-case the "How to use these tracks" heading. mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"), Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability ("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build scripts so regenerated stanzas carry the same formatting.
  • src/hg/makeDb/scripts/tad/buildTads3dgb.py - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/tad/buildTadsEncode.py - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/tad.ra - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/tads.html - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/tad.ra - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/tads.html - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/tads3dgb.ra - lines changed 464, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/tadsEncode.ra - lines changed 117, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/tad.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/tads.html - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/tads3dgb.ra - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/tadsEncode.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/tad.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/tads.html - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/tads3dgb.ra - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/tadsEncode.ra - lines changed 16, context: html, text, full: html, text

9a63ecfed718d4ad0b2c5212c7ad8844c9d23531 Mon Jun 29 14:21:07 2026 -0700

• lrSv: add GitHub source links (makedoc, scripts, trackDb.ra) to all description pages. refs #36258 Per the updated qa-track standard, link the track's UCSC source artifacts on github.com/ucscGenomeBrowser/kent from every lrSv description page: - Add the missing links to the lrSv supertrack page and colorsDbSv. - Backfill the trackDb.ra link (third artifact) across the subtrack pages that already linked the makedoc + scripts dir. lrSv1kLin is left as its placeholder (staged, not released).
  • src/hg/makeDb/trackDb/human/aou1kSv.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/aprSv.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chirmade101Sv.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/colorsDbSv.html - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/cpc1Sv.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/decodeSv.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/ga4kSv.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/gustafsonSv.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/han945Sv.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hgsvc2Sv.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hgsvc3Sv.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hprc2v21Sv.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSv.html - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSv1kgOnt.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSvAll.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/tommoJpSv.html - lines changed 1, context: html, text, full: html, text

fcb3dd044df301a3c0ea4588e1debf7068b00333 Mon Jun 29 15:43:06 2026 -0700

• lrSv: fresh-eyes audit fixes + multi-line HTML mouseOvers on all subtracks. refs #36258 Audit fixes: - lrSv.html summary table: recompute the per-dataset min/median/max SV-length columns from current data (length = max(svLen,insLen)); the old values came from the .ra filter bounds and were off by one in several rows. Fixes the stale lrSvAll Max (190,088,223 -> 57,207,413, left over from before KimPD was dropped from the merge) and the APR row's length convention. - decodeSv.html: align the opening Description to the displayed (deduped) counts (119,453 / 41,216 DEL) instead of the upstream release counts, noting the dedup from the 133,886-record release. - Drop dead svType filter options (CNV/BND/MEI/CTX) that appear in no subtrack, from the lrSv supertrack filterValues.svType and from lrSvAll (both the generated lrSvAll.ra and the lrSvMergeAll.py generator). Reformat the mouseOver of all 16 subtracks to the same multi-line bold-label HTML style as lrSvAll (Var / SV len / Ins len / per-track fields), using each track's existing fields.
  • src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/decodeSv.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSv.html - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSv.ra - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSvAll.ra - lines changed 1, context: html, text, full: html, text

5ad55adbb6a5cc72a393700130584aa87fef2c89 Tue Jun 30 06:15:44 2026 -0700

• varFreqs: add Top 3 source AFs to mouseOvers; audit excludes SGDP and SVatalog. refs #36642 Adds a Top 3 source AFs ranking to the varFreqsAffected and varFreqsBackground mouseOvers. Alongside the pooled allele frequency, the mouseOver now lists the three cohorts/arms with the highest per-source AF, formatted as "Source (AF), Source (AF), Source (AF)". Disease cohorts with phenotype splits carry the arm label (SPARK ASD, SCHEMA case, GREGoR unaffected); population cohorts use the bare key. Per-population sub-ancestries are deliberately excluded so a high sub-pop AF cannot crowd out actual project-level signals. vcfToBigBed.py adds a top_n_source_afs helper, collects per-arm AFs into affected_arm_afs / background_arm_afs, and emits two new fields topAffectedSources and topBackgroundSources. AS schema field count 163 -> 165. An AF-distribution sweep across all 28 source cohorts identified SGDP and SVatalog as encoding allele counts per genotyped individual (small N, AF defaults near 0.5), making their per-source AF unreliable for the ranking. Adds a skip_top_ranking column (col 9) to databases.tsv, set to 1 for SGDP and SVatalog, and gates the per-arm AF append in vcfToBigBed.py on this flag. Both cohorts still contribute to pooled backgroundAC/AN/AF and still appear in backgroundSources; they are only suppressed from the Top 3. Description pages varFreqsAffected.html and varFreqsBackground.html document the ranking; the latter also documents the SGDP/SVatalog exclusion. Build documentation in varFreqs.txt is updated.
  • src/hg/makeDb/doc/hg38/varFreqs.txt - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/databases.tsv - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/vcfToBigBed.py - lines changed 95, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqsAffected.html - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqsBackground.html - lines changed 29, context: html, text, full: html, text

