All File Changes

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

• docs/file-formats/autoSql.md
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    3c2b924e9bc0813d28535c66c7e46363723c96ab Wed Jul 15 10:41:34 2026 -0700
    changes to autoSql page based on CR, refs #37852
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    1ab91a0f05415ebbd3811e9723c13536bd9627bb Sat Jul 18 09:12:39 2026 -0700
    changes to autoSql page based on Automated CR, refs #37852
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
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    58d5745ceefe60d4d8c9f957f076533edb90d1fc Tue Jul 14 09:19:23 2026 -0700
    Fix typo from original lab's milestones
• src/hg/hgHubConnect/hooks/makefile
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    40de350c7aff82babf54c7a7eea41ff5c354bafc Tue Jul 14 11:15:31 2026 -0700
    Build shared objects once before parallel sub-makes in userAppMulti.mk. refs #37809 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/hgMenubar/hgMenubar.c
  • lines changed 18, context: html, text, full: html, text
    7be0d4bee5fc92c426382f480e06254e60f8bb9e Sat Jul 11 20:15:05 2026 -0700
    Cache-bust menu-bar CSS/JS on static pages, refs #10138 hgMenubar.c emitted nice_menu.css and topLinks.js as bare URLs with no version query, so browsers kept serving a stale cached nice_menu.css after commit c5a326f3 added the top-right links. The new #trToggle hamburger is hidden by a rule in that CSS, so on static pages (e.g. the homepage) it showed on first load and only disappeared after a manual force-reload. Append ?v=<file mtime> to those two URLs, the same idea CGIs get from webTimeStampedLinkToResource (which can't be reused here: it emits a ../-relative URL that is wrong for the arbitrary-depth static pages this menu bar is SSI-included into). Uses the existing fileModTime(), guarded by fileExists so a missing resource degrades to ?v=0 rather than aborting the menu bar.
• src/hg/hgTables/seqOut.c
  • lines changed 101, context: html, text, full: html, text
    b7a25f617b5e6fbdeb50ea890e0ff5872605d8d2 Thu Jul 16 00:22:46 2026 -0700
    Table Browser: on-the-fly mRNA and protein output for gene tracks without companion tables #Preview2 week - bugs introduced now will need a build patch to fix #Preview2 week - bugs introduced now will need a build patch to fix The Sequence output for a genePred/bigGenePred track only offered protein and mRNA when the trackDb type line named SQL peptide/mRNA tables (or the track was the hardcoded refGene). Assembly-hub bigGenePred tracks and ncbiRefSeq-style tracks therefore got genomic sequence only. Now those types always offer genomic, mRNA and protein. When no peptide/mRNA table is present, the mRNA is spliced from the assembly and the protein is translated from the CDS using the genetic code assigned to each sequence, so an assembly hub's codonTable setting is honored (chrM/chrMT still default to the mitochondrial code). Tracks that do have peptide/mRNA tables are unchanged. refs #21746
• src/hg/hgTracks/hgTracks.c
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    b551f6c3ac801dbb5b8a436d4ae646772d4eaded Wed Jul 15 16:42:58 2026 -0700
    Revert the "0 bases" -> "1 base" ruler scale-bar change from 94f9b53d3db. At single-base zoom the base-position scale bar reads "0 bases" again, as it does on the RR. QA reviewed the dev version and preferred the existing RR behavior over the reworked ruler text, so rather than keep iterating we match the RR. This touches only computeScaleBar; the two JavaScript click-behavior fixes from 94f9b53d3db (symmetric single-click recenter and the config-strip click fix) stay in place. refs #27113
• src/hg/hgTracks/hgTracks.h
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    a155f3262aa051b6b97e8c3ef0caba8304b992a0 Sat Jul 11 10:13:44 2026 -0700
    Comment: simpleFeature qStart/qEnd are only meaningful for alignment tracks They carry query-sequence coordinates for PSL/BAM/chain/snake features and are left 0 for gene models (genePred), where there is no query sequence. Noting this at the field so nobody assumes they are populated everywhere.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 87, context: html, text, full: html, text
    79764235e8868753201b1b5cd8278ff4f1dd1c08 Sat Jul 11 08:52:39 2026 -0700
    Add nucleotide-position indicator to UTR and non-coding exon mouseovers When zoomed to codon level, hovering a coding transcript's UTR now shows its HGVS position, c.-N in the 5' UTR (counting back to the start codon) and c.*N in the 3' UTR (counting forward from the stop). Non-coding transcripts, which have no codon boxes, get the same treatment on their exons using HGVS n. numbering from the transcript's 5' end. Distances are measured in spliced mRNA space, so introns don't inflate them and the numbering runs continuously across multi-exon UTRs. Previously these regions showed only strand, exon number and length, with no indication of which nucleotides they covered. refs #37866
• src/hg/hgc/hgc.c
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    e24258cb9af339295d713ab060cadcb284d2cb20 Thu Jul 16 18:05:51 2026 -0700
    Add db= to three more link builders found in QA follow-up. refs #37840 QA (Gerardo) found the "Go to <track> track controls" link on hgc feature pages still lacked db=; a completeness sweep of every hTrackUiForTrack caller turned up two more of the same idiom. Add the current-assembly db= to: hgc.c printTrackUiLink() (rendered via printTrackHtml on most hgc detail pages), lib/hui.c the related-tracks link, and lib/barChartUi.c the second isPopup "Change" link in barChartCfgUiSelectEachBar (twin of the one already fixed in barChartFacetedUi).
• src/hg/htdocs/ENCODE/downloads/index.html
  • lines changed 4, context: html, text, full: html, text
    332ac49b65ef9faeb07eb993d63424af77973a89 Fri Jul 17 14:18:07 2026 -0700
    Updating the *.cse.ucsc.edu domain to *.gi.ucsc.edu, refs #37880
• src/hg/htdocs/ENCODE/index.html
  • lines changed 1, context: html, text, full: html, text
    332ac49b65ef9faeb07eb993d63424af77973a89 Fri Jul 17 14:18:07 2026 -0700
    Updating the *.cse.ucsc.edu domain to *.gi.ucsc.edu, refs #37880
• src/hg/htdocs/ENCODE/news_archive.html
  • lines changed 1, context: html, text, full: html, text
    332ac49b65ef9faeb07eb993d63424af77973a89 Fri Jul 17 14:18:07 2026 -0700
    Updating the *.cse.ucsc.edu domain to *.gi.ucsc.edu, refs #37880
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 2, context: html, text, full: html, text
    e2a5a8c488681cd9560fdd13d80f10390a39d549 Tue Jul 14 09:33:07 2026 -0700
    Restoring the g=g2p link on the DDG2P news entry which was undone by my previous commit. No RM. Reported by Daily Code Review.
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    6d16cb32b992cc88362788b99ffc0fcc4c56d028 Tue Jul 14 10:33:07 2026 -0700
    Hiding the ENCODE4 cCREs/Regulation news post until it's ready to announce, refs #37845
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    9dc380d3c6aada6b12cbcd7a95d1d426b47ce86c Tue Jul 14 17:11:11 2026 -0700
    Add Long-read Structural Variants announcement (news archive + gateway news) and track pennantIcon. refs #36258 Add a July 16, 2026 news-archive entry announcing the Long-read Structural Variants container track on hg38 and hs1, with a UGT2B17 example image, and add the matching gateway indexNews item (dropping the oldest to keep six). Add a "New" pennantIcon on the longReadVariants supertrack linking to the post. Also move the still-unreleased ENCODE4 draft entry to July 22 and keep it commented out.
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    74385a9fce53d9b5c48e101f3a0fc89f899d4a47 Thu Jul 16 14:44:36 2026 -0700
    Add Eichler, Lin, Kim, Levin, and ASAP to Long-read SVs announcement acknowledgments per Max. refs #36258
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    008dba8f4169e0de018a6e102caf07193e4ad33c Thu Jul 16 14:56:03 2026 -0700
    Point hs1 linkouts in Long-read SVs announcement to hgTracks without g= (hs1 served as file/hub assembly). refs #36258
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    29c3c9a501f6cdefcc8e155f075523eb73e15ec9 Thu Jul 16 18:25:15 2026 -0700
    Uncommenting the staged ENCODE4 announcement now that long-read SVs is released, refs #37845
• src/hg/htdocs/images/longReadSVsAnnouncementImage.png
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    9dc380d3c6aada6b12cbcd7a95d1d426b47ce86c Tue Jul 14 17:11:11 2026 -0700
    Add Long-read Structural Variants announcement (news archive + gateway news) and track pennantIcon. refs #36258 Add a July 16, 2026 news-archive entry announcing the Long-read Structural Variants container track on hg38 and hs1, with a UGT2B17 example image, and add the matching gateway indexNews item (dropping the oldest to keep six). Add a "New" pennantIcon on the longReadVariants supertrack linking to the post. Also move the still-unreleased ENCODE4 draft entry to July 22 and keep it commented out.
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    b91db8547a0bb5431b4246b5faaf5696f73b2115 Thu Jul 16 11:25:35 2026 -0700
    hubSpace: add Hub Upload menu link, selection banner, and shareable hub links, refs #37705 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/inc/hgMyData.html
  • lines changed 7, context: html, text, full: html, text
    b91db8547a0bb5431b4246b5faaf5696f73b2115 Thu Jul 16 11:25:35 2026 -0700
    hubSpace: add Hub Upload menu link, selection banner, and shareable hub links, refs #37705 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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    94d7a6f6d8884db6fee1e7d9b95d9c2b409cb0ef Fri Jul 17 14:10:26 2026 -0700
    hubSpace: add Copy link to hub button to the hub-browsing banner, refs #37705 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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    dc34085c59de1a3a941e2c34318d9fd8af753579 Fri Jul 17 14:27:46 2026 -0700
    hubSpace: rename share buttons to Share hub, keep share banner always present, refs #37705 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    9dc380d3c6aada6b12cbcd7a95d1d426b47ce86c Tue Jul 14 17:11:11 2026 -0700
    Add Long-read Structural Variants announcement (news archive + gateway news) and track pennantIcon. refs #36258 Add a July 16, 2026 news-archive entry announcing the Long-read Structural Variants container track on hg38 and hs1, with a UGT2B17 example image, and add the matching gateway indexNews item (dropping the oldest to keep six). Add a "New" pennantIcon on the longReadVariants supertrack linking to the post. Also move the still-unreleased ENCODE4 draft entry to July 22 and keep it commented out.
