All File Changes

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

• confs/hgwdev.hg.conf
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    b32f95380141f3ca1f6b4b6561187642203cdc5c Sun Apr 19 01:11:15 2026 -0700
    Installing updated hg.conf files from UCSC servers
• src/CLAUDE.md
  • lines changed 16, context: html, text, full: html, text
    ab4a34f7bf395236e98a5d426d14e2108763526a Mon Apr 13 14:51:00 2026 -0700
    removing this in favor of putting it in a skill
  • lines changed 16, 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/hg/cgilib/cartEdit10.c
  • lines changed 17, context: html, text, full: html, text
    8c44bb1acda9ad5f13f7839d3994d6e4f07a2fa1 Sat Apr 18 11:27:44 2026 -0700
    Add cartVersion 10 to re-apply the encodeCcreCombined -> cCREs supertrack migration for carts saved while cartVersion was already 9 but before the trackDb switch to the new supertrack. refs #37383 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/cgilib/cartRewrite.c
  • lines changed 2, context: html, text, full: html, text
    8c44bb1acda9ad5f13f7839d3994d6e4f07a2fa1 Sat Apr 18 11:27:44 2026 -0700
    Add cartVersion 10 to re-apply the encodeCcreCombined -> cCREs supertrack migration for carts saved while cartVersion was already 9 but before the trackDb switch to the new supertrack. refs #37383 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/cgilib/makefile
  • lines changed 1, context: html, text, full: html, text
    8c44bb1acda9ad5f13f7839d3994d6e4f07a2fa1 Sat Apr 18 11:27:44 2026 -0700
    Add cartVersion 10 to re-apply the encodeCcreCombined -> cCREs supertrack migration for carts saved while cartVersion was already 9 but before the trackDb switch to the new supertrack. refs #37383 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 3, context: html, text, full: html, text
    77a4340b7205e040f0ae5298abc1271ce2f7ca33 Wed Apr 15 10:21:50 2026 -0700
    Adding 'subtrackUrl' trackDb option for faceted composites to specify a linkout url, refs #36320
  • lines changed 7, context: html, text, full: html, text
    6d78a8e2d7230272d15508db74169ad20cd76f3f Thu Apr 16 12:06:50 2026 -0700
    Restrict color override to supported track types; add palette icon; deduplicate type check, refs #20460 Note: palette.png must be installed to htdocs/images/ (new file). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/hgTracks/hgTracks.c
  • lines changed 6, context: html, text, full: html, text
    03550a41a3b40299ba1405770fdf548dd48a63a7 Mon Apr 13 15:51:11 2026 -0700
    Deduplicate and htmlEncode alias list in printAliases() refs #29201 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 3, context: html, text, full: html, text
    34a45f462f1b0e73015f60354ded50644bf629b7 Wed Apr 15 13:03:18 2026 -0700
    Apply colorOverride to track labels; add right-click "Change Track Color" dialog, refs #20460 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/hgTracks/imageV2.c
  • lines changed 17, context: html, text, full: html, text
    34a45f462f1b0e73015f60354ded50644bf629b7 Wed Apr 15 13:03:18 2026 -0700
    Apply colorOverride to track labels; add right-click "Change Track Color" dialog, refs #20460 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    6d78a8e2d7230272d15508db74169ad20cd76f3f Thu Apr 16 12:06:50 2026 -0700
    Restrict color override to supported track types; add palette icon; deduplicate type check, refs #20460 Note: palette.png must be installed to htdocs/images/ (new file). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    69a23e3d6507ff4d95c8bd99f97615e1159a0c17 Fri Apr 17 09:56:19 2026 -0700
    hgc: don't try to MySQL-connect to a GenArk source assembly in quickLift paths When a track has a quickLiftDb pointing to a GenArk accession (e.g. GCA_018466835.2), hgc crashed clicking on an item because genericClickHandlerPlus called hAllocConnTrack() on a db name that only exists as a hub assembly, not a MySQL database. The existing guard only skipped trackHubDatabase() entries (hubs registered in hubAssemblyHash), which doesn't include on-demand GenArk assemblies referenced by a quickLift chain. Extend the guard with isGenArk(), and apply the same fix in getTrackHtml() to avoid an "cannot find trackDb tables" warning on the subsequent description-HTML lookup. refs #37388
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 5, 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/trackDb/trackDbDoc.html
  • lines changed 4, context: html, text, full: html, text
    77a4340b7205e040f0ae5298abc1271ce2f7ca33 Wed Apr 15 10:21:50 2026 -0700
    Adding 'subtrackUrl' trackDb option for faceted composites to specify a linkout url, refs #36320
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 4, context: html, text, full: html, text
    77a4340b7205e040f0ae5298abc1271ce2f7ca33 Wed Apr 15 10:21:50 2026 -0700
    Adding 'subtrackUrl' trackDb option for faceted composites to specify a linkout url, refs #36320
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 17, context: html, text, full: html, text
    77a4340b7205e040f0ae5298abc1271ce2f7ca33 Wed Apr 15 10:21:50 2026 -0700
    Adding 'subtrackUrl' trackDb option for faceted composites to specify a linkout url, refs #36320
  • lines changed 2, context: html, text, full: html, text
    dbd0064a7a30cb9b1274501166f5d072811053a1 Wed Apr 15 12:12:39 2026 -0700
    Fixing typo for the subtrackUrl setting description, refs #36320
• src/hg/htdocs/images/palette.png
  • lines changed 0, context: html, text, full: html, text
    6d78a8e2d7230272d15508db74169ad20cd76f3f Thu Apr 16 12:06:50 2026 -0700
    Restrict color override to supported track types; add palette icon; deduplicate type check, refs #20460 Note: palette.png must be installed to htdocs/images/ (new file). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/inc/recTrackSets.hg19.tab
  • lines changed 1, context: html, text, full: html, text
    159988dc8595c08c87164253d8d09997c925661c Tue Apr 14 13:03:07 2026 -0700
    Creating a new RTS for the InSiGHT VCEP, refs #36582
• src/hg/htdocs/inc/recTrackSets.hg38.tab
  • lines changed 1, context: html, text, full: html, text
    159988dc8595c08c87164253d8d09997c925661c Tue Apr 14 13:03:07 2026 -0700
    Creating a new RTS for the InSiGHT VCEP, refs #36582
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    6d78a8e2d7230272d15508db74169ad20cd76f3f Thu Apr 16 12:06:50 2026 -0700
    Restrict color override to supported track types; add palette icon; deduplicate type check, refs #20460 Note: palette.png must be installed to htdocs/images/ (new file). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/js/facetedComposite.js
  • lines changed 12, context: html, text, full: html, text
    77a4340b7205e040f0ae5298abc1271ce2f7ca33 Wed Apr 15 10:21:50 2026 -0700
    Adding 'subtrackUrl' trackDb option for faceted composites to specify a linkout url, refs #36320
  • lines changed 4, context: html, text, full: html, text
    9abe0c1c7159998b51597ba166ee7a0e56fd48ca Wed Apr 15 12:17:09 2026 -0700
    Adding some error handling for faceted composites with missing or invalid primaryKey settings, refs #36320
• src/hg/js/hgTracks.js
  • lines changed 89, context: html, text, full: html, text
    34a45f462f1b0e73015f60354ded50644bf629b7 Wed Apr 15 13:03:18 2026 -0700
    Apply colorOverride to track labels; add right-click "Change Track Color" dialog, refs #20460 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    74b6045510bad42c806a64523d187c88f3e8565c Wed Apr 15 14:10:34 2026 -0700
    Fix right-click menu separator grouping broken by Change Track Color addition, refs #20460 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 48, context: html, text, full: html, text
    6c1b7e8cb87b181f3220efc0ed86dbb1ceea713e Thu Apr 16 10:36:16 2026 -0700
    hgTracks: harden Change Track Color dialog against XSS and invalid input, refs #20460 In response to findings from the nightly code review: inject hub-controlled shortLabel via .text() instead of HTML concatenation, validate the free-text color input with a hex regex before writing to the cart, and fold the duplicated Apply/Ok handlers into a shared closure.