aa5669fe641fb39d7711eb81ec05092d14f267fb Tue Jun 30 15:20:56 2026 -0700

• Adding Cardiomyopathy VCEP track hub build scripts and makedoc. refs #37446 Adds the 12 per-track build scripts under src/hg/makeDb/scripts/cardiomyopathyVCEP/ (gnomAD v4.1 allele frequencies, REVEL, CardioBoost, the hgVai consequence/HGVSp annotation layer, ClinGen EvRepo, ClinVar submitter 506161, Walsh 2019 curations, PM1 clinical-domain hotspots, MYBPC3 PVS1 caveats, Walsh 2017 PS4 odds-ratio track, Atlas PS4 per-variant OR, and the NON-FINAL provisional classifier) plus the build documentation at src/hg/makeDb/doc/Cardiomyopathy.txt. All ACMG thresholds are taken directly from the ClinGen Cardiomyopathy CSpecs (8 genes, affiliation 50002); no thresholds are invented in the build.
  • src/hg/makeDb/doc/Cardiomyopathy.txt - lines changed 502, context: html, text, full: html, text
  • src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPAFfrequencies.py - lines changed 253, context: html, text, full: html, text
  • src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPAnnotate.py - lines changed 189, context: html, text, full: html, text
  • src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPAtlasEF.py - lines changed 460, context: html, text, full: html, text
  • src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPCardioBoost.py - lines changed 136, context: html, text, full: html, text
  • src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPClinDomains.py - lines changed 339, context: html, text, full: html, text
  • src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPClinVar506161.py - lines changed 275, context: html, text, full: html, text
  • src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPEvRepo.py - lines changed 396, context: html, text, full: html, text
  • src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPPVS1.py - lines changed 217, context: html, text, full: html, text
  • src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPProvisionalClass.py - lines changed 554, context: html, text, full: html, text
  • src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPRevel.py - lines changed 188, context: html, text, full: html, text
  • src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPWalsh2019.py - lines changed 354, context: html, text, full: html, text
  • src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPWalshOR.py - lines changed 180, context: html, text, full: html, text

2dda14f9c5394e1d6fa30f3da69e74b8e8b84413 Tue Jun 30 15:34:05 2026 -0700

• Fix panelApp otto crash when reading Ensembl gene locations. The script hardcoded the Ensembl release sub-key (GRch37/82, GRch38/90) when pulling gene coordinates, but PanelApp Australia moved to releases 87/115. Every Australia gene then failed both assembly lookups, leaving the dataframes empty and raising a column-count ValueError. Added an ensemblBuild() helper that selects whichever release key the API returns, and routed all gene/STR coordinate and ensembl_id lookups through it. England (still on 82/90) is unaffected. No RM, refs otto
  • src/hg/utils/otto/panelApp/doPanelApp.py - lines changed 15, context: html, text, full: html, text

aaead1eeb6e454442e1a6c6dcb6a7c41cf3991d6 Tue Jun 30 16:49:27 2026 -0700

• varFreqs: July 1, 2026 release announcement, newsarch + indexNews + pennantIcon. refs #36642 Adds the New SNV Frequencies supertrack release entry to newsarch.html (anchor #070126) and indexNews.html for the upcoming July 1, 2026 release. The newsarch entry features rs4986893, the CYP2C19 East Asian founder stop-gained variant, as the screenshot example. Updates the varFreqs supertrack pennantIcon to point to the new anchor with hover text "Released Jul. 1, 2026".
  • src/hg/htdocs/goldenPath/newsarch.html - lines changed 100, context: html, text, full: html, text
  • src/hg/htdocs/images/snvFrequenciesNewsarch.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/htdocs/indexNews.html - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 1, context: html, text, full: html, text

