Commits for max

v501_preview2 to v501_base (2026-07-13 to 2026-07-20) v501

79764235e8868753201b1b5cd8278ff4f1dd1c08 Sat Jul 11 08:52:39 2026 -0700

• Add nucleotide-position indicator to UTR and non-coding exon mouseovers When zoomed to codon level, hovering a coding transcript's UTR now shows its HGVS position, c.-N in the 5' UTR (counting back to the start codon) and c.*N in the 3' UTR (counting forward from the stop). Non-coding transcripts, which have no codon boxes, get the same treatment on their exons using HGVS n. numbering from the transcript's 5' end. Distances are measured in spliced mRNA space, so introns don't inflate them and the numbering runs continuously across multi-exon UTRs. Previously these regions showed only strand, exon number and length, with no indication of which nucleotides they covered. refs #37866
  • src/hg/hgTracks/simpleTracks.c - lines changed 87, context: html, text, full: html, text

a155f3262aa051b6b97e8c3ef0caba8304b992a0 Sat Jul 11 10:13:44 2026 -0700

• Comment: simpleFeature qStart/qEnd are only meaningful for alignment tracks They carry query-sequence coordinates for PSL/BAM/chain/snake features and are left 0 for gene models (genePred), where there is no query sequence. Noting this at the field so nobody assumes they are populated everywhere.
  • src/hg/hgTracks/hgTracks.h - lines changed 2, context: html, text, full: html, text

7be0d4bee5fc92c426382f480e06254e60f8bb9e Sat Jul 11 20:15:05 2026 -0700

• Cache-bust menu-bar CSS/JS on static pages, refs #10138 hgMenubar.c emitted nice_menu.css and topLinks.js as bare URLs with no version query, so browsers kept serving a stale cached nice_menu.css after commit c5a326f3 added the top-right links. The new #trToggle hamburger is hidden by a rule in that CSS, so on static pages (e.g. the homepage) it showed on first load and only disappeared after a manual force-reload. Append ?v=<file mtime> to those two URLs, the same idea CGIs get from webTimeStampedLinkToResource (which can't be reused here: it emits a ../-relative URL that is wrong for the arbitrary-depth static pages this menu bar is SSI-included into). Uses the existing fileModTime(), guarded by fileExists so a missing resource degrades to ?v=0 rather than aborting the menu bar.
  • src/hg/hgMenubar/hgMenubar.c - lines changed 18, context: html, text, full: html, text

99764ad55bb121d285e9734de955bba41802ad06 Wed Jul 15 23:35:19 2026 -0700

• varFreqs: add gnomAD-Canada HostSeq SNV frequencies and fold into combined tracks, refs #36642 #Preview2 week - bugs introduced now will need a build patch to fix New "hostseq" vcfTabix subtrack of the SNV Frequencies container: gnomAD-Canada v1.0 / HostSeq, 10,487 Canadian COVID-19 WGS genomes on hg38. The release ships only as a ~104 GB Hail table, so hostseqHtToVcf.py reads it with Hail and flattens the freq array into a sites-only VCF with overall + 9 gnomAD ancestry-group AC/AN/AF, nhomalt, grpmax, dbSNP rsID and the variant filter status. 232,028,491 release rows -> 213,382,086 written (18,646,405 AC0 sites dropped). Registered HostSeq (is_disease=0) in databases.tsv and its 9 ancestry groups in populations.tsv, and rebuilt varFreqsAffected/varFreqsBackground so HostSeq feeds the background side (29 cohorts, 185 fields; merged set 1,374,129,993 variants). Added HostSeq to filterValues.backgroundSources.
  • src/hg/makeDb/doc/hg38/varFreqs.txt - lines changed 77, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/databases.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/hostseqHtToVcf.py - lines changed 165, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/populations.tsv - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hostseq.html - lines changed 114, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 28, context: html, text, full: html, text

c656fab2dcb67f0789af54ea1d04afcf6ab3d07b Wed Jul 15 23:38:55 2026 -0700

• varFreqs: expand SPARK phenotype-split documentation in makeDoc #Preview2 week - bugs introduced now will need a build patch to fix Rework the SFARI SPARK section of the varFreqs makeDoc to describe, step by step, what sparkMergeVcfAddCounts.sh does per chromosome (fill-tags overall + optional per-group AC/AN/AF, drop genotypes, concat) and how the individuals_registration TSV drives the ASD / non-ASD phenotype split.
  • src/hg/makeDb/doc/hg38/varFreqs.txt - lines changed 45, context: html, text, full: html, text