  • lines changed 1, context: html, text, full: html, text
    6d78a8e2d7230272d15508db74169ad20cd76f3f Thu Apr 16 12:06:50 2026 -0700
    Restrict color override to supported track types; add palette icon; deduplicate type check, refs #20460 Note: palette.png must be installed to htdocs/images/ (new file). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/lib/cart.c
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    349b74eb2b1d02e0d5f229f28d7a6529d0816ca9 Tue Apr 14 15:21:34 2026 -0700
    Shorten hyperlink text and add missing period in db-not-found error message, refs #37305 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/lib/hdb.c
  • lines changed 7, context: html, text, full: html, text
    9b8560a9176523093c93e05e5c40e294abec59d4 Mon Apr 13 06:37:15 2026 -0700
    Fix crash in hNibForChrom for assembly hubs by falling back to trackHubGetGenomeUndecorated before dereferencing genome pointer, refs #37356 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/lib/hgFind.c
  • lines changed 33, context: html, text, full: html, text
    4450e227ad04fd0176b28b6dffddabc0352a953f Mon Apr 13 14:28:42 2026 -0700
    Restore xref term in search result name/description for findSpec searches with an xrefTable. Commit 5197ebd63b5 batched the per-xref doQuery into one combined "or <idField> in (...)" query for performance, but dropped the id -> xrefTerm mapping: pos->name became the raw id and pos->description was no longer set for xref matches. Rebuild the mapping as a hash from xrefList and use it when processing each row to restore pos->name = xrefTerm and pos->description = "(id)". The two-query shape is preserved. refs #37345
• src/hg/lib/hui.c
  • lines changed 23, context: html, text, full: html, text
    c67551cbe58354d143a5a3f0a363f3a4f9c1fdc7 Mon Apr 13 15:11:42 2026 -0700
    Use Spectrum.js color picker for track color override in hui.c refs #20460 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 22, context: html, text, full: html, text
    6d78a8e2d7230272d15508db74169ad20cd76f3f Thu Apr 16 12:06:50 2026 -0700
    Restrict color override to supported track types; add palette icon; deduplicate type check, refs #20460 Note: palette.png must be installed to htdocs/images/ (new file). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    69a23e3d6507ff4d95c8bd99f97615e1159a0c17 Fri Apr 17 09:56:19 2026 -0700
    hgc: don't try to MySQL-connect to a GenArk source assembly in quickLift paths When a track has a quickLiftDb pointing to a GenArk accession (e.g. GCA_018466835.2), hgc crashed clicking on an item because genericClickHandlerPlus called hAllocConnTrack() on a db name that only exists as a hub assembly, not a MySQL database. The existing guard only skipped trackHubDatabase() entries (hubs registered in hubAssemblyHash), which doesn't include on-demand GenArk assemblies referenced by a quickLift chain. Extend the guard with isGenArk(), and apply the same fix in getTrackHtml() to avoid an "cannot find trackDb tables" warning on the subsequent description-HTML lookup. refs #37388
  • lines changed 2, context: html, text, full: html, text
    cb0c45df28d01afc48d55f91a642dc456e6fe478 Sat Apr 18 13:36:06 2026 -0700
    Add bigDbSnp to the list of track types that support the Change Track Color override; the bigDbSnp renderer goes through genericDrawItems/colorFromCart so the override takes effect by clearing the per-SNP functional-impact itemColor callback. refs #20460 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/InSiGHT.txt
  • lines changed 156, context: html, text, full: html, text
    ed3cb243b9151cae7d1859712148fa1d1e1a2196 Mon Apr 13 17:34:17 2026 -0700
    Adding makedoc and build scripts for InSiGHT VCEP track hub. refs #36582
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    dc7ac233e8848cee5087dca606f4d638ca8a3be1 Tue Apr 14 11:58:42 2026 -0700
    Update InSiGHT scripts per v2.0.0 CSpec: fix PMS2 BS1 threshold, add PMS2 PVS1 Moderate region. refs #36582
• src/hg/makeDb/doc/danRer11/bacEndPairsLift.txt
  • lines changed 39, 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/hg38/abelSv.txt
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    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/bacRearray32k.txt
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    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/encode4.regulation.txt
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    af291f82582af89f7c623eb4d13b8141d28e9862 Mon Apr 13 10:19:16 2026 -0700
    Update ENCODE4 makedocs with defaultSortField step. refs #34923
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    65189b08b3a2b7efe27670b30379feb200187541 Fri Apr 17 09:14:07 2026 -0700
    Link accession column to ENCODE portal for ENCODE4 Regulation bigComposites. refs #34923 Add subtrackUrl https://www.encodeproject.org/files/$$/ to all 6 hg38 and mm10 bigComposite tracks (Epigenetics, RnaSeq, TfChip). The new trackDb setting (refs #36320 note 157) replaces $$ with the value from the primaryKey column, making each accession in the configuration table a clickable link to the corresponding file details page on the ENCODE portal. Also added a note in the Data Access section of each composite's HTML, and updated both makedocs.
• src/hg/makeDb/doc/hg38/lrSv.txt
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    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>
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    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/strVar.txt
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    6ab7b1dfca6cc123dfe09a9e9f8afdf0c8cbdf31 Mon Apr 20 06:40:58 2026 -0700
    changes after code review, refs #37376
• src/hg/makeDb/doc/hg38/varFreqs.txt
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    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>
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    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/mm10.encode4.regulation.txt
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    af291f82582af89f7c623eb4d13b8141d28e9862 Mon Apr 13 10:19:16 2026 -0700
    Update ENCODE4 makedocs with defaultSortField step. refs #34923
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    65189b08b3a2b7efe27670b30379feb200187541 Fri Apr 17 09:14:07 2026 -0700
    Link accession column to ENCODE portal for ENCODE4 Regulation bigComposites. refs #34923 Add subtrackUrl https://www.encodeproject.org/files/$$/ to all 6 hg38 and mm10 bigComposite tracks (Epigenetics, RnaSeq, TfChip). The new trackDb setting (refs #36320 note 157) replaces $$ with the value from the primaryKey column, making each accession in the configuration table a clickable link to the corresponding file details page on the ENCODE portal. Also added a note in the Data Access section of each composite's HTML, and updated both makedocs.