b99548fc6477e8f2b46f571248147aab27d5766b Tue Jun 30 17:57:20 2026 -0700

• Add popEVE proteome-wide missense deleteriousness track for hg38. refs #37791 New heatmap bigBed track under the Deleteriousness Predictions superTrack, built from the UKBB-trained popEVE v1.1 GRCh38 VCF. One heatmap entry per protein (columns = amino acid positions at codon coordinates, rows = 20 amino acids), colored on a global, cross-gene gradient keyed to the raw popEVE score. Adds the conversion scripts (extractPopEve.py, vcfToPopEveHeatmap.py, popEve_heatmap.as), the makedoc, the trackDb stanza and description page, and gates the track alpha via an include in predictionScoresSuper.ra.
  • src/hg/makeDb/doc/hg38/popEve.txt - lines changed 79, context: html, text, full: html, text
  • src/hg/makeDb/scripts/popEve/extractPopEve.py - lines changed 99, context: html, text, full: html, text
  • src/hg/makeDb/scripts/popEve/popEve_heatmap.as - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/scripts/popEve/vcfToPopEveHeatmap.py - lines changed 268, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/popEve.html - lines changed 181, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/popEve.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/predictionScoresSuper.ra - lines changed 1, context: html, text, full: html, text

10c0695c8a4ff88a24ae2f446b4ef705fdbc37d8 Tue Jun 30 17:57:33 2026 -0700

• Add popEVE and EVE to the Deleteriousness Predictions page and related tracks. refs #37791 Document EVE and popEVE on the predictionScoresSuper description page, which previously listed the other member scores but not these two. Also add reciprocal relatedTracks cross-links between popEVE and EVE, AlphaMissense, PrimateAI-3D, ClinPred, and REVEL.
  • src/hg/makeDb/trackDb/human/predictionScoresSuper.html - lines changed 43, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/relatedTracks.ra - lines changed 12, context: html, text, full: html, text

30c0e2e97dc0f5391a58a3cc665f55697a3b6152 Tue Jun 30 18:03:44 2026 -0700

• varFreqs: newsarch, swap "supertrack" for "container track" and expand credits. refs #36642 Per Max's post-release feedback on the ticket: "supertrack" is jargon for end users, so all 4 mentions in the SNV Frequencies entry are swapped to "container track". Credits paragraph expanded to name the additional investigators and data-access teams who provided source variant files or helped shape the track (Sarah Tishkoff, Yanan Cao, Matthew Hobbs, Adam Ameur, Johan Viklund, Ameena Suliman, Julia Sommer, Cole Shanks, Qudsi Aljabiri). Also fixes "Insoo Jang" spelling to "Insu Jang" to match his own signature.
  • src/hg/htdocs/goldenPath/newsarch.html - lines changed 16, context: html, text, full: html, text

43697ed2271f7819ef6d6f1947c0b404a508539a Wed Jul 1 15:38:24 2026 -0700

• Make hgTracks decorators resolve the decoratedItem chrom through chromAlias so decorations link to their items when the decoratedItem field uses an alias (e.g. PanSN or accession names) rather than the native sequence name. refs #37803
  • src/hg/hgTracks/decorator.c - lines changed 33, context: html, text, full: html, text

b761e0e7b483d9fbb2832820c138c0baab13a869 Thu Jul 2 17:39:24 2026 -0700

• Fix Total out of memory metric in errorLogKeywordSearch.py to count only genuine events. refs #37699 A single needMem OOM failure recurses in the errAbort/warn handler (which itself allocates), re-emitting the "request size %llu bytes" format string many times per crash. The old grep "needMem: Out of memory" counted every one of those frames, inflating the weekly count ~60-175x (e.g. ~1070 reported vs ~18 genuine events for the week of 20260614). Restrict the match to lines with a numeric request size so only real allocation failures are counted.
  • src/utils/qa/errorLogKeywordSearch.py - lines changed 1, context: html, text, full: html, text