Commits for max

v497_preview2 to v497_base (2026-04-13 to 2026-04-20) v497

8efbcad3f2816dec50b5671a4445d2e6943f7f91 Mon Apr 13 07:57:41 2026 -0700

• Use light gray for monomorphic strVar loci (het=0), distinct from no-data gray, refs #36652 Add a separate color for loci where heterozygosity is exactly 0 (single allele observed) across all four strVar subtracks: light gray (200,200,200). This distinguishes them from the existing medium gray (128,128,128) used when no allele frequency data is available. Previously het=0 was lumped into the dark blue "nearly monomorphic" bin. Also expand the itemRgb field description in all four .as files to list the full color scheme. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • src/hg/makeDb/scripts/tommoStr/tommoStr.as - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/tommoStr/tommoStrToBed.py - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/scripts/trexplorer/trexplorer.as - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/trexplorer/trexplorerToBed.py - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/scripts/viennaVntr/viennaVntr.as - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/viennaVntr/viennaVntrToBed.py - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/scripts/webstr/webstr.as - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/webstr/webstrToBed.py - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/tommoStr.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trexplorer.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/viennaVntr.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/webstr.html - lines changed 5, context: html, text, full: html, text

9e4b6bdfe320b9def27f549f4928392e2b4d0937 Mon Apr 13 08:35:23 2026 -0700

• Add BCGSC Human BAC Re-Array (32k set) track on hg38, refs #35059 New subtrack under cloneEndSuper showing the curated 32k BAC clone tiling path provided by BACPAC Genomics (CHORI). Data is the pre-lifted hg38 custom track from bacpacresources.org, converted to bigBed5. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • src/hg/makeDb/doc/hg38/bacRearray32k.txt - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/bacRearray32k.html - lines changed 132, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.cloneEnd.ra - lines changed 17, context: html, text, full: html, text

c9093b16dc815c2b511c481ea404e89540ac525c Mon Apr 13 15:03:20 2026 -0700

• CLAUDE.md: move kent coding rules into the edit-kent-code skill Replace the full C/SQL/memory rule list with a short pointer to the edit-kent-code and make-track skills. Track-building sessions no longer pull C-specific rules into every context. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • src/CLAUDE.md - lines changed 16, context: html, text, full: html, text

e1886ca23647a83dfb58d5d5e02ac736563f903b Tue Apr 14 11:02:34 2026 -0700

• adding BAC End Pairs track to danRer11, lifted from danRer4, refs #35059 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • src/hg/makeDb/trackDb/zebrafish/danRer11/bacEndPairsLift.html - lines changed 76, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra - lines changed 9, context: html, text, full: html, text

ce8eb77d36cb9df0d68cd30ca2d74195dc8f5f91 Tue Apr 14 11:03:33 2026 -0700

• adding makedoc and build script for danRer11 bacEndPairsLift track, refs #35059 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • src/hg/makeDb/doc/danRer11/bacEndPairsLift.txt - lines changed 39, context: html, text, full: html, text
  • src/hg/makeDb/scripts/bacEndPairsLift/toBed12.py - lines changed 29, context: html, text, full: html, text

36d92a1a5471428caeab49221e1585b76537498d Wed Apr 15 06:06:47 2026 -0700

• fix zero-length items in NMD escape regions output, refs #33737 Two edge cases produced degenerate zero-length items in the BED output: - CDS boundary landing exactly on an exon boundary created zero-length cdsExons during construction - In outputExonsUpTo, when cumulative doneNs exactly hit the target n on a previous iteration, the next iteration entered the truncation branch with missBps=0, producing a zero-length region Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • src/hg/makeDb/scripts/nmd/genePredNmdEsc - lines changed 5, context: html, text, full: html, text

4fd9f828f80a223799ce69d7078ee22ffe8aabc5 Wed Apr 15 07:22:19 2026 -0700

• fixing up after claude, refs #35059
  • src/hg/makeDb/trackDb/human/cloneEnd.trackDb.ra - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.cloneEnd.ra - lines changed 17, context: html, text, full: html, text