• src/hg/makeDb/doc/mm10.txt
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    f5bb3841ce07863d41d9a41d99f44546e245c16a Thu Apr 16 12:23:26 2026 -0700
    Adding native mouse developmental timecourse bulk RNA-seq tracks for mm10 and mm39 from the Woldlab public hub using Claude, refs #37001
• src/hg/makeDb/doc/mm39/mouseDevTimecourse.txt
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    f5bb3841ce07863d41d9a41d99f44546e245c16a Thu Apr 16 12:23:26 2026 -0700
    Adding native mouse developmental timecourse bulk RNA-seq tracks for mm10 and mm39 from the Woldlab public hub using Claude, refs #37001
• src/hg/makeDb/scripts/abelSv/abelSv.as
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    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/scripts/abelSv/build.sh
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    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/scripts/abelSv/vcfToBed.py
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    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/scripts/bacEndPairsLift/toBed12.py
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    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/scripts/insight/buildInsightClinVar.py
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    ed3cb243b9151cae7d1859712148fa1d1e1a2196 Mon Apr 13 17:34:17 2026 -0700
    Adding makedoc and build scripts for InSiGHT VCEP track hub. refs #36582
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    55225be4fa1c5b6c1d886c524606b67701e86448 Tue Apr 14 10:32:57 2026 -0700
    Fix typo, comment error, and bare except in InSiGHT build scripts per code review. refs #36582
• src/hg/makeDb/scripts/insight/insightAFfrequencies.py
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    ed3cb243b9151cae7d1859712148fa1d1e1a2196 Mon Apr 13 17:34:17 2026 -0700
    Adding makedoc and build scripts for InSiGHT VCEP track hub. refs #36582
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    55225be4fa1c5b6c1d886c524606b67701e86448 Tue Apr 14 10:32:57 2026 -0700
    Fix typo, comment error, and bare except in InSiGHT build scripts per code review. refs #36582
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    dc7ac233e8848cee5087dca606f4d638ca8a3be1 Tue Apr 14 11:58:42 2026 -0700
    Update InSiGHT scripts per v2.0.0 CSpec: fix PMS2 BS1 threshold, add PMS2 PVS1 Moderate region. refs #36582
• src/hg/makeDb/scripts/insight/insightClinDomains.py
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    ed3cb243b9151cae7d1859712148fa1d1e1a2196 Mon Apr 13 17:34:17 2026 -0700
    Adding makedoc and build scripts for InSiGHT VCEP track hub. refs #36582
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    55225be4fa1c5b6c1d886c524606b67701e86448 Tue Apr 14 10:32:57 2026 -0700
    Fix typo, comment error, and bare except in InSiGHT build scripts per code review. refs #36582
• src/hg/makeDb/scripts/insight/insightFunctionalAssays.py
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    ed3cb243b9151cae7d1859712148fa1d1e1a2196 Mon Apr 13 17:34:17 2026 -0700
    Adding makedoc and build scripts for InSiGHT VCEP track hub. refs #36582
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    55225be4fa1c5b6c1d886c524606b67701e86448 Tue Apr 14 10:32:57 2026 -0700
    Fix typo, comment error, and bare except in InSiGHT build scripts per code review. refs #36582
• src/hg/makeDb/scripts/insight/insightHCIPriors.py
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    ed3cb243b9151cae7d1859712148fa1d1e1a2196 Mon Apr 13 17:34:17 2026 -0700
    Adding makedoc and build scripts for InSiGHT VCEP track hub. refs #36582
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    55225be4fa1c5b6c1d886c524606b67701e86448 Tue Apr 14 10:32:57 2026 -0700
    Fix typo, comment error, and bare except in InSiGHT build scripts per code review. refs #36582
• src/hg/makeDb/scripts/insight/insightPVS1.py
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    ed3cb243b9151cae7d1859712148fa1d1e1a2196 Mon Apr 13 17:34:17 2026 -0700
    Adding makedoc and build scripts for InSiGHT VCEP track hub. refs #36582
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    55225be4fa1c5b6c1d886c524606b67701e86448 Tue Apr 14 10:32:57 2026 -0700
    Fix typo, comment error, and bare except in InSiGHT build scripts per code review. refs #36582
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    dc7ac233e8848cee5087dca606f4d638ca8a3be1 Tue Apr 14 11:58:42 2026 -0700
    Update InSiGHT scripts per v2.0.0 CSpec: fix PMS2 BS1 threshold, add PMS2 PVS1 Moderate region. refs #36582
• src/hg/makeDb/scripts/lrSv/lrSv.as
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    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/scripts/lrSv/lrSv1kgOnt.as
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    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/scripts/lrSv/lrSv1kgOntVcfToBed.py
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    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/scripts/lrSv/lrSvAou1k.as
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    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/scripts/lrSv/lrSvAou1kCsvToBed.py
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    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/scripts/lrSv/lrSvApr.as
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    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/scripts/lrSv/lrSvAprBuild.sh
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    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/scripts/lrSv/lrSvAprVcfToBed.py
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    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/scripts/lrSv/lrSvChirmade101.as
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    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/scripts/lrSv/lrSvChirmade101TsvToBed.py
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    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/scripts/lrSv/lrSvCpc1.as
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    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/scripts/lrSv/lrSvCpc1Build.sh
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    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/scripts/lrSv/lrSvCpc1VcfToBed.py
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    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/scripts/lrSv/lrSvDecode.as
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    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/scripts/lrSv/lrSvDecodeVcfToBed.py
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    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/scripts/lrSv/lrSvGa4kSv.as
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    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/scripts/lrSv/lrSvGa4kSvVcfToBed.py
  • lines changed 84, 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/scripts/lrSv/lrSvHan945SuppVecToVcf.py
  • lines changed 64, 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/scripts/lrSv/lrSvHgsvc3.as
  • lines changed 26, 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/scripts/lrSv/lrSvHgsvc3TsvToBed.py
  • lines changed 132, 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/scripts/lrSv/lrSvKwanho.as
  • lines changed 42, 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/scripts/lrSv/lrSvKwanhoTsvToBed.py
  • lines changed 143, 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/scripts/lrSv/lrSvTommoJp.as
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    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/scripts/lrSv/lrSvTommoJpVcfToBed.py
  • lines changed 126, 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/scripts/lrSv/lrSvVcfToBed.py
  • lines changed 126, 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/scripts/nmd/genePredNmdEsc
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    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/tommoStr/tommoStr.as
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    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/tommoStrToBed.py
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    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/trexplorer/trexplorer.as
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    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/trexplorer/trexplorerToBed.py
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    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/viennaVntr/viennaVntr.as
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    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/viennaVntr/viennaVntrToBed.py
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    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/webstr/webstr.as
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    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/webstr/webstrToBed.py
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    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/trackDb/bacteria/staAur2/cons369way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/bushbaby/otoGar3/cons3way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/cat/felCat3/multiz4way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/cat/felCat4/cons6way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/chicken/galGal2/multiz7way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/chicken/galGal3/multiz7way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/chicken/galGal6/cons77way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/cow/bosTau4/multiz5way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/criGri/regenCho1/cons7way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/dog/canFam1/mzHg17Mm5_phast.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/dog/canFam2/multiz4way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/drosophila/dm2/multiz12way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/drosophila/dm2/multiz15way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/drosophila/dm2/multiz8way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/drosophila/dm2/multiz9way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/drosophila/dm3/multiz15way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/drosophila/dm6/cons124way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/drosophila/dm6/cons27way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/drosophila/mzDy1Dp2Ag1_phast.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/fugu/fr2/multiz5way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/fugu/fr3/cons8way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/galVar/galVar1/cons4way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/galVar/galVar1/cons5way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/galVar/galVar1/cons6way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/gorilla/gorGor3/cons11way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/guineaPig/cavPor3/cons5way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/guineaPig/cavPor3/cons6way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/horse/equCab2/multiz6way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/human/aou1kSv.html
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    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/trackDb/human/aprSv.html
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    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/trackDb/human/chirmade101Sv.html
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    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/trackDb/human/cloneEnd.trackDb.ra
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    4fd9f828f80a223799ce69d7078ee22ffe8aabc5 Wed Apr 15 07:22:19 2026 -0700
    fixing up after claude, refs #35059
• src/hg/makeDb/trackDb/human/colorsDbSnv.html
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    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/trackDb/human/cpc1Sv.html
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    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/trackDb/human/decodeSv.html
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    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/trackDb/human/ga4kSnv.html
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    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/trackDb/human/ga4kSv.html
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    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/trackDb/human/han945Sv.html
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    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/trackDb/human/hg18/multiz28way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/human/hg18/multizPrimate.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/human/hg38/abelSv.html
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    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/trackDb/human/hg38/abelSv.ra
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    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/trackDb/human/hg38/bacRearray32k.html
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    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/trackDb/human/hg38/cons17way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/human/hg38/cons20way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/human/hg38/cons27way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/human/hg38/cons30way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/human/hg38/cons4way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/human/hg38/cons5way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/human/hg38/cons7way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
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    3aec5f10b5edd6df96170253ddfe72a526586365 Fri Apr 10 16:39:59 2026 -0700
    Making it clear that the gnomAD str track was added, refs #35420
• src/hg/makeDb/trackDb/human/hg38/mane.alpha.ra
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    2f0deaf88df6e28e28ac768f9c600d46ae1966c1 Wed Apr 15 14:25:23 2026 -0700
    Deleting an old mane.alpha track from 2022, I accidentally bumped into it updating the MANE labels. No RM.