• src/hg/htdocs/license/index.html
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    332ac49b65ef9faeb07eb993d63424af77973a89 Fri Jul 17 14:18:07 2026 -0700
    Updating the *.cse.ucsc.edu domain to *.gi.ucsc.edu, refs #37880
• src/hg/htdocs/staff.html
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    3fbf5e889114d5dbf79728015b857d985d59a868 Fri Jul 17 14:02:03 2026 -0700
    Adding the interns to the Staff page, no Redmine
• src/hg/htdocs/store.html
  • lines changed 1, context: html, text, full: html, text
    332ac49b65ef9faeb07eb993d63424af77973a89 Fri Jul 17 14:18:07 2026 -0700
    Updating the *.cse.ucsc.edu domain to *.gi.ucsc.edu, refs #37880
• src/hg/js/hgHubConnect.js
  • lines changed 25, context: html, text, full: html, text
    b91db8547a0bb5431b4246b5faaf5696f73b2115 Thu Jul 16 11:25:35 2026 -0700
    hubSpace: add Hub Upload menu link, selection banner, and shareable hub links, refs #37705 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/js/hgMyData.js
  • lines changed 97, context: html, text, full: html, text
    b91db8547a0bb5431b4246b5faaf5696f73b2115 Thu Jul 16 11:25:35 2026 -0700
    hubSpace: add Hub Upload menu link, selection banner, and shareable hub links, refs #37705 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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    94d7a6f6d8884db6fee1e7d9b95d9c2b409cb0ef Fri Jul 17 14:10:26 2026 -0700
    hubSpace: add Copy link to hub button to the hub-browsing banner, refs #37705 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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    dc34085c59de1a3a941e2c34318d9fd8af753579 Fri Jul 17 14:27:46 2026 -0700
    hubSpace: rename share buttons to Share hub, keep share banner always present, refs #37705 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/lib/barChartUi.c
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    e24258cb9af339295d713ab060cadcb284d2cb20 Thu Jul 16 18:05:51 2026 -0700
    Add db= to three more link builders found in QA follow-up. refs #37840 QA (Gerardo) found the "Go to <track> track controls" link on hgc feature pages still lacked db=; a completeness sweep of every hTrackUiForTrack caller turned up two more of the same idiom. Add the current-assembly db= to: hgc.c printTrackUiLink() (rendered via printTrackHtml on most hgc detail pages), lib/hui.c the related-tracks link, and lib/barChartUi.c the second isPopup "Change" link in barChartCfgUiSelectEachBar (twin of the one already fixed in barChartFacetedUi).
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    e24258cb9af339295d713ab060cadcb284d2cb20 Thu Jul 16 18:05:51 2026 -0700
    Add db= to three more link builders found in QA follow-up. refs #37840 QA (Gerardo) found the "Go to <track> track controls" link on hgc feature pages still lacked db=; a completeness sweep of every hTrackUiForTrack caller turned up two more of the same idiom. Add the current-assembly db= to: hgc.c printTrackUiLink() (rendered via printTrackHtml on most hgc detail pages), lib/hui.c the related-tracks link, and lib/barChartUi.c the second isPopup "Change" link in barChartCfgUiSelectEachBar (twin of the one already fixed in barChartFacetedUi).
• src/hg/lib/straw/cStraw.cpp
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    006f538b5a95fd704a106546add7b6cd9bd77fa3 Sun Jul 19 22:26:32 2026 -0700
    Muting warnings when retrieving hic data for a region not in the hic file, refs #36444
• src/hg/lib/straw/straw.cpp
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    006f538b5a95fd704a106546add7b6cd9bd77fa3 Sun Jul 19 22:26:32 2026 -0700
    Muting warnings when retrieving hic data for a region not in the hic file, refs #36444
• src/hg/lib/straw/straw.h
  • lines changed 9, context: html, text, full: html, text
    006f538b5a95fd704a106546add7b6cd9bd77fa3 Sun Jul 19 22:26:32 2026 -0700
    Muting warnings when retrieving hic data for a region not in the hic file, refs #36444
• src/hg/makeDb/doc/hg38/clinvarMapped.txt
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    5fe93cbef0d7692552e37e62bbf394cc7d222a28 Thu Jul 16 00:32:55 2026 -0700
    ClinVar Mapped track: map ClinVar coding variants through paralog alignments #Preview2 week - bugs introduced now will need a build patch to fix Adds the clinvarMapped composite (hg38) with two subtracks: - clinvarMappedParalog: every protein-changing ClinVar variant projected onto the equivalent (aligned) residue of each of its gene's paralogs - clinvarMappedParalogAln: the pairwise protein alignments used to do the mapping, as bigPsl, so the evidence for each projection can be inspected Pipeline: paralog pairs from Ensembl BioMart, one representative transcript per gene from MANE Select, pairwise global protein alignment (BLOSUM62) for pairs at >=20% identity, variants projected residue-to-residue and mapped back to the paralog's genomic codon. Colors and filters mirror the ClinVar track; the map track is filterable by source gene, classification, review stars, residue conservation and percent identity. refs #37883
• src/hg/makeDb/doc/hg38/eve.txt
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    9f9a96ab068a76799311c09a2813b0b28f8e7712 Mon Jul 13 12:52:41 2026 -0700
    Order EVE heatmap amino acid rows by class to match the MaveDB track. refs #37763 Change the heatmap row order from alphabetical to physicochemical-amino-acid-class order (A V L I M F Y W R H K D E S T N Q G C P), matching the MaveDB Experiments heatmap so the tracks can be compared row-for-row. Rebuilds eve.bb; updates the makedoc, the AutoSql row label comment, and the description page.
• src/hg/makeDb/doc/hg38/hprc2.txt
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    04456b0be37a7d7b57551e0d9596e3ef0b8f0393 Thu Jul 16 00:34:37 2026 -0700
    Add HPRC Release 2 hg38 native tracks (alignments, coverage, breaks, rearrangements, chains), refs #35415 #Preview2 week - bugs introduced now will need a build patch to fix New pan-genome track container (group hprc) derived from the HPRC Release 2 per-assembly chains to GRCh38 (462 haplotypes), running in parallel to the existing HPRC release 1 tracks: - hprc2Coverage: fraction of assemblies aligning across GRCh38 - hprc2Breaks: alignment breaks, colored by prevalence - hprc2Rearr: insertions/deletions/inversions/duplications/complex indels, lrSv color palette, numeric size field, 50 bp default filter - hprc2Chains: per-haplotype bigChain composite, grouped by superpopulation Container hidden by default. Scripts, autoSql, and makeDoc included.
• src/hg/makeDb/doc/hg38/lrSv.txt
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    95208355e2c667d194b29ee78c8ca8a09c2c2596 Fri Jul 17 08:51:28 2026 -0700
    lrSv: add NIH CARD long-read SV subtrack (cardSv) #Preview2 week - bugs introduced now will need a build patch to fix Add the NIH CARD Long-Read Initiative structural-variant catalogue (351 post-mortem brain samples: 205 NABEC European ancestry, 146 HBCC African/African-admixed) as a new subtrack of the Long-read SVs container. The provider bigBed is re-derived into the shared lrSv schema: signed svLen made positive (reference span), an explicit insLen added, the single DUP:TANDEM folded to DUP, and colors remapped to the container's shared svColor() palette. All 228,855 provider records are carried through 1:1. Adds the converter and autoSql, the trackDb stanza with filters consistent with the sibling subtracks, a full description page, a summary row and blurb on the container page, and a makeDoc section. refs #36258
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    3bf9e1a841206d3bf5902e06791ef5be2dbdbd39 Fri Jul 17 09:09:47 2026 -0700
    lrSv: add Noyvert multi-ancestry long-read SV subtrack (noyvertSv) #Preview2 week - bugs introduced now will need a build patch to fix 888 Oxford Nanopore 1000 Genomes genomes, Sniffles2 v2.0.7, 107,445 SVs with per-superpopulation allele frequencies, imputation-accuracy metrics and UK Biobank SV-WAS associations. Converter approximates AC/AN from AF and the genotype missing rate (source has no allele count), stores BND mate breakends, and follows the shared lrSv svType/svLen/insLen/AC field convention so the container-level filters apply. refs #36258
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    d92e36dbbee172d6bb81a751eb8bb935f356890c Fri Jul 17 09:31:28 2026 -0700
    lrSv: add cardSv and noyvertSv to the lrSvAll merged track #Preview2 week - bugs introduced now will need a build patch to fix Append NIH CARD 351 (AC/alleleFreq) and Noyvert 888 (AC/AF) to databases.tsv and re-run lrSvMergeAll.py: 16 source databases now, 3,018,404 input variants merged to 2,582,278 (was 14 dbs, 2,317,508). Regenerated lrSvAll.ra (filterValues.sources + sourceCount 1:16) and updated the container summary table. refs #36258
• src/hg/makeDb/doc/hg38/popEve.txt
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    3d194de4d74f67c1a453035e20c4769d88bec4c4 Mon Jul 13 12:52:57 2026 -0700
    Order popEVE heatmap amino acid rows by class to match the MaveDB track. refs #37791 Change the heatmap row order from alphabetical to physicochemical-amino-acid-class order (A V L I M F Y W R H K D E S T N Q G C P), matching the MaveDB Experiments heatmap so the tracks can be compared row-for-row. Rebuilds popEve.bb; updates the makedoc, the AutoSql row label comment, and the description page.
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    15bdf707a4bde0a281109bb810499a2fa98ef6ac Tue Jul 14 07:48:05 2026 -0700
    Fix stale "row Y" reference in popEVE trailingFix comment per CR feedback. refs #37791 The amino acid row reorder made P the last row, not Y, but the trailingFix explanation in the converter comment and the makedoc still said "row Y, last column". Reworded both to be order-agnostic ("last row, last column"). Documentation only; the code already operates positionally on labelParts[-1].
• src/hg/makeDb/doc/hg38/varFreqs.txt
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    99764ad55bb121d285e9734de955bba41802ad06 Wed Jul 15 23:35:19 2026 -0700
    varFreqs: add gnomAD-Canada HostSeq SNV frequencies and fold into combined tracks, refs #36642 #Preview2 week - bugs introduced now will need a build patch to fix New "hostseq" vcfTabix subtrack of the SNV Frequencies container: gnomAD-Canada v1.0 / HostSeq, 10,487 Canadian COVID-19 WGS genomes on hg38. The release ships only as a ~104 GB Hail table, so hostseqHtToVcf.py reads it with Hail and flattens the freq array into a sites-only VCF with overall + 9 gnomAD ancestry-group AC/AN/AF, nhomalt, grpmax, dbSNP rsID and the variant filter status. 232,028,491 release rows -> 213,382,086 written (18,646,405 AC0 sites dropped). Registered HostSeq (is_disease=0) in databases.tsv and its 9 ancestry groups in populations.tsv, and rebuilt varFreqsAffected/varFreqsBackground so HostSeq feeds the background side (29 cohorts, 185 fields; merged set 1,374,129,993 variants). Added HostSeq to filterValues.backgroundSources.
