Commits for lrnassar

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

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/InSiGHT.txt - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/scripts/insight/buildInsightClinVar.py - lines changed 298, 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/clinPred.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/predictionScoresSuper.html - lines changed 73, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.html - lines changed 5, 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/wgEncodeReg4RnaSeq.html - lines changed 99, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.html - lines changed 65, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.ra - lines changed 2463, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.html - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra - lines changed 168, 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/mpra.ra - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/mprabase.html - lines changed 25, 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/hs1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/locusSpec.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/mucins.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/umdTp53.html - lines changed 140, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/umdTp53.ra - lines changed 28, context: html, text, full: html, text
  • src/hg/utils/otto/umdTp53/README.md - lines changed 76, context: html, text, full: html, text
  • src/hg/utils/otto/umdTp53/checkAndLoad.sh - lines changed 96, context: html, text, full: html, text
  • src/hg/utils/otto/umdTp53/doUmdTp53Update.sh - lines changed 43, context: html, text, full: html, text
  • src/hg/utils/otto/umdTp53/download.sh - lines changed 88, context: html, text, full: html, text
  • src/hg/utils/otto/umdTp53/makefile - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/otto/umdTp53/umdTp53.as - lines changed 56, context: html, text, full: html, text
  • src/hg/utils/otto/umdTp53/umdTp53ToBed.py - lines changed 466, context: html, text, full: html, text

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/mlqAutomate.py - lines changed 20, context: html, text, full: html, text

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
  • src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 5, 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/goldenPath/newsarch.html - lines changed 96, context: html, text, full: html, text
  • src/hg/htdocs/images/mpraNewsImage.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/hg38/mpra.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/mpra.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/mpraVarDb.html - lines changed 2, 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/wgEncodeReg4Epigenetics.ra - lines changed 4770, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.ra - lines changed 5004, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra - lines changed 902, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra - lines changed 334, 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/evaSnp9.txt - lines changed 95, context: html, text, full: html, text
  • src/hg/makeDb/scripts/evaSnp/evaSnp9.py - lines changed 2473, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/evaSnp.ra - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/evaSnpContainer.html - lines changed 29, context: html, text, full: html, text