• src/hg/makeDb/trackDb/human/hg38/mane.ra
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    01428b5a058a1d0ebdd0582235ad05ddd13e6528 Wed Apr 15 15:33:19 2026 -0700
    Adding new improved label matches on search results to MANE, refs #37299
• src/hg/makeDb/trackDb/human/hg38/mb2.ra
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    6dc2c9cfeea520480c21f04ee957c5297c0ee64f Wed Apr 15 10:25:45 2026 -0700
    Further label changes to MethBase 2, still a work in progress, refs #36320
• src/hg/makeDb/trackDb/human/hg38/mb2_2.ra
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    6dc2c9cfeea520480c21f04ee957c5297c0ee64f Wed Apr 15 10:25:45 2026 -0700
    Further label changes to MethBase 2, still a work in progress, refs #36320
• src/hg/makeDb/trackDb/human/hg38/nmd.html
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    04b359f6abe6b9c526f19fe7a59cda77d8daed51 Tue Apr 14 16:35:37 2026 -0700
    QA fixes for NMD Escape supertrack: labels, HTML descriptions, PMIDs. refs #33737 Fix shortLabels exceeding 20 chars and longLabels exceeding 80 chars across all subtracks. Fix wrong PMIDs for Nagy and Kurosaki references in nmd.html. Reorder references alphabetically and add DOI/PMC links. Add Data Access and Credits sections to all three description pages.
• src/hg/makeDb/trackDb/human/hg38/nmd.ra
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    04b359f6abe6b9c526f19fe7a59cda77d8daed51 Tue Apr 14 16:35:37 2026 -0700
    QA fixes for NMD Escape supertrack: labels, HTML descriptions, PMIDs. refs #33737 Fix shortLabels exceeding 20 chars and longLabels exceeding 80 chars across all subtracks. Fix wrong PMIDs for Nagy and Kurosaki references in nmd.html. Reorder references alphabetically and add DOI/PMC links. Add Data Access and Credits sections to all three description pages.
• src/hg/makeDb/trackDb/human/hg38/nmdDetective.html
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    04b359f6abe6b9c526f19fe7a59cda77d8daed51 Tue Apr 14 16:35:37 2026 -0700
    QA fixes for NMD Escape supertrack: labels, HTML descriptions, PMIDs. refs #33737 Fix shortLabels exceeding 20 chars and longLabels exceeding 80 chars across all subtracks. Fix wrong PMIDs for Nagy and Kurosaki references in nmd.html. Reorder references alphabetically and add DOI/PMC links. Add Data Access and Credits sections to all three description pages.
• src/hg/makeDb/trackDb/human/hg38/nmdEscTranscripts.html
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    04b359f6abe6b9c526f19fe7a59cda77d8daed51 Tue Apr 14 16:35:37 2026 -0700
    QA fixes for NMD Escape supertrack: labels, HTML descriptions, PMIDs. refs #33737 Fix shortLabels exceeding 20 chars and longLabels exceeding 80 chars across all subtracks. Fix wrong PMIDs for Nagy and Kurosaki references in nmd.html. Reorder references alphabetically and add DOI/PMC links. Add Data Access and Credits sections to all three description pages.
• src/hg/makeDb/trackDb/human/hg38/tommoStr.html
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    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/trackDb/human/hg38/trackDb.cloneEnd.ra
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    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>
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    4fd9f828f80a223799ce69d7078ee22ffe8aabc5 Wed Apr 15 07:22:19 2026 -0700
    fixing up after claude, refs #35059
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    38549bf61d05dc874b81c0d33c2e27a620e51d52 Mon Apr 13 13:39:20 2026 -0700
    initial view of the VGP 577-way cactus alignment refs #34370
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    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/trackDb/human/hg38/trexplorer.html
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    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/trackDb/human/hg38/vgp577way.trackDb.ra
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    38549bf61d05dc874b81c0d33c2e27a620e51d52 Mon Apr 13 13:39:20 2026 -0700
    initial view of the VGP 577-way cactus alignment refs #34370
• src/hg/makeDb/trackDb/human/hg38/viennaVntr.html
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    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/trackDb/human/hg38/webstr.html
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    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/trackDb/human/hg38/wgEncodeReg4Epigenetics.html
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    65189b08b3a2b7efe27670b30379feb200187541 Fri Apr 17 09:14:07 2026 -0700
    Link accession column to ENCODE portal for ENCODE4 Regulation bigComposites. refs #34923 Add subtrackUrl https://www.encodeproject.org/files/$$/ to all 6 hg38 and mm10 bigComposite tracks (Epigenetics, RnaSeq, TfChip). The new trackDb setting (refs #36320 note 157) replaces $$ with the value from the primaryKey column, making each accession in the configuration table a clickable link to the corresponding file details page on the ENCODE portal. Also added a note in the Data Access section of each composite's HTML, and updated both makedocs.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra
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    925304757ea50469b4f20b5880ba58e2667e29db Mon Apr 13 10:18:21 2026 -0700
    Add defaultSortField to ENCODE4 bigComposite tracks to group peak/signal pairs. refs #34923 Added _Experiment column (hidden from facets via underscore prefix) to metadata TSVs for hg38 and mm10 Epigenetics and TF ChIP composites. Set defaultSortField to _Experiment so peak and signal subtracks from the same experiment sort adjacent. Also fixed pre-existing CRLF line endings in three metadata TSVs.