b7a25f617b5e6fbdeb50ea890e0ff5872605d8d2 Thu Jul 16 00:22:46 2026 -0700

• Table Browser: on-the-fly mRNA and protein output for gene tracks without companion tables #Preview2 week - bugs introduced now will need a build patch to fix #Preview2 week - bugs introduced now will need a build patch to fix The Sequence output for a genePred/bigGenePred track only offered protein and mRNA when the trackDb type line named SQL peptide/mRNA tables (or the track was the hardcoded refGene). Assembly-hub bigGenePred tracks and ncbiRefSeq-style tracks therefore got genomic sequence only. Now those types always offer genomic, mRNA and protein. When no peptide/mRNA table is present, the mRNA is spliced from the assembly and the protein is translated from the CDS using the genetic code assigned to each sequence, so an assembly hub's codonTable setting is honored (chrM/chrMT still default to the mitochondrial code). Tracks that do have peptide/mRNA tables are unchanged. refs #21746
  • src/hg/hgTables/seqOut.c - lines changed 101, context: html, text, full: html, text

5fe93cbef0d7692552e37e62bbf394cc7d222a28 Thu Jul 16 00:32:55 2026 -0700

• ClinVar Mapped track: map ClinVar coding variants through paralog alignments #Preview2 week - bugs introduced now will need a build patch to fix Adds the clinvarMapped composite (hg38) with two subtracks: - clinvarMappedParalog: every protein-changing ClinVar variant projected onto the equivalent (aligned) residue of each of its gene's paralogs - clinvarMappedParalogAln: the pairwise protein alignments used to do the mapping, as bigPsl, so the evidence for each projection can be inspected Pipeline: paralog pairs from Ensembl BioMart, one representative transcript per gene from MANE Select, pairwise global protein alignment (BLOSUM62) for pairs at >=20% identity, variants projected residue-to-residue and mapped back to the paralog's genomic codon. Colors and filters mirror the ClinVar track; the map track is filterable by source gene, classification, review stars, residue conservation and percent identity. refs #37883
  • src/hg/makeDb/doc/hg38/clinvarMapped.txt - lines changed 89, context: html, text, full: html, text
  • src/hg/makeDb/scripts/clinvarMapped/clinvarMappedCodons.py - lines changed 224, context: html, text, full: html, text
  • src/hg/makeDb/scripts/clinvarMapped/clinvarMappedMane.sh - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/scripts/clinvarMapped/clinvarMappedParalog.as - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/scripts/clinvarMapped/clinvarMappedParalogAlign.py - lines changed 112, context: html, text, full: html, text
  • src/hg/makeDb/scripts/clinvarMapped/clinvarMappedParalogAlnPsl.py - lines changed 164, context: html, text, full: html, text
  • src/hg/makeDb/scripts/clinvarMapped/clinvarMappedParalogPairs.sh - lines changed 58, context: html, text, full: html, text
  • src/hg/makeDb/scripts/clinvarMapped/clinvarMappedParalogProject.py - lines changed 207, context: html, text, full: html, text
  • src/hg/makeDb/scripts/clinvarMapped/clinvarMappedParalogStats.sh - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/clinvarMapped.html - lines changed 171, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/clinvarMapped.ra - lines changed 60, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 2, context: html, text, full: html, text