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    c656fab2dcb67f0789af54ea1d04afcf6ab3d07b Wed Jul 15 23:38:55 2026 -0700
    varFreqs: expand SPARK phenotype-split documentation in makeDoc #Preview2 week - bugs introduced now will need a build patch to fix Rework the SFARI SPARK section of the varFreqs makeDoc to describe, step by step, what sparkMergeVcfAddCounts.sh does per chromosome (fill-tags overall + optional per-group AC/AN/AF, drop genotypes, concat) and how the individuals_registration TSV drives the ASD / non-ASD phenotype split.
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
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    cb6c90791625bb8103f90f0b1bca76828117983d Fri Jul 17 13:51:50 2026 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
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    cb6c90791625bb8103f90f0b1bca76828117983d Fri Jul 17 13:51:50 2026 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/mm10.txt
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    e6bafe04b348ec643f503c1600ab336c56870214 Tue Jul 14 18:01:27 2026 -0700
    Adding the mouseDevTimecourse bigWig signal composite for mm10, including its track description page, build scripts, and makedoc documentation, using Claude, refs #37001
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
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    cb6c90791625bb8103f90f0b1bca76828117983d Fri Jul 17 13:51:50 2026 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/ucscGenes/hg19.gencodeV50lift37.sh
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    65b9e931d649064e568d5826f636f0ab24d6ac19 Thu Jul 16 07:34:15 2026 -0700
    Makedoc and trackDb for hg19 GENCODE V50 knownGene, refs #37393
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    58972c744024ac33cca07b80375635aff97315f3 Sun Jul 19 21:17:20 2026 -0700
    Noting for knownGene builds that we're not building gnfU95Distance now, as hgNearData isn't listing it as an option. refs #37395, #37393
• src/hg/makeDb/doc/ucscGenes/hg38.gencodeV50.sh
  • lines changed 37, context: html, text, full: html, text
    f7003f9a6744e9c1d0ec6cef2226a1035d2b2b06 Wed Jul 15 22:08:51 2026 -0700
    TrackDb and makedoc for UCSC Genes version of GENCODE V50, refs #37395
  • lines changed 2, context: html, text, full: html, text
    58972c744024ac33cca07b80375635aff97315f3 Sun Jul 19 21:17:20 2026 -0700
    Noting for knownGene builds that we're not building gnfU95Distance now, as hgNearData isn't listing it as an option. refs #37395, #37393
• src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM39.sh
  • lines changed 53, context: html, text, full: html, text
    10fb7902ebfda7cdddb0b410d506bf2f571b4ec6 Wed Jul 15 21:20:24 2026 -0700
    TrackDb and makedoc for UCSC Genes version of GENCODE VM39, refs #37391
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    cb6c90791625bb8103f90f0b1bca76828117983d Fri Jul 17 13:51:50 2026 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPAFfrequencies.py
  • lines changed 13, context: html, text, full: html, text
    6577d5ee1319bbea85988c1c89179436b4a94edf Tue Jul 14 11:27:59 2026 -0700
    Address code-review feedback on the Cardiomyopathy VCEP build scripts. refs #37446 - cmpVCEPCardioBoost.py: add the standard --db/--output-dir CLI. It previously hardcoded the working directory for both its input TSV and its output (unlike the 11 sibling scripts, and contrary to the makedoc's documented interface); the build loop's flags were silently ignored. Output is unchanged (31,236 variants per assembly). - Decode leftover HTML entities (arrows, >=, <=, +/-, x) in print/stderr diagnostics, comments, and docstrings across all scripts so build logs read cleanly. The mouseOver / bigBed display strings intentionally keep their entities. - cmpVCEPWalsh2019.py: fix the stale docstring that described the ClinVar-unmatched entries as "deferred" (they are mapped via the hgvsToVcf fallback, item L) and drop the unverified "163 rows" count. Per code-review feedback on commit aa5669fe64. No track data changed.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPAnnotate.py
  • lines changed 4, context: html, text, full: html, text
    6577d5ee1319bbea85988c1c89179436b4a94edf Tue Jul 14 11:27:59 2026 -0700
    Address code-review feedback on the Cardiomyopathy VCEP build scripts. refs #37446 - cmpVCEPCardioBoost.py: add the standard --db/--output-dir CLI. It previously hardcoded the working directory for both its input TSV and its output (unlike the 11 sibling scripts, and contrary to the makedoc's documented interface); the build loop's flags were silently ignored. Output is unchanged (31,236 variants per assembly). - Decode leftover HTML entities (arrows, >=, <=, +/-, x) in print/stderr diagnostics, comments, and docstrings across all scripts so build logs read cleanly. The mouseOver / bigBed display strings intentionally keep their entities. - cmpVCEPWalsh2019.py: fix the stale docstring that described the ClinVar-unmatched entries as "deferred" (they are mapped via the hgvsToVcf fallback, item L) and drop the unverified "163 rows" count. Per code-review feedback on commit aa5669fe64. No track data changed.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPAtlasEF.py
  • lines changed 14, context: html, text, full: html, text
    6577d5ee1319bbea85988c1c89179436b4a94edf Tue Jul 14 11:27:59 2026 -0700
    Address code-review feedback on the Cardiomyopathy VCEP build scripts. refs #37446 - cmpVCEPCardioBoost.py: add the standard --db/--output-dir CLI. It previously hardcoded the working directory for both its input TSV and its output (unlike the 11 sibling scripts, and contrary to the makedoc's documented interface); the build loop's flags were silently ignored. Output is unchanged (31,236 variants per assembly). - Decode leftover HTML entities (arrows, >=, <=, +/-, x) in print/stderr diagnostics, comments, and docstrings across all scripts so build logs read cleanly. The mouseOver / bigBed display strings intentionally keep their entities. - cmpVCEPWalsh2019.py: fix the stale docstring that described the ClinVar-unmatched entries as "deferred" (they are mapped via the hgvsToVcf fallback, item L) and drop the unverified "163 rows" count. Per code-review feedback on commit aa5669fe64. No track data changed.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPCardioBoost.py
  • lines changed 23, context: html, text, full: html, text
    6577d5ee1319bbea85988c1c89179436b4a94edf Tue Jul 14 11:27:59 2026 -0700
    Address code-review feedback on the Cardiomyopathy VCEP build scripts. refs #37446 - cmpVCEPCardioBoost.py: add the standard --db/--output-dir CLI. It previously hardcoded the working directory for both its input TSV and its output (unlike the 11 sibling scripts, and contrary to the makedoc's documented interface); the build loop's flags were silently ignored. Output is unchanged (31,236 variants per assembly). - Decode leftover HTML entities (arrows, >=, <=, +/-, x) in print/stderr diagnostics, comments, and docstrings across all scripts so build logs read cleanly. The mouseOver / bigBed display strings intentionally keep their entities. - cmpVCEPWalsh2019.py: fix the stale docstring that described the ClinVar-unmatched entries as "deferred" (they are mapped via the hgvsToVcf fallback, item L) and drop the unverified "163 rows" count. Per code-review feedback on commit aa5669fe64. No track data changed.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPClinDomains.py
  • lines changed 10, context: html, text, full: html, text
    6577d5ee1319bbea85988c1c89179436b4a94edf Tue Jul 14 11:27:59 2026 -0700
    Address code-review feedback on the Cardiomyopathy VCEP build scripts. refs #37446 - cmpVCEPCardioBoost.py: add the standard --db/--output-dir CLI. It previously hardcoded the working directory for both its input TSV and its output (unlike the 11 sibling scripts, and contrary to the makedoc's documented interface); the build loop's flags were silently ignored. Output is unchanged (31,236 variants per assembly). - Decode leftover HTML entities (arrows, >=, <=, +/-, x) in print/stderr diagnostics, comments, and docstrings across all scripts so build logs read cleanly. The mouseOver / bigBed display strings intentionally keep their entities. - cmpVCEPWalsh2019.py: fix the stale docstring that described the ClinVar-unmatched entries as "deferred" (they are mapped via the hgvsToVcf fallback, item L) and drop the unverified "163 rows" count. Per code-review feedback on commit aa5669fe64. No track data changed.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPClinVar506161.py
  • lines changed 8, context: html, text, full: html, text
    6577d5ee1319bbea85988c1c89179436b4a94edf Tue Jul 14 11:27:59 2026 -0700
    Address code-review feedback on the Cardiomyopathy VCEP build scripts. refs #37446 - cmpVCEPCardioBoost.py: add the standard --db/--output-dir CLI. It previously hardcoded the working directory for both its input TSV and its output (unlike the 11 sibling scripts, and contrary to the makedoc's documented interface); the build loop's flags were silently ignored. Output is unchanged (31,236 variants per assembly). - Decode leftover HTML entities (arrows, >=, <=, +/-, x) in print/stderr diagnostics, comments, and docstrings across all scripts so build logs read cleanly. The mouseOver / bigBed display strings intentionally keep their entities. - cmpVCEPWalsh2019.py: fix the stale docstring that described the ClinVar-unmatched entries as "deferred" (they are mapped via the hgvsToVcf fallback, item L) and drop the unverified "163 rows" count. Per code-review feedback on commit aa5669fe64. No track data changed.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPEvRepo.py
  • lines changed 10, context: html, text, full: html, text
    6577d5ee1319bbea85988c1c89179436b4a94edf Tue Jul 14 11:27:59 2026 -0700
    Address code-review feedback on the Cardiomyopathy VCEP build scripts. refs #37446 - cmpVCEPCardioBoost.py: add the standard --db/--output-dir CLI. It previously hardcoded the working directory for both its input TSV and its output (unlike the 11 sibling scripts, and contrary to the makedoc's documented interface); the build loop's flags were silently ignored. Output is unchanged (31,236 variants per assembly). - Decode leftover HTML entities (arrows, >=, <=, +/-, x) in print/stderr diagnostics, comments, and docstrings across all scripts so build logs read cleanly. The mouseOver / bigBed display strings intentionally keep their entities. - cmpVCEPWalsh2019.py: fix the stale docstring that described the ClinVar-unmatched entries as "deferred" (they are mapped via the hgvsToVcf fallback, item L) and drop the unverified "163 rows" count. Per code-review feedback on commit aa5669fe64. No track data changed.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPPVS1.py
  • lines changed 10, context: html, text, full: html, text
    6577d5ee1319bbea85988c1c89179436b4a94edf Tue Jul 14 11:27:59 2026 -0700