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    65189b08b3a2b7efe27670b30379feb200187541 Fri Apr 17 09:14:07 2026 -0700
    Link accession column to ENCODE portal for ENCODE4 Regulation bigComposites. refs #34923 Add subtrackUrl https://www.encodeproject.org/files/$$/ to all 6 hg38 and mm10 bigComposite tracks (Epigenetics, RnaSeq, TfChip). The new trackDb setting (refs #36320 note 157) replaces $$ with the value from the primaryKey column, making each accession in the configuration table a clickable link to the corresponding file details page on the ENCODE portal. Also added a note in the Data Access section of each composite's HTML, and updated both makedocs.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.html
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    65189b08b3a2b7efe27670b30379feb200187541 Fri Apr 17 09:14:07 2026 -0700
    Link accession column to ENCODE portal for ENCODE4 Regulation bigComposites. refs #34923 Add subtrackUrl https://www.encodeproject.org/files/$$/ to all 6 hg38 and mm10 bigComposite tracks (Epigenetics, RnaSeq, TfChip). The new trackDb setting (refs #36320 note 157) replaces $$ with the value from the primaryKey column, making each accession in the configuration table a clickable link to the corresponding file details page on the ENCODE portal. Also added a note in the Data Access section of each composite's HTML, and updated both makedocs.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.ra
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    65189b08b3a2b7efe27670b30379feb200187541 Fri Apr 17 09:14:07 2026 -0700
    Link accession column to ENCODE portal for ENCODE4 Regulation bigComposites. refs #34923 Add subtrackUrl https://www.encodeproject.org/files/$$/ to all 6 hg38 and mm10 bigComposite tracks (Epigenetics, RnaSeq, TfChip). The new trackDb setting (refs #36320 note 157) replaces $$ with the value from the primaryKey column, making each accession in the configuration table a clickable link to the corresponding file details page on the ENCODE portal. Also added a note in the Data Access section of each composite's HTML, and updated both makedocs.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.html
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    65189b08b3a2b7efe27670b30379feb200187541 Fri Apr 17 09:14:07 2026 -0700
    Link accession column to ENCODE portal for ENCODE4 Regulation bigComposites. refs #34923 Add subtrackUrl https://www.encodeproject.org/files/$$/ to all 6 hg38 and mm10 bigComposite tracks (Epigenetics, RnaSeq, TfChip). The new trackDb setting (refs #36320 note 157) replaces $$ with the value from the primaryKey column, making each accession in the configuration table a clickable link to the corresponding file details page on the ENCODE portal. Also added a note in the Data Access section of each composite's HTML, and updated both makedocs.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.ra
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    925304757ea50469b4f20b5880ba58e2667e29db Mon Apr 13 10:18:21 2026 -0700
    Add defaultSortField to ENCODE4 bigComposite tracks to group peak/signal pairs. refs #34923 Added _Experiment column (hidden from facets via underscore prefix) to metadata TSVs for hg38 and mm10 Epigenetics and TF ChIP composites. Set defaultSortField to _Experiment so peak and signal subtracks from the same experiment sort adjacent. Also fixed pre-existing CRLF line endings in three metadata TSVs.
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    65189b08b3a2b7efe27670b30379feb200187541 Fri Apr 17 09:14:07 2026 -0700
    Link accession column to ENCODE portal for ENCODE4 Regulation bigComposites. refs #34923 Add subtrackUrl https://www.encodeproject.org/files/$$/ to all 6 hg38 and mm10 bigComposite tracks (Epigenetics, RnaSeq, TfChip). The new trackDb setting (refs #36320 note 157) replaces $$ with the value from the primaryKey column, making each accession in the configuration table a clickable link to the corresponding file details page on the ENCODE portal. Also added a note in the Data Access section of each composite's HTML, and updated both makedocs.
• src/hg/makeDb/trackDb/human/hgsvc3Sv.html
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    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/trackDb/human/hs1/trackDb.ra
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    38549bf61d05dc874b81c0d33c2e27a620e51d52 Mon Apr 13 13:39:20 2026 -0700
    initial view of the VGP 577-way cactus alignment refs #34370
• src/hg/makeDb/trackDb/human/hs1/vgp577way.trackDb.ra
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    38549bf61d05dc874b81c0d33c2e27a620e51d52 Mon Apr 13 13:39:20 2026 -0700
    initial view of the VGP 577-way cactus alignment refs #34370
• src/hg/makeDb/trackDb/human/kwanhoSv.html
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    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/trackDb/human/longReadVariants.ra
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    6ab7b1dfca6cc123dfe09a9e9f8afdf0c8cbdf31 Mon Apr 20 06:40:58 2026 -0700
    changes after code review, refs #37376
• src/hg/makeDb/trackDb/human/lrSv.html
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    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/trackDb/human/lrSv.ra
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    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>
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    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/trackDb/human/tommoJpSv.html
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    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/trackDb/human/trackDb.ra
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    ac1e5ad678524308ef32df6154f7f1632a54a266 Fri Apr 17 10:27:56 2026 -0700
    Adding snowflake pennantIcon to AVADA pointing to the VARAICO news archive release, and adding reciprocal relatedTracks entries between AVADA and Varaico for hg19 and hg38. No RM.
• src/hg/makeDb/trackDb/human/varFreqs.html
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    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>
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    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/trackDb/human/varFreqs.ra
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    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>
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    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/trackDb/lamprey/petMar1/multiz6way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/lancelet/braFlo1/multiz5way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/lizard/anoCar2/cons7way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/medaka/oryLat2/multiz5way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html
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    367b855aad5d40c853edb4c5286dd91749314cd3 Tue Apr 14 17:09:52 2026 -0700
    Updating mm10 ENCODE4 cCREs track description pages and trackDb settings, refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/cCREsSuper.html
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    367b855aad5d40c853edb4c5286dd91749314cd3 Tue Apr 14 17:09:52 2026 -0700
    Updating mm10 ENCODE4 cCREs track description pages and trackDb settings, refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/cons4way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/mouse/mm10/coreCollection.html
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    367b855aad5d40c853edb4c5286dd91749314cd3 Tue Apr 14 17:09:52 2026 -0700
    Updating mm10 ENCODE4 cCREs track description pages and trackDb settings, refs #37131
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    be7a61203ddd2ae5a51aed21ee093b2e712a0312 Fri Apr 17 10:04:18 2026 -0700
    Fix Core Collection cCRE class list in mm10 description to match actual data: rename 'Chromatin accessibility (CA)' to 'CA-only' and remove 'Transcription factor (TF)' (TF class is Registry-only, not present in any of the 18 Core Collection bigBeds). refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/developmentTimecourseM21mm10FPKM.html