04456b0be37a7d7b57551e0d9596e3ef0b8f0393 Thu Jul 16 00:34:37 2026 -0700

• Add HPRC Release 2 hg38 native tracks (alignments, coverage, breaks, rearrangements, chains), refs #35415 #Preview2 week - bugs introduced now will need a build patch to fix New pan-genome track container (group hprc) derived from the HPRC Release 2 per-assembly chains to GRCh38 (462 haplotypes), running in parallel to the existing HPRC release 1 tracks: - hprc2Coverage: fraction of assemblies aligning across GRCh38 - hprc2Breaks: alignment breaks, colored by prevalence - hprc2Rearr: insertions/deletions/inversions/duplications/complex indels, lrSv color palette, numeric size field, 50 bp default filter - hprc2Chains: per-haplotype bigChain composite, grouped by superpopulation Container hidden by default. Scripts, autoSql, and makeDoc included.
  • src/hg/makeDb/doc/hg38/hprc2.txt - lines changed 92, context: html, text, full: html, text
  • src/hg/makeDb/scripts/hprc2/hprc2Aggregate.sh - lines changed 123, context: html, text, full: html, text
  • src/hg/makeDb/scripts/hprc2/hprc2Arrange.as - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/scripts/hprc2/hprc2Chains.sh - lines changed 75, context: html, text, full: html, text
  • src/hg/makeDb/scripts/hprc2/hprc2Download.sh - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/scripts/hprc2/hprc2ProcessAll.sh - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/scripts/hprc2/hprc2ProcessOne.sh - lines changed 71, context: html, text, full: html, text
  • src/hg/makeDb/scripts/hprc2/hprc2SampleSuperpop.py - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hprc2.html - lines changed 123, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hprc2.ra - lines changed 91, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hprc2Chains.ra - lines changed 4636, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 2, context: html, text, full: html, text

95208355e2c667d194b29ee78c8ca8a09c2c2596 Fri Jul 17 08:51:28 2026 -0700

• lrSv: add NIH CARD long-read SV subtrack (cardSv) #Preview2 week - bugs introduced now will need a build patch to fix Add the NIH CARD Long-Read Initiative structural-variant catalogue (351 post-mortem brain samples: 205 NABEC European ancestry, 146 HBCC African/African-admixed) as a new subtrack of the Long-read SVs container. The provider bigBed is re-derived into the shared lrSv schema: signed svLen made positive (reference span), an explicit insLen added, the single DUP:TANDEM folded to DUP, and colors remapped to the container's shared svColor() palette. All 228,855 provider records are carried through 1:1. Adds the converter and autoSql, the trackDb stanza with filters consistent with the sibling subtracks, a full description page, a summary row and blurb on the container page, and a makeDoc section. refs #36258
  • src/hg/makeDb/doc/hg38/lrSv.txt - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvCard.as - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvCardBbToBed.py - lines changed 117, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/cardSv.html - lines changed 139, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSv.html - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSv.ra - lines changed 32, context: html, text, full: html, text

3bf9e1a841206d3bf5902e06791ef5be2dbdbd39 Fri Jul 17 09:09:47 2026 -0700

• lrSv: add Noyvert multi-ancestry long-read SV subtrack (noyvertSv) #Preview2 week - bugs introduced now will need a build patch to fix 888 Oxford Nanopore 1000 Genomes genomes, Sniffles2 v2.0.7, 107,445 SVs with per-superpopulation allele frequencies, imputation-accuracy metrics and UK Biobank SV-WAS associations. Converter approximates AC/AN from AF and the genotype missing rate (source has no allele count), stores BND mate breakends, and follows the shared lrSv svType/svLen/insLen/AC field convention so the container-level filters apply. refs #36258
  • src/hg/makeDb/doc/hg38/lrSv.txt - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvNoyvert.as - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvNoyvertTsvToBed.py - lines changed 205, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSv.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSv.ra - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/noyvertSv.html - lines changed 130, context: html, text, full: html, text

d92e36dbbee172d6bb81a751eb8bb935f356890c Fri Jul 17 09:31:28 2026 -0700

• lrSv: add cardSv and noyvertSv to the lrSvAll merged track #Preview2 week - bugs introduced now will need a build patch to fix Append NIH CARD 351 (AC/alleleFreq) and Noyvert 888 (AC/AF) to databases.tsv and re-run lrSvMergeAll.py: 16 source databases now, 3,018,404 input variants merged to 2,582,278 (was 14 dbs, 2,317,508). Regenerated lrSvAll.ra (filterValues.sources + sourceCount 1:16) and updated the container summary table. refs #36258
  • src/hg/makeDb/doc/hg38/lrSv.txt - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/databases.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSv.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSvAll.ra - lines changed 2, context: html, text, full: html, text

12c38f63e39d562ab77060346429068f97e32c25 Fri Jul 17 23:59:34 2026 -0700

• lrsv docs change after feedback from Jonas Gustavsson jgust1@uw.edu
  • src/hg/makeDb/trackDb/human/lrSv.html - lines changed 5, context: html, text, full: html, text

af24c692f12ca0c3fcbf639e63040e61cfb684a5 Sat Jul 18 00:17:03 2026 -0700

• small lrsv docs changes
  • src/hg/makeDb/trackDb/human/lrSv.html - lines changed 2, context: html, text, full: html, text