Commits for lrnassar

v501_base to v502_preview (2026-07-20 to 2026-07-27) v502

ff04ae9d89641156d7b93d03e1d6162c8e070355 Mon Jul 20 17:01:25 2026 -0700

• Fix TP53 Provisional Classification bigBed type declaration from 9+9 to 9+10. The AUTOSQL and emitted data have 10 extra fields, and the trackDb declares bigBed 9 + 10, but the bedToBigBed -type arg and the docstring said 9+9. Corrected both so the bigBed header extraFieldCount is right and the script is self-consistent. refs #37399
  • src/hg/makeDb/scripts/tp53/tp53ProvisionalClass.py - lines changed 2, context: html, text, full: html, text

7753691572e05914d2d184bd295c9076cc9da463 Tue Jul 21 18:49:22 2026 -0700

• Skip active dbDb entries with no local database in runCheckHgFindSpec. refs #37836 The new GenArk hub assemblies added for #37836 are pure hub pointers (nibPath "hub:...") with no companion local MySQL database, unlike earlier additions such as rn8/hs1/mpxvRivers. The loop ran "hgsql $db" on every active dbDb name, which failed with "Unknown database" for these entries and tripped the QA cron with stderr noise. Guard the loop on the set of databases that actually exist so hub-only entries are skipped cleanly; the set of databases actually checked is unchanged.
  • src/utils/qa/runCheckHgFindSpec - lines changed 7, context: html, text, full: html, text

d10aba5d8ac8abc3655c599b9e421538a8a7e32e Wed Jul 22 10:56:04 2026 -0700

• Releasing GENCODE V50 knownGene tracks for hg38, hg19 (V50lift37), and mm39 (VM39). Promote knownGene from the alpha-gated staging file to the released trackDb: bump shortLabel/longLabel, bigDataUrl, html, and searchTrix to the new version; collapse the include to a single untagged knownGene.ra; and remove the knownGene.alpha.ra files. refs #37395 #37393 #37391
  • src/hg/makeDb/trackDb/human/hg19/knownGene.alpha.ra - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/knownGene.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra - lines changed 47, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/knownGene.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/knownGene.alpha.ra - lines changed 41, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra - lines changed 2, context: html, text, full: html, text

028e5a86ab2f9731bceae8eb1676488c175871f3 Wed Jul 22 10:56:04 2026 -0700

• Hiding previous GENCODE versions track now that V50/VM39 is released. Set visibility hide on wgEncodeGencodeV49 (hg38), wgEncodeGencodeV49lift37 (hg19), and wgEncodeGencodeVM38 (mm39) so the new version is the default shown in the GENCODE Versions container. refs #37396 #37394 #37392
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV49lift37.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV49.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM38.ra - lines changed 1, context: html, text, full: html, text

e6b7a180acff63d77b0d6d4cfba98a2298a7889e Wed Jul 22 11:25:18 2026 -0700

• Adding GENCODE V50/VM39 release notes to the GENCODE Versions container description page. The per-version subtrack pages were updated for the new release but the wgEncodeGencodeSuper container page Release Notes still topped out at the previous version. Add the new version-to-Ensembl correspondence line (V50/V50lift37/VM39 -> Ensembl 116) for hg38, hg19, and mm39. refs #37396 #37394 #37392
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeSuper.html - lines changed 4, context: html, text, full: html, text

7485753cb34c1c3fd4a3f7b8894d993110db50ff Thu Jul 23 14:03:39 2026 -0700

• Rebuild popEVE heatmap with the full per-amino-acid matrix. refs #37791 The track was built from the genomic single-nucleotide VCF, so each column showed only the ~6 of 19 substitutions reachable by a single nucleotide change. The popEVE authors confirmed the per-transcript CSV download carries the complete matrix, so the converter now takes the all-19 scores from those CSVs while reusing the genomic codon coordinates, strand, and blocks derived from the VCF. Proteins absent from the (older) CSV release fall back to the sparse VCF scores. Color anchors recomputed over the full-matrix distribution, and the mouseover's raw EVE field is relabeled "EVE index" to distinguish it from the EVE track's 0-1 score. Updates the description page and makedoc to match.
  • src/hg/makeDb/doc/hg38/popEve.txt - lines changed 41, context: html, text, full: html, text
  • src/hg/makeDb/scripts/popEve/vcfToPopEveHeatmap.py - lines changed 95, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/popEve.html - lines changed 15, context: html, text, full: html, text

9a56fd00c6ee9cba19d36d6fe4ae0222523cdcd8 Thu Jul 23 14:10:55 2026 -0700

• Update popEVE color-legend anchors to the dense-rebuild values. refs #37791 The description page's color table still showed the sparse build's saturation anchors (-5.74 / -2.29); the dense rebuild recomputed them to -6.04 / -2.41. Caught in visual QA.
  • src/hg/makeDb/trackDb/human/popEve.html - lines changed 2, context: html, text, full: html, text

798b37017a4e1b95f3ccdf7c8b477dfb5446a324 Fri Jul 24 15:22:34 2026 -0700

• lrSv: QA fixes for cardSv/noyvertSv additions - BND filter, makedoc, link targets. refs #37888 Add BND to filterValues.svType on the longReadVariants supertrack and the merged lrSvAll track (and the lrSvMergeAll.py generator) so the breakend variants that noyvertSv contributes are filterable. Correct a stale makedoc comment that said CARD was not in the lrSvAll merge (it is). Add target="_blank" to the API and hgdownload links in cardSv.html and noyvertSv.html.
  • src/hg/makeDb/doc/hg38/lrSv.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/cardSv.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSv.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSvAll.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/noyvertSv.html - lines changed 2, context: html, text, full: html, text

bbddaf74c88b5e590f0943b73dd5c0d40f42e42d Fri Jul 24 15:22:34 2026 -0700

• Update Long-read SVs announcement counts for cardSv/noyvertSv additions. refs #37888 Bump the container from 14 to 16 studies and roughly 2.3 to 2.6 million merged SV sites, and add NIH CARD (Americas) and Noyvert 888 (1000 Genomes) to the region summary table.
  • src/hg/htdocs/goldenPath/newsarch.html - lines changed 4, context: html, text, full: html, text

d5302bd1e0cf296545df9ad3e0d3ab57859a51eb Fri Jul 24 17:17:17 2026 -0700

• varFreqs: post-QA polish on new hostseq subtrack. refs #37882 Findings from the qa-track pass on the gnomAD-Canada HostSeq subtrack added in 99764ad55bb: - hostseq.html: fix non-ASCII byte in Alföldi (Alföldi), swap hardcoded hg38 for $db in the hgdownload URL, extend the FILTER enumeration to include InbreedingCoeff;RF (34,540 sites), add nhomalt and grpmax to the Display Conventions details-page list, and add an "Effective sample size per ancestry group" subsection warning that AF_fin (~4 individuals) and AF_mid (~72) are too sparse to be reliable population estimates. Collapsed a stray double blank line between refs. - populations.tsv, hostseqHtToVcf.py: harmonize the "oth" group label to "Remaining individuals" per the gnomAD README. The existing VCF header still shows the old label; it picks up the new one on the next re-emit (not worth re-running the 104 GB Hail table just for this). - varFreqs.ra: hostseq priority 2 -> 33 to break the sort-order collision with allofus (also at priority 2).
  • src/hg/makeDb/scripts/varFreqs/hostseqHtToVcf.py - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/populations.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hostseq.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 1, context: html, text, full: html, text