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    f5bb3841ce07863d41d9a41d99f44546e245c16a Thu Apr 16 12:23:26 2026 -0700
    Adding native mouse developmental timecourse bulk RNA-seq tracks for mm10 and mm39 from the Woldlab public hub using Claude, refs #37001
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    4d5b62e7f9485f7e595d22d2ebe0824c548897d5 Thu Apr 16 16:15:36 2026 -0700
    Updating mouseDevTimecourse track description pages and longLabels using Claude. refs #37001
• src/hg/makeDb/trackDb/mouse/mm10/developmentTimecourseM21mm10TPM.html
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    f5bb3841ce07863d41d9a41d99f44546e245c16a Thu Apr 16 12:23:26 2026 -0700
    Adding native mouse developmental timecourse bulk RNA-seq tracks for mm10 and mm39 from the Woldlab public hub using Claude, refs #37001
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    4d5b62e7f9485f7e595d22d2ebe0824c548897d5 Thu Apr 16 16:15:36 2026 -0700
    Updating mouseDevTimecourse track description pages and longLabels using Claude. refs #37001
• src/hg/makeDb/trackDb/mouse/mm10/developmentTimecourseM4mm10FPKM.html
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    f5bb3841ce07863d41d9a41d99f44546e245c16a Thu Apr 16 12:23:26 2026 -0700
    Adding native mouse developmental timecourse bulk RNA-seq tracks for mm10 and mm39 from the Woldlab public hub using Claude, refs #37001
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    4d5b62e7f9485f7e595d22d2ebe0824c548897d5 Thu Apr 16 16:15:36 2026 -0700
    Updating mouseDevTimecourse track description pages and longLabels using Claude. refs #37001
• src/hg/makeDb/trackDb/mouse/mm10/developmentTimecourseM4mm10TPM.html
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    f5bb3841ce07863d41d9a41d99f44546e245c16a Thu Apr 16 12:23:26 2026 -0700
    Adding native mouse developmental timecourse bulk RNA-seq tracks for mm10 and mm39 from the Woldlab public hub using Claude, refs #37001
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    4d5b62e7f9485f7e595d22d2ebe0824c548897d5 Thu Apr 16 16:15:36 2026 -0700
    Updating mouseDevTimecourse track description pages and longLabels using Claude. refs #37001
• src/hg/makeDb/trackDb/mouse/mm10/encode.cCREs.override.ra
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    367b855aad5d40c853edb4c5286dd91749314cd3 Tue Apr 14 17:09:52 2026 -0700
    Updating mm10 ENCODE4 cCREs track description pages and trackDb settings, refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/encode4.ccres.ra
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    367b855aad5d40c853edb4c5286dd91749314cd3 Tue Apr 14 17:09:52 2026 -0700
    Updating mm10 ENCODE4 cCREs track description pages and trackDb settings, refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.html
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    65189b08b3a2b7efe27670b30379feb200187541 Fri Apr 17 09:14:07 2026 -0700
    Link accession column to ENCODE portal for ENCODE4 Regulation bigComposites. refs #34923 Add subtrackUrl https://www.encodeproject.org/files/$$/ to all 6 hg38 and mm10 bigComposite tracks (Epigenetics, RnaSeq, TfChip). The new trackDb setting (refs #36320 note 157) replaces $$ with the value from the primaryKey column, making each accession in the configuration table a clickable link to the corresponding file details page on the ENCODE portal. Also added a note in the Data Access section of each composite's HTML, and updated both makedocs.
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra
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    925304757ea50469b4f20b5880ba58e2667e29db Mon Apr 13 10:18:21 2026 -0700
    Add defaultSortField to ENCODE4 bigComposite tracks to group peak/signal pairs. refs #34923 Added _Experiment column (hidden from facets via underscore prefix) to metadata TSVs for hg38 and mm10 Epigenetics and TF ChIP composites. Set defaultSortField to _Experiment so peak and signal subtracks from the same experiment sort adjacent. Also fixed pre-existing CRLF line endings in three metadata TSVs.
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    65189b08b3a2b7efe27670b30379feb200187541 Fri Apr 17 09:14:07 2026 -0700
    Link accession column to ENCODE portal for ENCODE4 Regulation bigComposites. refs #34923 Add subtrackUrl https://www.encodeproject.org/files/$$/ to all 6 hg38 and mm10 bigComposite tracks (Epigenetics, RnaSeq, TfChip). The new trackDb setting (refs #36320 note 157) replaces $$ with the value from the primaryKey column, making each accession in the configuration table a clickable link to the corresponding file details page on the ENCODE portal. Also added a note in the Data Access section of each composite's HTML, and updated both makedocs.
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.html
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    65189b08b3a2b7efe27670b30379feb200187541 Fri Apr 17 09:14:07 2026 -0700
    Link accession column to ENCODE portal for ENCODE4 Regulation bigComposites. refs #34923 Add subtrackUrl https://www.encodeproject.org/files/$$/ to all 6 hg38 and mm10 bigComposite tracks (Epigenetics, RnaSeq, TfChip). The new trackDb setting (refs #36320 note 157) replaces $$ with the value from the primaryKey column, making each accession in the configuration table a clickable link to the corresponding file details page on the ENCODE portal. Also added a note in the Data Access section of each composite's HTML, and updated both makedocs.
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.ra
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    65189b08b3a2b7efe27670b30379feb200187541 Fri Apr 17 09:14:07 2026 -0700
    Link accession column to ENCODE portal for ENCODE4 Regulation bigComposites. refs #34923 Add subtrackUrl https://www.encodeproject.org/files/$$/ to all 6 hg38 and mm10 bigComposite tracks (Epigenetics, RnaSeq, TfChip). The new trackDb setting (refs #36320 note 157) replaces $$ with the value from the primaryKey column, making each accession in the configuration table a clickable link to the corresponding file details page on the ENCODE portal. Also added a note in the Data Access section of each composite's HTML, and updated both makedocs.
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.html
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    65189b08b3a2b7efe27670b30379feb200187541 Fri Apr 17 09:14:07 2026 -0700
    Link accession column to ENCODE portal for ENCODE4 Regulation bigComposites. refs #34923 Add subtrackUrl https://www.encodeproject.org/files/$$/ to all 6 hg38 and mm10 bigComposite tracks (Epigenetics, RnaSeq, TfChip). The new trackDb setting (refs #36320 note 157) replaces $$ with the value from the primaryKey column, making each accession in the configuration table a clickable link to the corresponding file details page on the ENCODE portal. Also added a note in the Data Access section of each composite's HTML, and updated both makedocs.
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra
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    925304757ea50469b4f20b5880ba58e2667e29db Mon Apr 13 10:18:21 2026 -0700
    Add defaultSortField to ENCODE4 bigComposite tracks to group peak/signal pairs. refs #34923 Added _Experiment column (hidden from facets via underscore prefix) to metadata TSVs for hg38 and mm10 Epigenetics and TF ChIP composites. Set defaultSortField to _Experiment so peak and signal subtracks from the same experiment sort adjacent. Also fixed pre-existing CRLF line endings in three metadata TSVs.
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    65189b08b3a2b7efe27670b30379feb200187541 Fri Apr 17 09:14:07 2026 -0700
    Link accession column to ENCODE portal for ENCODE4 Regulation bigComposites. refs #34923 Add subtrackUrl https://www.encodeproject.org/files/$$/ to all 6 hg38 and mm10 bigComposite tracks (Epigenetics, RnaSeq, TfChip). The new trackDb setting (refs #36320 note 157) replaces $$ with the value from the primaryKey column, making each accession in the configuration table a clickable link to the corresponding file details page on the ENCODE portal. Also added a note in the Data Access section of each composite's HTML, and updated both makedocs.