    Address code-review feedback on the Cardiomyopathy VCEP build scripts. refs #37446 - cmpVCEPCardioBoost.py: add the standard --db/--output-dir CLI. It previously hardcoded the working directory for both its input TSV and its output (unlike the 11 sibling scripts, and contrary to the makedoc's documented interface); the build loop's flags were silently ignored. Output is unchanged (31,236 variants per assembly). - Decode leftover HTML entities (arrows, >=, <=, +/-, x) in print/stderr diagnostics, comments, and docstrings across all scripts so build logs read cleanly. The mouseOver / bigBed display strings intentionally keep their entities. - cmpVCEPWalsh2019.py: fix the stale docstring that described the ClinVar-unmatched entries as "deferred" (they are mapped via the hgvsToVcf fallback, item L) and drop the unverified "163 rows" count. Per code-review feedback on commit aa5669fe64. No track data changed.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPProvisionalClass.py
  • lines changed 14, context: html, text, full: html, text
    6577d5ee1319bbea85988c1c89179436b4a94edf Tue Jul 14 11:27:59 2026 -0700
    Address code-review feedback on the Cardiomyopathy VCEP build scripts. refs #37446 - cmpVCEPCardioBoost.py: add the standard --db/--output-dir CLI. It previously hardcoded the working directory for both its input TSV and its output (unlike the 11 sibling scripts, and contrary to the makedoc's documented interface); the build loop's flags were silently ignored. Output is unchanged (31,236 variants per assembly). - Decode leftover HTML entities (arrows, >=, <=, +/-, x) in print/stderr diagnostics, comments, and docstrings across all scripts so build logs read cleanly. The mouseOver / bigBed display strings intentionally keep their entities. - cmpVCEPWalsh2019.py: fix the stale docstring that described the ClinVar-unmatched entries as "deferred" (they are mapped via the hgvsToVcf fallback, item L) and drop the unverified "163 rows" count. Per code-review feedback on commit aa5669fe64. No track data changed.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPRevel.py
  • lines changed 4, context: html, text, full: html, text
    6577d5ee1319bbea85988c1c89179436b4a94edf Tue Jul 14 11:27:59 2026 -0700
    Address code-review feedback on the Cardiomyopathy VCEP build scripts. refs #37446 - cmpVCEPCardioBoost.py: add the standard --db/--output-dir CLI. It previously hardcoded the working directory for both its input TSV and its output (unlike the 11 sibling scripts, and contrary to the makedoc's documented interface); the build loop's flags were silently ignored. Output is unchanged (31,236 variants per assembly). - Decode leftover HTML entities (arrows, >=, <=, +/-, x) in print/stderr diagnostics, comments, and docstrings across all scripts so build logs read cleanly. The mouseOver / bigBed display strings intentionally keep their entities. - cmpVCEPWalsh2019.py: fix the stale docstring that described the ClinVar-unmatched entries as "deferred" (they are mapped via the hgvsToVcf fallback, item L) and drop the unverified "163 rows" count. Per code-review feedback on commit aa5669fe64. No track data changed.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPWalsh2019.py
  • lines changed 13, context: html, text, full: html, text
    6577d5ee1319bbea85988c1c89179436b4a94edf Tue Jul 14 11:27:59 2026 -0700
    Address code-review feedback on the Cardiomyopathy VCEP build scripts. refs #37446 - cmpVCEPCardioBoost.py: add the standard --db/--output-dir CLI. It previously hardcoded the working directory for both its input TSV and its output (unlike the 11 sibling scripts, and contrary to the makedoc's documented interface); the build loop's flags were silently ignored. Output is unchanged (31,236 variants per assembly). - Decode leftover HTML entities (arrows, >=, <=, +/-, x) in print/stderr diagnostics, comments, and docstrings across all scripts so build logs read cleanly. The mouseOver / bigBed display strings intentionally keep their entities. - cmpVCEPWalsh2019.py: fix the stale docstring that described the ClinVar-unmatched entries as "deferred" (they are mapped via the hgvsToVcf fallback, item L) and drop the unverified "163 rows" count. Per code-review feedback on commit aa5669fe64. No track data changed.
• src/hg/makeDb/scripts/cardiomyopathyVCEP/cmpVCEPWalshOR.py
  • lines changed 4, context: html, text, full: html, text
    6577d5ee1319bbea85988c1c89179436b4a94edf Tue Jul 14 11:27:59 2026 -0700
    Address code-review feedback on the Cardiomyopathy VCEP build scripts. refs #37446 - cmpVCEPCardioBoost.py: add the standard --db/--output-dir CLI. It previously hardcoded the working directory for both its input TSV and its output (unlike the 11 sibling scripts, and contrary to the makedoc's documented interface); the build loop's flags were silently ignored. Output is unchanged (31,236 variants per assembly). - Decode leftover HTML entities (arrows, >=, <=, +/-, x) in print/stderr diagnostics, comments, and docstrings across all scripts so build logs read cleanly. The mouseOver / bigBed display strings intentionally keep their entities. - cmpVCEPWalsh2019.py: fix the stale docstring that described the ClinVar-unmatched entries as "deferred" (they are mapped via the hgvsToVcf fallback, item L) and drop the unverified "163 rows" count. Per code-review feedback on commit aa5669fe64. No track data changed.
• src/hg/makeDb/scripts/clinvarMapped/clinvarMappedCodons.py
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    5fe93cbef0d7692552e37e62bbf394cc7d222a28 Thu Jul 16 00:32:55 2026 -0700
    ClinVar Mapped track: map ClinVar coding variants through paralog alignments #Preview2 week - bugs introduced now will need a build patch to fix Adds the clinvarMapped composite (hg38) with two subtracks: - clinvarMappedParalog: every protein-changing ClinVar variant projected onto the equivalent (aligned) residue of each of its gene's paralogs - clinvarMappedParalogAln: the pairwise protein alignments used to do the mapping, as bigPsl, so the evidence for each projection can be inspected Pipeline: paralog pairs from Ensembl BioMart, one representative transcript per gene from MANE Select, pairwise global protein alignment (BLOSUM62) for pairs at >=20% identity, variants projected residue-to-residue and mapped back to the paralog's genomic codon. Colors and filters mirror the ClinVar track; the map track is filterable by source gene, classification, review stars, residue conservation and percent identity. refs #37883
• src/hg/makeDb/scripts/clinvarMapped/clinvarMappedMane.sh
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    5fe93cbef0d7692552e37e62bbf394cc7d222a28 Thu Jul 16 00:32:55 2026 -0700
    ClinVar Mapped track: map ClinVar coding variants through paralog alignments #Preview2 week - bugs introduced now will need a build patch to fix Adds the clinvarMapped composite (hg38) with two subtracks: - clinvarMappedParalog: every protein-changing ClinVar variant projected onto the equivalent (aligned) residue of each of its gene's paralogs - clinvarMappedParalogAln: the pairwise protein alignments used to do the mapping, as bigPsl, so the evidence for each projection can be inspected Pipeline: paralog pairs from Ensembl BioMart, one representative transcript per gene from MANE Select, pairwise global protein alignment (BLOSUM62) for pairs at >=20% identity, variants projected residue-to-residue and mapped back to the paralog's genomic codon. Colors and filters mirror the ClinVar track; the map track is filterable by source gene, classification, review stars, residue conservation and percent identity. refs #37883
• src/hg/makeDb/scripts/clinvarMapped/clinvarMappedParalog.as
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    5fe93cbef0d7692552e37e62bbf394cc7d222a28 Thu Jul 16 00:32:55 2026 -0700
    ClinVar Mapped track: map ClinVar coding variants through paralog alignments #Preview2 week - bugs introduced now will need a build patch to fix Adds the clinvarMapped composite (hg38) with two subtracks: - clinvarMappedParalog: every protein-changing ClinVar variant projected onto the equivalent (aligned) residue of each of its gene's paralogs - clinvarMappedParalogAln: the pairwise protein alignments used to do the mapping, as bigPsl, so the evidence for each projection can be inspected Pipeline: paralog pairs from Ensembl BioMart, one representative transcript per gene from MANE Select, pairwise global protein alignment (BLOSUM62) for pairs at >=20% identity, variants projected residue-to-residue and mapped back to the paralog's genomic codon. Colors and filters mirror the ClinVar track; the map track is filterable by source gene, classification, review stars, residue conservation and percent identity. refs #37883
• src/hg/makeDb/scripts/clinvarMapped/clinvarMappedParalogAlign.py
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    5fe93cbef0d7692552e37e62bbf394cc7d222a28 Thu Jul 16 00:32:55 2026 -0700
    ClinVar Mapped track: map ClinVar coding variants through paralog alignments #Preview2 week - bugs introduced now will need a build patch to fix Adds the clinvarMapped composite (hg38) with two subtracks: - clinvarMappedParalog: every protein-changing ClinVar variant projected onto the equivalent (aligned) residue of each of its gene's paralogs - clinvarMappedParalogAln: the pairwise protein alignments used to do the mapping, as bigPsl, so the evidence for each projection can be inspected Pipeline: paralog pairs from Ensembl BioMart, one representative transcript per gene from MANE Select, pairwise global protein alignment (BLOSUM62) for pairs at >=20% identity, variants projected residue-to-residue and mapped back to the paralog's genomic codon. Colors and filters mirror the ClinVar track; the map track is filterable by source gene, classification, review stars, residue conservation and percent identity. refs #37883
• src/hg/makeDb/scripts/clinvarMapped/clinvarMappedParalogAlnPsl.py
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    5fe93cbef0d7692552e37e62bbf394cc7d222a28 Thu Jul 16 00:32:55 2026 -0700
    ClinVar Mapped track: map ClinVar coding variants through paralog alignments #Preview2 week - bugs introduced now will need a build patch to fix Adds the clinvarMapped composite (hg38) with two subtracks: - clinvarMappedParalog: every protein-changing ClinVar variant projected onto the equivalent (aligned) residue of each of its gene's paralogs - clinvarMappedParalogAln: the pairwise protein alignments used to do the mapping, as bigPsl, so the evidence for each projection can be inspected Pipeline: paralog pairs from Ensembl BioMart, one representative transcript per gene from MANE Select, pairwise global protein alignment (BLOSUM62) for pairs at >=20% identity, variants projected residue-to-residue and mapped back to the paralog's genomic codon. Colors and filters mirror the ClinVar track; the map track is filterable by source gene, classification, review stars, residue conservation and percent identity. refs #37883
• src/hg/makeDb/scripts/clinvarMapped/clinvarMappedParalogPairs.sh