86744c40b7e7f18792d287aedf9cf5da543e2d5a Fri Apr 17 07:22:27 2026 -0700

• Add GA4K (Genomic Answers for Kids) small-variant subtrack to the Variant Frequencies supertrack for hg38. #Preview2 week - bugs introduced now will need a build patch to fix Children's Mercy pediatric rare-disease cohort: ~36.2M SNVs and short indels from 552 PacBio HiFi long-read samples (DeepVariant/GLnexus), filtered to variants replicated in >=2 unrelated GA4K individuals or an HPRC variant. Ref: Cohen et al. 2022, Genet Med, PMID 35305867. refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • src/hg/makeDb/doc/hg38/varFreqs.txt - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/ga4kSnv.html - lines changed 81, 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 9, context: html, text, full: html, text

7594507ca126d5242346787e42e13c52ea7709b1 Fri Apr 17 08:40:31 2026 -0700

• Add lrSv supertrack: long-read structural variants from 9 studies (hg38). #Preview2 week - bugs introduced now will need a build patch to fix Sub-tracks (all bigBed 9+): han945Sv - 945 Han Chinese, ONT (Gong 2025, PMID 39929826) lrSv1kgOnt - 1019 1000 Genomes, ONT, SVAN-annotated (Schloissnig 2025, PMID 40702182; lifted from hs1) tommoJpSv - 333 Japanese (111 trios), ONT (Otsuki 2022, PMID 36127505) aou1kSv - 1027 All of Us, PacBio HiFi (Garimella 2025, PMID 41256123) ga4kSv - 502 GA4K pediatric rare disease, PacBio HiFi (Cohen 2022, PMID 35305867) decodeSv - 3622 Icelanders, ONT (Beyter 2021, PMID 33972781) hgsvc3Sv - 65 HGSVC3 diverse haplotype-resolved assemblies, HiFi+ONT (Logsdon 2025, PMID 40702183; merges insdel+inv tables) kwanhoSv - 100 post-mortem brains (PD/ILBD/HC), PacBio HiFi (Kim 2026, PMID 41929179) chirmade101Sv - 101 long-read WGS GWAS SVatalog cohort (Chirmade 2026, PMID 41203876) Includes per-track conversion scripts and autoSql under scripts/lrSv/, the supertrack summary table in lrSv.html, and a consolidated makeDoc at doc/hg38/lrSv.txt. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • src/hg/makeDb/doc/hg38/lrSv.txt - lines changed 252, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSv.as - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSv1kgOnt.as - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSv1kgOntVcfToBed.py - lines changed 228, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvAou1k.as - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvAou1kCsvToBed.py - lines changed 130, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvChirmade101.as - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvChirmade101TsvToBed.py - lines changed 118, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvDecode.as - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvDecodeVcfToBed.py - lines changed 86, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvGa4kSv.as - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvGa4kSvVcfToBed.py - lines changed 84, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvHan945SuppVecToVcf.py - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvHgsvc3.as - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvHgsvc3TsvToBed.py - lines changed 132, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvKwanho.as - lines changed 42, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvKwanhoTsvToBed.py - lines changed 143, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvTommoJp.as - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvTommoJpVcfToBed.py - lines changed 126, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvVcfToBed.py - lines changed 126, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/aou1kSv.html - lines changed 95, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chirmade101Sv.html - lines changed 97, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/decodeSv.html - lines changed 94, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/ga4kSv.html - lines changed 103, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/han945Sv.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hgsvc3Sv.html - lines changed 115, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/kwanhoSv.html - lines changed 106, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSv.html - lines changed 308, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSv.ra - lines changed 126, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/tommoJpSv.html - lines changed 81, context: html, text, full: html, text