• src/hg/makeDb/trackDb/mouse/mm10/mouseDevTimecourse.html
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    f5bb3841ce07863d41d9a41d99f44546e245c16a Thu Apr 16 12:23:26 2026 -0700
    Adding native mouse developmental timecourse bulk RNA-seq tracks for mm10 and mm39 from the Woldlab public hub using Claude, refs #37001
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    4d5b62e7f9485f7e595d22d2ebe0824c548897d5 Thu Apr 16 16:15:36 2026 -0700
    Updating mouseDevTimecourse track description pages and longLabels using Claude. refs #37001
• src/hg/makeDb/trackDb/mouse/mm10/mouseDevTimecourse.ra
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    f5bb3841ce07863d41d9a41d99f44546e245c16a Thu Apr 16 12:23:26 2026 -0700
    Adding native mouse developmental timecourse bulk RNA-seq tracks for mm10 and mm39 from the Woldlab public hub using Claude, refs #37001
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    4d5b62e7f9485f7e595d22d2ebe0824c548897d5 Thu Apr 16 16:15:36 2026 -0700
    Updating mouseDevTimecourse track description pages and longLabels using Claude. refs #37001
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.ra
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    0bce85c1c28d45448a957ba5e9054eed75132096 Fri Apr 17 15:53:54 2026 -0700
    Staging the mm10 ENCODE4 cCREs track on hgwbeta; moved encodeCcreCombined.old.ra out of trackDb.encode3.ra into trackDb.ra since updating the release tag to public-only caused a make beta build error, refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    f5bb3841ce07863d41d9a41d99f44546e245c16a Thu Apr 16 12:23:26 2026 -0700
    Adding native mouse developmental timecourse bulk RNA-seq tracks for mm10 and mm39 from the Woldlab public hub using Claude, refs #37001
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    0bce85c1c28d45448a957ba5e9054eed75132096 Fri Apr 17 15:53:54 2026 -0700
    Staging the mm10 ENCODE4 cCREs track on hgwbeta; moved encodeCcreCombined.old.ra out of trackDb.encode3.ra into trackDb.ra since updating the release tag to public-only caused a make beta build error, refs #37131
• src/hg/makeDb/trackDb/mouse/mm39/cons35way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/mouse/mm39/developmentTimecourseM21mm39FPKM.html
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    f5bb3841ce07863d41d9a41d99f44546e245c16a Thu Apr 16 12:23:26 2026 -0700
    Adding native mouse developmental timecourse bulk RNA-seq tracks for mm10 and mm39 from the Woldlab public hub using Claude, refs #37001
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    4d5b62e7f9485f7e595d22d2ebe0824c548897d5 Thu Apr 16 16:15:36 2026 -0700
    Updating mouseDevTimecourse track description pages and longLabels using Claude. refs #37001
• src/hg/makeDb/trackDb/mouse/mm39/developmentTimecourseM21mm39TPM.html
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    f5bb3841ce07863d41d9a41d99f44546e245c16a Thu Apr 16 12:23:26 2026 -0700
    Adding native mouse developmental timecourse bulk RNA-seq tracks for mm10 and mm39 from the Woldlab public hub using Claude, refs #37001
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    4d5b62e7f9485f7e595d22d2ebe0824c548897d5 Thu Apr 16 16:15:36 2026 -0700
    Updating mouseDevTimecourse track description pages and longLabels using Claude. refs #37001
• src/hg/makeDb/trackDb/mouse/mm39/mouseDevTimecourse.html
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    f5bb3841ce07863d41d9a41d99f44546e245c16a Thu Apr 16 12:23:26 2026 -0700
    Adding native mouse developmental timecourse bulk RNA-seq tracks for mm10 and mm39 from the Woldlab public hub using Claude, refs #37001
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    4d5b62e7f9485f7e595d22d2ebe0824c548897d5 Thu Apr 16 16:15:36 2026 -0700
    Updating mouseDevTimecourse track description pages and longLabels using Claude. refs #37001
• src/hg/makeDb/trackDb/mouse/mm39/mouseDevTimecourse.ra
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    f5bb3841ce07863d41d9a41d99f44546e245c16a Thu Apr 16 12:23:26 2026 -0700
    Adding native mouse developmental timecourse bulk RNA-seq tracks for mm10 and mm39 from the Woldlab public hub using Claude, refs #37001
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    4d5b62e7f9485f7e595d22d2ebe0824c548897d5 Thu Apr 16 16:15:36 2026 -0700
    Updating mouseDevTimecourse track description pages and longLabels using Claude. refs #37001
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
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    f5bb3841ce07863d41d9a41d99f44546e245c16a Thu Apr 16 12:23:26 2026 -0700
    Adding native mouse developmental timecourse bulk RNA-seq tracks for mm10 and mm39 from the Woldlab public hub using Claude, refs #37001
• src/hg/makeDb/trackDb/mouse/mm7/multiz17way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/mouse/mm8/multiz17way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/mouse/mm9/multiz30way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/mouseLemur/micMur3/cons3way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/opossum/monDom4/multiz7way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/opossum/monDom5/multiz9way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/opossum/multiz5way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/orangutan/ponAbe2/multiz8way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/platypus/ornAna1/multiz6way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/rat/regenRn1/cons7way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/rat/rn4/multiz9way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/rat/rn5/cons13way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/rat/rn6/cons20way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/relatedTracks.ra
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    ac1e5ad678524308ef32df6154f7f1632a54a266 Fri Apr 17 10:27:56 2026 -0700
    Adding snowflake pennantIcon to AVADA pointing to the VARAICO news archive release, and adding reciprocal relatedTracks entries between AVADA and Varaico for hg19 and hg38. No RM.
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    e8cfed22bdb02ca22850d6a33f82370df0d4b24f Mon Apr 20 06:42:15 2026 -0700
    adding related tracks from the long read sv supertrack
• src/hg/makeDb/trackDb/sacCer/multizYeast.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/sacCer/sacCer2/multiz7way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/sacCer/sacCer3/multiz7way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/stickleback/gasAcu1/multiz8way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/tagTypes.tab
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    4b55654dd73a403c1f30eeefbe37489a3bb4153f Mon Apr 13 13:41:50 2026 -0700
    initial view of the VGP 577-way cactus alignment refs #34370
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    77a4340b7205e040f0ae5298abc1271ce2f7ca33 Wed Apr 15 10:21:50 2026 -0700
    Adding 'subtrackUrl' trackDb option for faceted composites to specify a linkout url, refs #36320
• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons17way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons20way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/trackDb.encode3.ra
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    8c44bb1acda9ad5f13f7839d3994d6e4f07a2fa1 Sat Apr 18 11:27:44 2026 -0700
    Add cartVersion 10 to re-apply the encodeCcreCombined -> cCREs supertrack migration for carts saved while cartVersion was already 9 but before the trackDb switch to the new supertrack. refs #37383 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/treeShrew/tupChi1/cons4way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/treeShrew/tupChi1/cons5way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/virus/wuhCor1/cons119way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/virus/wuhCor1/cons44way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/virus/wuhCor1/cons7way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/worm/ce10/cons7way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/worm/ce10/cons9way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/worm/ce11/cons135way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/worm/ce11/cons26way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/worm/ce2/c_briggsae_pwMaf.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/worm/ce4/multiz5way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/worm/ce6/multiz6way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/xenTro/xenTro2/multiz7way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/xenTro/xenTro9/cons11way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/zebrafish/danRer10/cons12way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/zebrafish/danRer11/bacEndPairsLift.html