  • lines changed 58, context: html, text, full: html, text
    5fe93cbef0d7692552e37e62bbf394cc7d222a28 Thu Jul 16 00:32:55 2026 -0700
    ClinVar Mapped track: map ClinVar coding variants through paralog alignments #Preview2 week - bugs introduced now will need a build patch to fix Adds the clinvarMapped composite (hg38) with two subtracks: - clinvarMappedParalog: every protein-changing ClinVar variant projected onto the equivalent (aligned) residue of each of its gene's paralogs - clinvarMappedParalogAln: the pairwise protein alignments used to do the mapping, as bigPsl, so the evidence for each projection can be inspected Pipeline: paralog pairs from Ensembl BioMart, one representative transcript per gene from MANE Select, pairwise global protein alignment (BLOSUM62) for pairs at >=20% identity, variants projected residue-to-residue and mapped back to the paralog's genomic codon. Colors and filters mirror the ClinVar track; the map track is filterable by source gene, classification, review stars, residue conservation and percent identity. refs #37883
• src/hg/makeDb/scripts/clinvarMapped/clinvarMappedParalogProject.py
  • lines changed 207, context: html, text, full: html, text
    5fe93cbef0d7692552e37e62bbf394cc7d222a28 Thu Jul 16 00:32:55 2026 -0700
    ClinVar Mapped track: map ClinVar coding variants through paralog alignments #Preview2 week - bugs introduced now will need a build patch to fix Adds the clinvarMapped composite (hg38) with two subtracks: - clinvarMappedParalog: every protein-changing ClinVar variant projected onto the equivalent (aligned) residue of each of its gene's paralogs - clinvarMappedParalogAln: the pairwise protein alignments used to do the mapping, as bigPsl, so the evidence for each projection can be inspected Pipeline: paralog pairs from Ensembl BioMart, one representative transcript per gene from MANE Select, pairwise global protein alignment (BLOSUM62) for pairs at >=20% identity, variants projected residue-to-residue and mapped back to the paralog's genomic codon. Colors and filters mirror the ClinVar track; the map track is filterable by source gene, classification, review stars, residue conservation and percent identity. refs #37883
• src/hg/makeDb/scripts/clinvarMapped/clinvarMappedParalogStats.sh
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    5fe93cbef0d7692552e37e62bbf394cc7d222a28 Thu Jul 16 00:32:55 2026 -0700
    ClinVar Mapped track: map ClinVar coding variants through paralog alignments #Preview2 week - bugs introduced now will need a build patch to fix Adds the clinvarMapped composite (hg38) with two subtracks: - clinvarMappedParalog: every protein-changing ClinVar variant projected onto the equivalent (aligned) residue of each of its gene's paralogs - clinvarMappedParalogAln: the pairwise protein alignments used to do the mapping, as bigPsl, so the evidence for each projection can be inspected Pipeline: paralog pairs from Ensembl BioMart, one representative transcript per gene from MANE Select, pairwise global protein alignment (BLOSUM62) for pairs at >=20% identity, variants projected residue-to-residue and mapped back to the paralog's genomic codon. Colors and filters mirror the ClinVar track; the map track is filterable by source gene, classification, review stars, residue conservation and percent identity. refs #37883
• src/hg/makeDb/scripts/eve/eve_heatmap.as
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    9f9a96ab068a76799311c09a2813b0b28f8e7712 Mon Jul 13 12:52:41 2026 -0700
    Order EVE heatmap amino acid rows by class to match the MaveDB track. refs #37763 Change the heatmap row order from alphabetical to physicochemical-amino-acid-class order (A V L I M F Y W R H K D E S T N Q G C P), matching the MaveDB Experiments heatmap so the tracks can be compared row-for-row. Rebuilds eve.bb; updates the makedoc, the AutoSql row label comment, and the description page.
• src/hg/makeDb/scripts/eve/vcfToEveHeatmap.py
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    9f9a96ab068a76799311c09a2813b0b28f8e7712 Mon Jul 13 12:52:41 2026 -0700
    Order EVE heatmap amino acid rows by class to match the MaveDB track. refs #37763 Change the heatmap row order from alphabetical to physicochemical-amino-acid-class order (A V L I M F Y W R H K D E S T N Q G C P), matching the MaveDB Experiments heatmap so the tracks can be compared row-for-row. Rebuilds eve.bb; updates the makedoc, the AutoSql row label comment, and the description page.
• src/hg/makeDb/scripts/hprc2/hprc2Aggregate.sh
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    04456b0be37a7d7b57551e0d9596e3ef0b8f0393 Thu Jul 16 00:34:37 2026 -0700
    Add HPRC Release 2 hg38 native tracks (alignments, coverage, breaks, rearrangements, chains), refs #35415 #Preview2 week - bugs introduced now will need a build patch to fix New pan-genome track container (group hprc) derived from the HPRC Release 2 per-assembly chains to GRCh38 (462 haplotypes), running in parallel to the existing HPRC release 1 tracks: - hprc2Coverage: fraction of assemblies aligning across GRCh38 - hprc2Breaks: alignment breaks, colored by prevalence - hprc2Rearr: insertions/deletions/inversions/duplications/complex indels, lrSv color palette, numeric size field, 50 bp default filter - hprc2Chains: per-haplotype bigChain composite, grouped by superpopulation Container hidden by default. Scripts, autoSql, and makeDoc included.
• src/hg/makeDb/scripts/hprc2/hprc2Arrange.as
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    04456b0be37a7d7b57551e0d9596e3ef0b8f0393 Thu Jul 16 00:34:37 2026 -0700
    Add HPRC Release 2 hg38 native tracks (alignments, coverage, breaks, rearrangements, chains), refs #35415 #Preview2 week - bugs introduced now will need a build patch to fix New pan-genome track container (group hprc) derived from the HPRC Release 2 per-assembly chains to GRCh38 (462 haplotypes), running in parallel to the existing HPRC release 1 tracks: - hprc2Coverage: fraction of assemblies aligning across GRCh38 - hprc2Breaks: alignment breaks, colored by prevalence - hprc2Rearr: insertions/deletions/inversions/duplications/complex indels, lrSv color palette, numeric size field, 50 bp default filter - hprc2Chains: per-haplotype bigChain composite, grouped by superpopulation Container hidden by default. Scripts, autoSql, and makeDoc included.
• src/hg/makeDb/scripts/hprc2/hprc2Chains.sh
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    04456b0be37a7d7b57551e0d9596e3ef0b8f0393 Thu Jul 16 00:34:37 2026 -0700
    Add HPRC Release 2 hg38 native tracks (alignments, coverage, breaks, rearrangements, chains), refs #35415 #Preview2 week - bugs introduced now will need a build patch to fix New pan-genome track container (group hprc) derived from the HPRC Release 2 per-assembly chains to GRCh38 (462 haplotypes), running in parallel to the existing HPRC release 1 tracks: - hprc2Coverage: fraction of assemblies aligning across GRCh38 - hprc2Breaks: alignment breaks, colored by prevalence - hprc2Rearr: insertions/deletions/inversions/duplications/complex indels, lrSv color palette, numeric size field, 50 bp default filter - hprc2Chains: per-haplotype bigChain composite, grouped by superpopulation Container hidden by default. Scripts, autoSql, and makeDoc included.
• src/hg/makeDb/scripts/hprc2/hprc2Download.sh
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    04456b0be37a7d7b57551e0d9596e3ef0b8f0393 Thu Jul 16 00:34:37 2026 -0700
    Add HPRC Release 2 hg38 native tracks (alignments, coverage, breaks, rearrangements, chains), refs #35415 #Preview2 week - bugs introduced now will need a build patch to fix New pan-genome track container (group hprc) derived from the HPRC Release 2 per-assembly chains to GRCh38 (462 haplotypes), running in parallel to the existing HPRC release 1 tracks: - hprc2Coverage: fraction of assemblies aligning across GRCh38 - hprc2Breaks: alignment breaks, colored by prevalence - hprc2Rearr: insertions/deletions/inversions/duplications/complex indels, lrSv color palette, numeric size field, 50 bp default filter - hprc2Chains: per-haplotype bigChain composite, grouped by superpopulation Container hidden by default. Scripts, autoSql, and makeDoc included.
• src/hg/makeDb/scripts/hprc2/hprc2ProcessAll.sh
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    04456b0be37a7d7b57551e0d9596e3ef0b8f0393 Thu Jul 16 00:34:37 2026 -0700
    Add HPRC Release 2 hg38 native tracks (alignments, coverage, breaks, rearrangements, chains), refs #35415 #Preview2 week - bugs introduced now will need a build patch to fix New pan-genome track container (group hprc) derived from the HPRC Release 2 per-assembly chains to GRCh38 (462 haplotypes), running in parallel to the existing HPRC release 1 tracks: - hprc2Coverage: fraction of assemblies aligning across GRCh38 - hprc2Breaks: alignment breaks, colored by prevalence - hprc2Rearr: insertions/deletions/inversions/duplications/complex indels, lrSv color palette, numeric size field, 50 bp default filter - hprc2Chains: per-haplotype bigChain composite, grouped by superpopulation Container hidden by default. Scripts, autoSql, and makeDoc included.
• src/hg/makeDb/scripts/hprc2/hprc2ProcessOne.sh
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    04456b0be37a7d7b57551e0d9596e3ef0b8f0393 Thu Jul 16 00:34:37 2026 -0700
    Add HPRC Release 2 hg38 native tracks (alignments, coverage, breaks, rearrangements, chains), refs #35415 #Preview2 week - bugs introduced now will need a build patch to fix New pan-genome track container (group hprc) derived from the HPRC Release 2 per-assembly chains to GRCh38 (462 haplotypes), running in parallel to the existing HPRC release 1 tracks: - hprc2Coverage: fraction of assemblies aligning across GRCh38 - hprc2Breaks: alignment breaks, colored by prevalence - hprc2Rearr: insertions/deletions/inversions/duplications/complex indels, lrSv color palette, numeric size field, 50 bp default filter - hprc2Chains: per-haplotype bigChain composite, grouped by superpopulation Container hidden by default. Scripts, autoSql, and makeDoc included.
• src/hg/makeDb/scripts/hprc2/hprc2SampleSuperpop.py
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    04456b0be37a7d7b57551e0d9596e3ef0b8f0393 Thu Jul 16 00:34:37 2026 -0700
    Add HPRC Release 2 hg38 native tracks (alignments, coverage, breaks, rearrangements, chains), refs #35415 #Preview2 week - bugs introduced now will need a build patch to fix New pan-genome track container (group hprc) derived from the HPRC Release 2 per-assembly chains to GRCh38 (462 haplotypes), running in parallel to the existing HPRC release 1 tracks: - hprc2Coverage: fraction of assemblies aligning across GRCh38 - hprc2Breaks: alignment breaks, colored by prevalence - hprc2Rearr: insertions/deletions/inversions/duplications/complex indels, lrSv color palette, numeric size field, 50 bp default filter - hprc2Chains: per-haplotype bigChain composite, grouped by superpopulation Container hidden by default. Scripts, autoSql, and makeDoc included.