6ab7b1dfca6cc123dfe09a9e9f8afdf0c8cbdf31 Mon Apr 20 06:40:58 2026 -0700

• changes after code review, refs #37376
  • src/hg/htdocs/goldenPath/help/bigBed.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/strVar.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/longReadVariants.ra - lines changed 1, context: html, text, full: html, text

e8cfed22bdb02ca22850d6a33f82370df0d4b24f Mon Apr 20 06:42:15 2026 -0700

• adding related tracks from the long read sv supertrack
  • src/hg/makeDb/trackDb/relatedTracks.ra - lines changed 10, context: html, text, full: html, text

4d9c385e230b4cc8bd55815aa7ba37dea97d4c0a Mon Apr 20 08:49:42 2026 -0700

• abelSv: new track for CCDG 17,795 structural variants (hg38) Add site-frequency track for the Abel et al. 2020 Nature SV callset (PMID 32460305): 737,998 SVs from 17,795 deeply sequenced genomes. Includes the B38 native callset (14,623 samples) and B37 lifted to hg38 (8,417 samples). Track is colored by SV type (DEL/DUP/INV/MEI/BND) with filters for type, callset, filter status, AC, AF, SV length, and MSQ. BND secondary mate records are suppressed so translocation pairs appear only once. refs #36258
  • src/hg/makeDb/doc/hg38/abelSv.txt - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/scripts/abelSv/abelSv.as - lines changed 41, context: html, text, full: html, text
  • src/hg/makeDb/scripts/abelSv/build.sh - lines changed 51, context: html, text, full: html, text
  • src/hg/makeDb/scripts/abelSv/vcfToBed.py - lines changed 192, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/abelSv.html - lines changed 141, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/abelSv.ra - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 2, context: html, text, full: html, text

526213b2893134217a300ff913e11b4e98d67991 Mon Apr 20 08:50:10 2026 -0700

• lrSv: add cpc1Sv and aprSv pangenome SV subtracks (hg38, hs1) cpc1Sv: 97,205 SVs from the CPC + HPRC Phase 1 pangenome (Gao et al 2023, Nature; PMID 37316654) built on T2T-CHM13v2, with 53 Chinese and 47 HPRC samples. Each graph snarl site is shown as one item with alt alleles classified by length delta (INS/DEL/CPX, 50 bp threshold) and collapsed. aprSv: 103,077 SVs from the Arabic Pangenome Reference (Nassir et al. 2025, Nat Commun; PMID 40707445) built on T2T-CHM13v2 from 53 UAE-resident Arab individuals. Same multi-allele classification as cpc1Sv, with alt alleles iterated within each multi-allelic row. Both tracks load natively on hs1 and are lifted to hg38 with hs1ToHg38.over.chain.gz. refs #36258
  • src/hg/makeDb/doc/hg38/lrSv.txt - lines changed 162, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvApr.as - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvAprBuild.sh - lines changed 38, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvAprVcfToBed.py - lines changed 169, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvCpc1.as - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvCpc1Build.sh - lines changed 41, context: html, text, full: html, text
  • src/hg/makeDb/scripts/lrSv/lrSvCpc1VcfToBed.py - lines changed 204, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/aprSv.html - lines changed 103, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/cpc1Sv.html - lines changed 120, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/lrSv.ra - lines changed 206, context: html, text, full: html, text

e89a2c6a10b38da2591e8e4e7132fe29a4b1fbd7 Mon Apr 20 09:31:08 2026 -0700

• varFreqs: add colorsDbSnv subtrack (hg38 and hs1) CoLoRSdb v1.2.0 long-read SNV/indel population-frequency VCFs from 1,027 PacBio HiFi whole genomes, joint-called with DeepVariant and GLnexus. The GRCh38 release is shown on hg38 and the CHM13 release on hs1 (both are native, not lifted). This is the first varFreqs subtrack that renders on hs1. refs #36642
  • src/hg/makeDb/doc/hg38/varFreqs.txt - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/colorsDbSnv.html - lines changed 74, 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 10, context: html, text, full: html, text