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    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/trackDb.ra
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    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/danRer3/multiz5way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/zebrafish/danRer4/multiz7way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/makeDb/trackDb/zebrafish/danRer7/cons8way.html
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    8813ac251245d677748cb32ae7462a9a851ec4de Tue Apr 14 12:08:50 2026 -0700
    Adding Phylogenetic Hidden Markov Models link in 92 conservation track descriptions. Jairo's feedback through an email. This work was done as part of #37324
• src/hg/utils/automation/doBlastzChainNet.pl
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    bc8249599cb2e1365b24e7e331f5b61a2e6c73ff Fri Apr 17 08:57:06 2026 -0700
    rais ram limit during chain run to 64g to prevent out of memory crashes
• src/hg/utils/automation/doXenoRefGene.pl
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    cd2eb699ee42cfe22aa6d1587ed3ac444953d8e9 Fri Apr 17 13:00:43 2026 -0700
    fixup to get geneName2 column correctly populated refs #14450
• src/hg/utils/automation/kegAlign.json.ga
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    2cbbc4621cd9e83ffd450178330665df5ae36fe0 Wed Apr 15 16:56:37 2026 -0700
    closing in on a galaxy lastz workflow that may be useful refs #31811
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    fda87ad3679538899bf2adecc27a6e9c0bc678c8 Sun Apr 19 10:37:42 2026 -0700
    correctly naming the liftOver and liftOverSwap file outputs refs #31811
• src/hg/utils/automation/kegAlignLastz.sh
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    9de971b5871aa13f6aaac9928fcb456b75a8359c Mon Apr 13 15:55:21 2026 -0700
    initial shell to run galaxy kegAlign lastz - to be cleaned up refs #31811
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    f08a32f711b71809d508587d53612a3d701b8749 Mon Apr 13 16:23:53 2026 -0700
    adding processing of the result into bigBed files and in the usual lastz output locations refs #31811
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    032903d6adc6d0c49cbedf17c51f4319052cb8ef Thu Apr 16 12:43:59 2026 -0700
    improved variable naming fixup problems process in work refs #31811
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    fd4b9f71e184d33ced4948ba1ba8618faed8d576 Thu Apr 16 13:42:54 2026 -0700
    make it possible to run either the galaxy kegAlign or the classic UCSC process, function up the bigBed creation and featureBits calculations, make everything in the kegAlign process reentrant so the script can be run repeatedly to fix broken issues refs #31811
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    c6b00020d3775552377ee3fda1a77d9cb39c453d Fri Apr 17 15:16:44 2026 -0700
    correct specification for the linearGap and scoreMatrix inputs refs #31811
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    7edafbf8e253dec09305b4c540ebff3cd9557837 Fri Apr 17 16:30:08 2026 -0700
    add the genark verification check and fixup errors in the scripting refs #31811
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    c078aaab1bcbfbc23b26931b850430af6f352c3f Sun Apr 19 10:41:30 2026 -0700
    correctly naming the liftOver and liftOverSwap file outputs refs #31811
• src/hg/utils/automation/pairLastz.sh
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    87eb4afb1cb9d39eb4d175462a467c23306f091c Fri Apr 17 14:59:00 2026 -0700
    logs should accumulate only, never overwrite
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    96adb44e8265446fccbaac39dd13bae7217d4825 Fri Apr 17 15:13:38 2026 -0700
    verify given GenArk assemblies actually exist in GenArk before proceeding refs #37380
• src/hg/utils/otto/genCC/doGenCC.py
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    d0dafe3247d2e3c5c892c498784e4065590df665 Wed Apr 15 12:14:43 2026 -0700
    Adding a flag to continue with the script if the item count is more than 10% (after QA approves), no redmine.
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    4ff781d4f74a99c1b6a05a5a6ef61e4e7819c220 Wed Apr 15 12:35:55 2026 -0700
    Move prevSubmission.tsv update to after item count checks in genCC otto, no redmine. Previously the mv ran before checkItemCounts, so a failed run would mark the update as done and prevent re-runs with --force from detecting the change. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    9364a4054ae5065f07014618eef211a85a4b8c1f Wed Apr 15 13:07:01 2026 -0700
    Have --force bypass the md5sum update check in genCC otto, no redmine. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    74b022cc616762a29b67e4eedc96242e040740ac Wed Apr 15 13:18:30 2026 -0700
    Fixing spacing for when the message is printed, no Redmine
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    bb1f29a4c6d5222beb5d51c05486fefaa763da51 Wed Apr 15 13:27:07 2026 -0700
    Printing out how to force the update if the itemCheck fails for genCC, no Redmine
• src/hg/utils/otto/otto.crontab
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    444a2b070e48370587223105f4428d94cb796e51 Tue Apr 14 15:09:09 2026 -0700
    Adding weekly otto cron for InSiGHT ClinVar curated variants track, Tuesdays 3:08am. refs #36582
• src/utils/qa/checkAllStaticLinks.csh
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    bf2f9d1f4a880c335a01977a6645855f0c835028 Wed Apr 15 11:47:29 2026 -0700
    Fix checkAllStaticLinks and checkStaticLinks cron scripts: use https for hgwbeta baseUrl since hgwbeta now redirects HTTP to HTTPS, and suppress progress output to reduce cron email noise. No RM.
• src/utils/qa/checkStaticLinks.csh
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    bf2f9d1f4a880c335a01977a6645855f0c835028 Wed Apr 15 11:47:29 2026 -0700
    Fix checkAllStaticLinks and checkStaticLinks cron scripts: use https for hgwbeta baseUrl since hgwbeta now redirects HTTP to HTTPS, and suppress progress output to reduce cron email noise. No RM.
• src/utils/qa/checkUiLinks.py
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    fba554ebc73d05957c3c7431163f18d7f25a3ee9 Tue Apr 14 10:49:06 2026 -0700
    Remove hs1 and mpxvRivers curated hubs from today's ui link check. No RM.
• src/utils/qa/hubCheckDraftEmails.py
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    014a8807f791774e378297827c0fc7cb119607b0 Sun Apr 19 14:25:53 2026 -0700
    Updating hubCheckDraftEmails.py cron to pull contact emails from hubPublic.email with curl+grep as fallback, and to only draft one email per hub when a hub has both "Couldn't open" and "missing description page" errors. No RM
• src/utils/redmineCli
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    eff4c5c82d82b41a6dc377aa4c48b65c1a4ce135 Mon Apr 13 18:30:27 2026 -0700
    Add track ticket custom field support to redmineCli update subcommand. refs #37339 New named options: --release-log-text, --release-log-url, --released-to-rr, --file-list, --table-list, --assemblies. Also adds generic --custom-field ID=VALUE for arbitrary custom fields.
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    87340d09edb5b6ce0fe39d99f574b62d70dc8c0e Wed Apr 15 12:25:35 2026 -0700
    Add 'note' subcommand to redmineCli to fetch a specific note from a ticket, refs #20460 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    33daea3fc1defaeddf990265711fb9905b4917b1 Thu Apr 16 11:27:53 2026 -0700
    redmineCli: add --target-version to update, resolves name against ticket's project versions Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    eb370c5173537bdffaeff3e3368531a6dff3f9a0 Fri Apr 17 10:05:46 2026 -0700
    redmineCli: try version name lookup before treating numeric input as ID Redmine version names are often bare numbers (e.g. "497" for the v497 release), and the version's internal ID (e.g. 261) differs. resolve_version was short-circuiting on isdigit() before any name lookup, so passing a name like "497" sent fixed_version_id=497 — which Redmine rejected as "not in the list". Flip the order: try name lookup first, only fall through to treating the input as a literal ID if it's digits and nothing matched by name. Also drop the parallel isdigit() short-circuit in cmd_update so it always goes through the resolver. refs #37339

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