• src/hg/makeDb/scripts/hprc2X/README.txt
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    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/buildDel.sh
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    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/buildFullXref.sh
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    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/buildSample.sh
  • lines changed 24, context: html, text, full: html, text
    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/dbsnpStats.sh
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    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/dumpAbsentFixed.py
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    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/hprc2XArrange.as
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    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/hprc2XIndelsAll.sh
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    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/hprc2XIndelsOne.sh
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    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/leftNormDel.py
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    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/normHprc.sh
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    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/normHprc1.sh
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    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/presentInRel2.py
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    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/runSamples.sh
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    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/windowMatch.py
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    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/xrefDbSnp.sh
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    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/lrSv/databases.tsv
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    d92e36dbbee172d6bb81a751eb8bb935f356890c Fri Jul 17 09:31:28 2026 -0700
    lrSv: add cardSv and noyvertSv to the lrSvAll merged track #Preview2 week - bugs introduced now will need a build patch to fix Append NIH CARD 351 (AC/alleleFreq) and Noyvert 888 (AC/AF) to databases.tsv and re-run lrSvMergeAll.py: 16 source databases now, 3,018,404 input variants merged to 2,582,278 (was 14 dbs, 2,317,508). Regenerated lrSvAll.ra (filterValues.sources + sourceCount 1:16) and updated the container summary table. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvCard.as
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    95208355e2c667d194b29ee78c8ca8a09c2c2596 Fri Jul 17 08:51:28 2026 -0700
    lrSv: add NIH CARD long-read SV subtrack (cardSv) #Preview2 week - bugs introduced now will need a build patch to fix Add the NIH CARD Long-Read Initiative structural-variant catalogue (351 post-mortem brain samples: 205 NABEC European ancestry, 146 HBCC African/African-admixed) as a new subtrack of the Long-read SVs container. The provider bigBed is re-derived into the shared lrSv schema: signed svLen made positive (reference span), an explicit insLen added, the single DUP:TANDEM folded to DUP, and colors remapped to the container's shared svColor() palette. All 228,855 provider records are carried through 1:1. Adds the converter and autoSql, the trackDb stanza with filters consistent with the sibling subtracks, a full description page, a summary row and blurb on the container page, and a makeDoc section. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvCardBbToBed.py
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    95208355e2c667d194b29ee78c8ca8a09c2c2596 Fri Jul 17 08:51:28 2026 -0700
    lrSv: add NIH CARD long-read SV subtrack (cardSv) #Preview2 week - bugs introduced now will need a build patch to fix Add the NIH CARD Long-Read Initiative structural-variant catalogue (351 post-mortem brain samples: 205 NABEC European ancestry, 146 HBCC African/African-admixed) as a new subtrack of the Long-read SVs container. The provider bigBed is re-derived into the shared lrSv schema: signed svLen made positive (reference span), an explicit insLen added, the single DUP:TANDEM folded to DUP, and colors remapped to the container's shared svColor() palette. All 228,855 provider records are carried through 1:1. Adds the converter and autoSql, the trackDb stanza with filters consistent with the sibling subtracks, a full description page, a summary row and blurb on the container page, and a makeDoc section. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvNoyvert.as
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    3bf9e1a841206d3bf5902e06791ef5be2dbdbd39 Fri Jul 17 09:09:47 2026 -0700
    lrSv: add Noyvert multi-ancestry long-read SV subtrack (noyvertSv) #Preview2 week - bugs introduced now will need a build patch to fix 888 Oxford Nanopore 1000 Genomes genomes, Sniffles2 v2.0.7, 107,445 SVs with per-superpopulation allele frequencies, imputation-accuracy metrics and UK Biobank SV-WAS associations. Converter approximates AC/AN from AF and the genotype missing rate (source has no allele count), stores BND mate breakends, and follows the shared lrSv svType/svLen/insLen/AC field convention so the container-level filters apply. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvNoyvertTsvToBed.py
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    3bf9e1a841206d3bf5902e06791ef5be2dbdbd39 Fri Jul 17 09:09:47 2026 -0700
    lrSv: add Noyvert multi-ancestry long-read SV subtrack (noyvertSv) #Preview2 week - bugs introduced now will need a build patch to fix 888 Oxford Nanopore 1000 Genomes genomes, Sniffles2 v2.0.7, 107,445 SVs with per-superpopulation allele frequencies, imputation-accuracy metrics and UK Biobank SV-WAS associations. Converter approximates AC/AN from AF and the genotype missing rate (source has no allele count), stores BND mate breakends, and follows the shared lrSv svType/svLen/insLen/AC field convention so the container-level filters apply. refs #36258
• src/hg/makeDb/scripts/mouseDevTimecourse/downloadBigwigs.sh
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    e6bafe04b348ec643f503c1600ab336c56870214 Tue Jul 14 18:01:27 2026 -0700
    Adding the mouseDevTimecourse bigWig signal composite for mm10, including its track description page, build scripts, and makedoc documentation, using Claude, refs #37001
• src/hg/makeDb/scripts/mouseDevTimecourse/generateBigwigTrackDb.py
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    e6bafe04b348ec643f503c1600ab336c56870214 Tue Jul 14 18:01:27 2026 -0700
    Adding the mouseDevTimecourse bigWig signal composite for mm10, including its track description page, build scripts, and makedoc documentation, using Claude, refs #37001
• src/hg/makeDb/scripts/popEve/popEve_heatmap.as
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    3d194de4d74f67c1a453035e20c4769d88bec4c4 Mon Jul 13 12:52:57 2026 -0700
    Order popEVE heatmap amino acid rows by class to match the MaveDB track. refs #37791 Change the heatmap row order from alphabetical to physicochemical-amino-acid-class order (A V L I M F Y W R H K D E S T N Q G C P), matching the MaveDB Experiments heatmap so the tracks can be compared row-for-row. Rebuilds popEve.bb; updates the makedoc, the AutoSql row label comment, and the description page.
• src/hg/makeDb/scripts/popEve/vcfToPopEveHeatmap.py
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    3d194de4d74f67c1a453035e20c4769d88bec4c4 Mon Jul 13 12:52:57 2026 -0700
    Order popEVE heatmap amino acid rows by class to match the MaveDB track. refs #37791 Change the heatmap row order from alphabetical to physicochemical-amino-acid-class order (A V L I M F Y W R H K D E S T N Q G C P), matching the MaveDB Experiments heatmap so the tracks can be compared row-for-row. Rebuilds popEve.bb; updates the makedoc, the AutoSql row label comment, and the description page.
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    15bdf707a4bde0a281109bb810499a2fa98ef6ac Tue Jul 14 07:48:05 2026 -0700
    Fix stale "row Y" reference in popEVE trailingFix comment per CR feedback. refs #37791 The amino acid row reorder made P the last row, not Y, but the trailingFix explanation in the converter comment and the makedoc still said "row Y, last column". Reworded both to be order-agnostic ("last row, last column"). Documentation only; the code already operates positionally on labelParts[-1].
• src/hg/makeDb/scripts/varFreqs/databases.tsv
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    99764ad55bb121d285e9734de955bba41802ad06 Wed Jul 15 23:35:19 2026 -0700
    varFreqs: add gnomAD-Canada HostSeq SNV frequencies and fold into combined tracks, refs #36642 #Preview2 week - bugs introduced now will need a build patch to fix New "hostseq" vcfTabix subtrack of the SNV Frequencies container: gnomAD-Canada v1.0 / HostSeq, 10,487 Canadian COVID-19 WGS genomes on hg38. The release ships only as a ~104 GB Hail table, so hostseqHtToVcf.py reads it with Hail and flattens the freq array into a sites-only VCF with overall + 9 gnomAD ancestry-group AC/AN/AF, nhomalt, grpmax, dbSNP rsID and the variant filter status. 232,028,491 release rows -> 213,382,086 written (18,646,405 AC0 sites dropped). Registered HostSeq (is_disease=0) in databases.tsv and its 9 ancestry groups in populations.tsv, and rebuilt varFreqsAffected/varFreqsBackground so HostSeq feeds the background side (29 cohorts, 185 fields; merged set 1,374,129,993 variants). Added HostSeq to filterValues.backgroundSources.
• src/hg/makeDb/scripts/varFreqs/hostseqHtToVcf.py
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    99764ad55bb121d285e9734de955bba41802ad06 Wed Jul 15 23:35:19 2026 -0700
    varFreqs: add gnomAD-Canada HostSeq SNV frequencies and fold into combined tracks, refs #36642 #Preview2 week - bugs introduced now will need a build patch to fix New "hostseq" vcfTabix subtrack of the SNV Frequencies container: gnomAD-Canada v1.0 / HostSeq, 10,487 Canadian COVID-19 WGS genomes on hg38. The release ships only as a ~104 GB Hail table, so hostseqHtToVcf.py reads it with Hail and flattens the freq array into a sites-only VCF with overall + 9 gnomAD ancestry-group AC/AN/AF, nhomalt, grpmax, dbSNP rsID and the variant filter status. 232,028,491 release rows -> 213,382,086 written (18,646,405 AC0 sites dropped). Registered HostSeq (is_disease=0) in databases.tsv and its 9 ancestry groups in populations.tsv, and rebuilt varFreqsAffected/varFreqsBackground so HostSeq feeds the background side (29 cohorts, 185 fields; merged set 1,374,129,993 variants). Added HostSeq to filterValues.backgroundSources.
• src/hg/makeDb/scripts/varFreqs/populations.tsv
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    99764ad55bb121d285e9734de955bba41802ad06 Wed Jul 15 23:35:19 2026 -0700
    varFreqs: add gnomAD-Canada HostSeq SNV frequencies and fold into combined tracks, refs #36642 #Preview2 week - bugs introduced now will need a build patch to fix New "hostseq" vcfTabix subtrack of the SNV Frequencies container: gnomAD-Canada v1.0 / HostSeq, 10,487 Canadian COVID-19 WGS genomes on hg38. The release ships only as a ~104 GB Hail table, so hostseqHtToVcf.py reads it with Hail and flattens the freq array into a sites-only VCF with overall + 9 gnomAD ancestry-group AC/AN/AF, nhomalt, grpmax, dbSNP rsID and the variant filter status. 232,028,491 release rows -> 213,382,086 written (18,646,405 AC0 sites dropped). Registered HostSeq (is_disease=0) in databases.tsv and its 9 ancestry groups in populations.tsv, and rebuilt varFreqsAffected/varFreqsBackground so HostSeq feeds the background side (29 cohorts, 185 fields; merged set 1,374,129,993 variants). Added HostSeq to filterValues.backgroundSources.
• src/hg/makeDb/trackDb/dog/canFam6/canFam6.susScr11.chainNet.ra
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    1f772d81ca29eb447e034a476369b573bc3e7909 Tue Jul 14 19:53:26 2026 -0700
    chainNet trackDb for canFam6 susScr11, otto liftOver
• src/hg/makeDb/trackDb/dog/canFam6/trackDb.ra
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    1f772d81ca29eb447e034a476369b573bc3e7909 Tue Jul 14 19:53:26 2026 -0700
    chainNet trackDb for canFam6 susScr11, otto liftOver
• src/hg/makeDb/trackDb/human/cardSv.html
  • lines changed 139, context: html, text, full: html, text
    95208355e2c667d194b29ee78c8ca8a09c2c2596 Fri Jul 17 08:51:28 2026 -0700
    lrSv: add NIH CARD long-read SV subtrack (cardSv) #Preview2 week - bugs introduced now will need a build patch to fix Add the NIH CARD Long-Read Initiative structural-variant catalogue (351 post-mortem brain samples: 205 NABEC European ancestry, 146 HBCC African/African-admixed) as a new subtrack of the Long-read SVs container. The provider bigBed is re-derived into the shared lrSv schema: signed svLen made positive (reference span), an explicit insLen added, the single DUP:TANDEM folded to DUP, and colors remapped to the container's shared svColor() palette. All 228,855 provider records are carried through 1:1. Adds the converter and autoSql, the trackDb stanza with filters consistent with the sibling subtracks, a full description page, a summary row and blurb on the container page, and a makeDoc section. refs #36258
• src/hg/makeDb/trackDb/human/eve.html
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    9f9a96ab068a76799311c09a2813b0b28f8e7712 Mon Jul 13 12:52:41 2026 -0700
    Order EVE heatmap amino acid rows by class to match the MaveDB track. refs #37763 Change the heatmap row order from alphabetical to physicochemical-amino-acid-class order (A V L I M F Y W R H K D E S T N Q G C P), matching the MaveDB Experiments heatmap so the tracks can be compared row-for-row. Rebuilds eve.bb; updates the makedoc, the AutoSql row label comment, and the description page.
• src/hg/makeDb/trackDb/human/hg19/knownGene.alpha.ra
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    65b9e931d649064e568d5826f636f0ab24d6ac19 Thu Jul 16 07:34:15 2026 -0700
    Makedoc and trackDb for hg19 GENCODE V50 knownGene, refs #37393
• src/hg/makeDb/trackDb/human/hg19/knownGeneArchive.ra
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    65b9e931d649064e568d5826f636f0ab24d6ac19 Thu Jul 16 07:34:15 2026 -0700
    Makedoc and trackDb for hg19 GENCODE V50 knownGene, refs #37393
• src/hg/makeDb/trackDb/human/hg19/knownGeneV50lift37.html
  • lines changed 167, context: html, text, full: html, text
    65b9e931d649064e568d5826f636f0ab24d6ac19 Thu Jul 16 07:34:15 2026 -0700
    Makedoc and trackDb for hg19 GENCODE V50 knownGene, refs #37393
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    65b9e931d649064e568d5826f636f0ab24d6ac19 Thu Jul 16 07:34:15 2026 -0700
    Makedoc and trackDb for hg19 GENCODE V50 knownGene, refs #37393
• src/hg/makeDb/trackDb/human/hg38/cCREregistry.html
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    1f43db197e0e58c47901a1d9f00531ecb08cacf0 Wed Jul 15 23:40:36 2026 -0700
    Updating hg38 ENCODE4 cCREs description pages to match mm10 (max-Z threshold, ATAC caveat, Core Collection link, Low-DNase/CA-only classes), fixing a filterValues typo and a few broken links along the way, and restoring the mm10 ENCODE4 Regulation links since ENCODE4 is on the RR. refs #37845 refs #37131
• src/hg/makeDb/trackDb/human/hg38/cCREsSuper.html
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    1f43db197e0e58c47901a1d9f00531ecb08cacf0 Wed Jul 15 23:40:36 2026 -0700
    Updating hg38 ENCODE4 cCREs description pages to match mm10 (max-Z threshold, ATAC caveat, Core Collection link, Low-DNase/CA-only classes), fixing a filterValues typo and a few broken links along the way, and restoring the mm10 ENCODE4 Regulation links since ENCODE4 is on the RR. refs #37845 refs #37131
• src/hg/makeDb/trackDb/human/hg38/clinvarMapped.html
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    5fe93cbef0d7692552e37e62bbf394cc7d222a28 Thu Jul 16 00:32:55 2026 -0700
    ClinVar Mapped track: map ClinVar coding variants through paralog alignments #Preview2 week - bugs introduced now will need a build patch to fix Adds the clinvarMapped composite (hg38) with two subtracks: - clinvarMappedParalog: every protein-changing ClinVar variant projected onto the equivalent (aligned) residue of each of its gene's paralogs - clinvarMappedParalogAln: the pairwise protein alignments used to do the mapping, as bigPsl, so the evidence for each projection can be inspected Pipeline: paralog pairs from Ensembl BioMart, one representative transcript per gene from MANE Select, pairwise global protein alignment (BLOSUM62) for pairs at >=20% identity, variants projected residue-to-residue and mapped back to the paralog's genomic codon. Colors and filters mirror the ClinVar track; the map track is filterable by source gene, classification, review stars, residue conservation and percent identity. refs #37883
• src/hg/makeDb/trackDb/human/hg38/clinvarMapped.ra
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    5fe93cbef0d7692552e37e62bbf394cc7d222a28 Thu Jul 16 00:32:55 2026 -0700
    ClinVar Mapped track: map ClinVar coding variants through paralog alignments #Preview2 week - bugs introduced now will need a build patch to fix Adds the clinvarMapped composite (hg38) with two subtracks: - clinvarMappedParalog: every protein-changing ClinVar variant projected onto the equivalent (aligned) residue of each of its gene's paralogs - clinvarMappedParalogAln: the pairwise protein alignments used to do the mapping, as bigPsl, so the evidence for each projection can be inspected Pipeline: paralog pairs from Ensembl BioMart, one representative transcript per gene from MANE Select, pairwise global protein alignment (BLOSUM62) for pairs at >=20% identity, variants projected residue-to-residue and mapped back to the paralog's genomic codon. Colors and filters mirror the ClinVar track; the map track is filterable by source gene, classification, review stars, residue conservation and percent identity. refs #37883
• src/hg/makeDb/trackDb/human/hg38/coreCollection.html
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    1f43db197e0e58c47901a1d9f00531ecb08cacf0 Wed Jul 15 23:40:36 2026 -0700
    Updating hg38 ENCODE4 cCREs description pages to match mm10 (max-Z threshold, ATAC caveat, Core Collection link, Low-DNase/CA-only classes), fixing a filterValues typo and a few broken links along the way, and restoring the mm10 ENCODE4 Regulation links since ENCODE4 is on the RR. refs #37845 refs #37131
• src/hg/makeDb/trackDb/human/hg38/encode.cCREs.override.ra
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    1f43db197e0e58c47901a1d9f00531ecb08cacf0 Wed Jul 15 23:40:36 2026 -0700
    Updating hg38 ENCODE4 cCREs description pages to match mm10 (max-Z threshold, ATAC caveat, Core Collection link, Low-DNase/CA-only classes), fixing a filterValues typo and a few broken links along the way, and restoring the mm10 ENCODE4 Regulation links since ENCODE4 is on the RR. refs #37845 refs #37131
• src/hg/makeDb/trackDb/human/hg38/hprc2.html
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    04456b0be37a7d7b57551e0d9596e3ef0b8f0393 Thu Jul 16 00:34:37 2026 -0700
    Add HPRC Release 2 hg38 native tracks (alignments, coverage, breaks, rearrangements, chains), refs #35415 #Preview2 week - bugs introduced now will need a build patch to fix New pan-genome track container (group hprc) derived from the HPRC Release 2 per-assembly chains to GRCh38 (462 haplotypes), running in parallel to the existing HPRC release 1 tracks: - hprc2Coverage: fraction of assemblies aligning across GRCh38 - hprc2Breaks: alignment breaks, colored by prevalence - hprc2Rearr: insertions/deletions/inversions/duplications/complex indels, lrSv color palette, numeric size field, 50 bp default filter - hprc2Chains: per-haplotype bigChain composite, grouped by superpopulation Container hidden by default. Scripts, autoSql, and makeDoc included.
• src/hg/makeDb/trackDb/human/hg38/hprc2.ra
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    04456b0be37a7d7b57551e0d9596e3ef0b8f0393 Thu Jul 16 00:34:37 2026 -0700
    Add HPRC Release 2 hg38 native tracks (alignments, coverage, breaks, rearrangements, chains), refs #35415 #Preview2 week - bugs introduced now will need a build patch to fix New pan-genome track container (group hprc) derived from the HPRC Release 2 per-assembly chains to GRCh38 (462 haplotypes), running in parallel to the existing HPRC release 1 tracks: - hprc2Coverage: fraction of assemblies aligning across GRCh38 - hprc2Breaks: alignment breaks, colored by prevalence - hprc2Rearr: insertions/deletions/inversions/duplications/complex indels, lrSv color palette, numeric size field, 50 bp default filter - hprc2Chains: per-haplotype bigChain composite, grouped by superpopulation Container hidden by default. Scripts, autoSql, and makeDoc included.
• src/hg/makeDb/trackDb/human/hg38/hprc2Chains.ra
  • lines changed 4636, context: html, text, full: html, text
    04456b0be37a7d7b57551e0d9596e3ef0b8f0393 Thu Jul 16 00:34:37 2026 -0700
    Add HPRC Release 2 hg38 native tracks (alignments, coverage, breaks, rearrangements, chains), refs #35415 #Preview2 week - bugs introduced now will need a build patch to fix New pan-genome track container (group hprc) derived from the HPRC Release 2 per-assembly chains to GRCh38 (462 haplotypes), running in parallel to the existing HPRC release 1 tracks: - hprc2Coverage: fraction of assemblies aligning across GRCh38 - hprc2Breaks: alignment breaks, colored by prevalence - hprc2Rearr: insertions/deletions/inversions/duplications/complex indels, lrSv color palette, numeric size field, 50 bp default filter - hprc2Chains: per-haplotype bigChain composite, grouped by superpopulation Container hidden by default. Scripts, autoSql, and makeDoc included.
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
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    f7003f9a6744e9c1d0ec6cef2226a1035d2b2b06 Wed Jul 15 22:08:51 2026 -0700
    TrackDb and makedoc for UCSC Genes version of GENCODE V50, refs #37395
• src/hg/makeDb/trackDb/human/hg38/knownGeneArchive.ra
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    f7003f9a6744e9c1d0ec6cef2226a1035d2b2b06 Wed Jul 15 22:08:51 2026 -0700
    TrackDb and makedoc for UCSC Genes version of GENCODE V50, refs #37395
• src/hg/makeDb/trackDb/human/hg38/knownGeneV50.html
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    f7003f9a6744e9c1d0ec6cef2226a1035d2b2b06 Wed Jul 15 22:08:51 2026 -0700
    TrackDb and makedoc for UCSC Genes version of GENCODE V50, refs #37395
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    f7003f9a6744e9c1d0ec6cef2226a1035d2b2b06 Wed Jul 15 22:08:51 2026 -0700
    TrackDb and makedoc for UCSC Genes version of GENCODE V50, refs #37395
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    5fe93cbef0d7692552e37e62bbf394cc7d222a28 Thu Jul 16 00:32:55 2026 -0700
    ClinVar Mapped track: map ClinVar coding variants through paralog alignments #Preview2 week - bugs introduced now will need a build patch to fix Adds the clinvarMapped composite (hg38) with two subtracks: - clinvarMappedParalog: every protein-changing ClinVar variant projected onto the equivalent (aligned) residue of each of its gene's paralogs - clinvarMappedParalogAln: the pairwise protein alignments used to do the mapping, as bigPsl, so the evidence for each projection can be inspected Pipeline: paralog pairs from Ensembl BioMart, one representative transcript per gene from MANE Select, pairwise global protein alignment (BLOSUM62) for pairs at >=20% identity, variants projected residue-to-residue and mapped back to the paralog's genomic codon. Colors and filters mirror the ClinVar track; the map track is filterable by source gene, classification, review stars, residue conservation and percent identity. refs #37883
  • lines changed 2, context: html, text, full: html, text
    04456b0be37a7d7b57551e0d9596e3ef0b8f0393 Thu Jul 16 00:34:37 2026 -0700
    Add HPRC Release 2 hg38 native tracks (alignments, coverage, breaks, rearrangements, chains), refs #35415 #Preview2 week - bugs introduced now will need a build patch to fix New pan-genome track container (group hprc) derived from the HPRC Release 2 per-assembly chains to GRCh38 (462 haplotypes), running in parallel to the existing HPRC release 1 tracks: - hprc2Coverage: fraction of assemblies aligning across GRCh38 - hprc2Breaks: alignment breaks, colored by prevalence - hprc2Rearr: insertions/deletions/inversions/duplications/complex indels, lrSv color palette, numeric size field, 50 bp default filter - hprc2Chains: per-haplotype bigChain composite, grouped by superpopulation Container hidden by default. Scripts, autoSql, and makeDoc included.
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    c1e6abaa73026fe77039279711797accf2215a13 Fri Jul 17 13:06:26 2026 -0700
    Removing accidential commit of a trackDb include for a test file, no ticket
• src/hg/makeDb/trackDb/human/hostseq.html
  • lines changed 114, context: html, text, full: html, text
    99764ad55bb121d285e9734de955bba41802ad06 Wed Jul 15 23:35:19 2026 -0700
    varFreqs: add gnomAD-Canada HostSeq SNV frequencies and fold into combined tracks, refs #36642 #Preview2 week - bugs introduced now will need a build patch to fix New "hostseq" vcfTabix subtrack of the SNV Frequencies container: gnomAD-Canada v1.0 / HostSeq, 10,487 Canadian COVID-19 WGS genomes on hg38. The release ships only as a ~104 GB Hail table, so hostseqHtToVcf.py reads it with Hail and flattens the freq array into a sites-only VCF with overall + 9 gnomAD ancestry-group AC/AN/AF, nhomalt, grpmax, dbSNP rsID and the variant filter status. 232,028,491 release rows -> 213,382,086 written (18,646,405 AC0 sites dropped). Registered HostSeq (is_disease=0) in databases.tsv and its 9 ancestry groups in populations.tsv, and rebuilt varFreqsAffected/varFreqsBackground so HostSeq feeds the background side (29 cohorts, 185 fields; merged set 1,374,129,993 variants). Added HostSeq to filterValues.backgroundSources.
• src/hg/makeDb/trackDb/human/lrSv.html
  • lines changed 36, context: html, text, full: html, text
    95208355e2c667d194b29ee78c8ca8a09c2c2596 Fri Jul 17 08:51:28 2026 -0700
    lrSv: add NIH CARD long-read SV subtrack (cardSv) #Preview2 week - bugs introduced now will need a build patch to fix Add the NIH CARD Long-Read Initiative structural-variant catalogue (351 post-mortem brain samples: 205 NABEC European ancestry, 146 HBCC African/African-admixed) as a new subtrack of the Long-read SVs container. The provider bigBed is re-derived into the shared lrSv schema: signed svLen made positive (reference span), an explicit insLen added, the single DUP:TANDEM folded to DUP, and colors remapped to the container's shared svColor() palette. All 228,855 provider records are carried through 1:1. Adds the converter and autoSql, the trackDb stanza with filters consistent with the sibling subtracks, a full description page, a summary row and blurb on the container page, and a makeDoc section. refs #36258
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    3bf9e1a841206d3bf5902e06791ef5be2dbdbd39 Fri Jul 17 09:09:47 2026 -0700
    lrSv: add Noyvert multi-ancestry long-read SV subtrack (noyvertSv) #Preview2 week - bugs introduced now will need a build patch to fix 888 Oxford Nanopore 1000 Genomes genomes, Sniffles2 v2.0.7, 107,445 SVs with per-superpopulation allele frequencies, imputation-accuracy metrics and UK Biobank SV-WAS associations. Converter approximates AC/AN from AF and the genotype missing rate (source has no allele count), stores BND mate breakends, and follows the shared lrSv svType/svLen/insLen/AC field convention so the container-level filters apply. refs #36258
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    d92e36dbbee172d6bb81a751eb8bb935f356890c Fri Jul 17 09:31:28 2026 -0700
    lrSv: add cardSv and noyvertSv to the lrSvAll merged track #Preview2 week - bugs introduced now will need a build patch to fix Append NIH CARD 351 (AC/alleleFreq) and Noyvert 888 (AC/AF) to databases.tsv and re-run lrSvMergeAll.py: 16 source databases now, 3,018,404 input variants merged to 2,582,278 (was 14 dbs, 2,317,508). Regenerated lrSvAll.ra (filterValues.sources + sourceCount 1:16) and updated the container summary table. refs #36258
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    12c38f63e39d562ab77060346429068f97e32c25 Fri Jul 17 23:59:34 2026 -0700
    lrsv docs change after feedback from Jonas Gustavsson jgust1@uw.edu
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    af24c692f12ca0c3fcbf639e63040e61cfb684a5 Sat Jul 18 00:17:03 2026 -0700
    small lrsv docs changes
• src/hg/makeDb/trackDb/human/lrSv.ra
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    9dc380d3c6aada6b12cbcd7a95d1d426b47ce86c Tue Jul 14 17:11:11 2026 -0700
    Add Long-read Structural Variants announcement (news archive + gateway news) and track pennantIcon. refs #36258 Add a July 16, 2026 news-archive entry announcing the Long-read Structural Variants container track on hg38 and hs1, with a UGT2B17 example image, and add the matching gateway indexNews item (dropping the oldest to keep six). Add a "New" pennantIcon on the longReadVariants supertrack linking to the post. Also move the still-unreleased ENCODE4 draft entry to July 22 and keep it commented out.
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    95208355e2c667d194b29ee78c8ca8a09c2c2596 Fri Jul 17 08:51:28 2026 -0700
    lrSv: add NIH CARD long-read SV subtrack (cardSv) #Preview2 week - bugs introduced now will need a build patch to fix Add the NIH CARD Long-Read Initiative structural-variant catalogue (351 post-mortem brain samples: 205 NABEC European ancestry, 146 HBCC African/African-admixed) as a new subtrack of the Long-read SVs container. The provider bigBed is re-derived into the shared lrSv schema: signed svLen made positive (reference span), an explicit insLen added, the single DUP:TANDEM folded to DUP, and colors remapped to the container's shared svColor() palette. All 228,855 provider records are carried through 1:1. Adds the converter and autoSql, the trackDb stanza with filters consistent with the sibling subtracks, a full description page, a summary row and blurb on the container page, and a makeDoc section. refs #36258
  • lines changed 54, context: html, text, full: html, text
    3bf9e1a841206d3bf5902e06791ef5be2dbdbd39 Fri Jul 17 09:09:47 2026 -0700
    lrSv: add Noyvert multi-ancestry long-read SV subtrack (noyvertSv) #Preview2 week - bugs introduced now will need a build patch to fix 888 Oxford Nanopore 1000 Genomes genomes, Sniffles2 v2.0.7, 107,445 SVs with per-superpopulation allele frequencies, imputation-accuracy metrics and UK Biobank SV-WAS associations. Converter approximates AC/AN from AF and the genotype missing rate (source has no allele count), stores BND mate breakends, and follows the shared lrSv svType/svLen/insLen/AC field convention so the container-level filters apply. refs #36258
• src/hg/makeDb/trackDb/human/lrSvAll.ra
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    d92e36dbbee172d6bb81a751eb8bb935f356890c Fri Jul 17 09:31:28 2026 -0700
    lrSv: add cardSv and noyvertSv to the lrSvAll merged track #Preview2 week - bugs introduced now will need a build patch to fix Append NIH CARD 351 (AC/alleleFreq) and Noyvert 888 (AC/AF) to databases.tsv and re-run lrSvMergeAll.py: 16 source databases now, 3,018,404 input variants merged to 2,582,278 (was 14 dbs, 2,317,508). Regenerated lrSvAll.ra (filterValues.sources + sourceCount 1:16) and updated the container summary table. refs #36258
• src/hg/makeDb/trackDb/human/noyvertSv.html
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    3bf9e1a841206d3bf5902e06791ef5be2dbdbd39 Fri Jul 17 09:09:47 2026 -0700
    lrSv: add Noyvert multi-ancestry long-read SV subtrack (noyvertSv) #Preview2 week - bugs introduced now will need a build patch to fix 888 Oxford Nanopore 1000 Genomes genomes, Sniffles2 v2.0.7, 107,445 SVs with per-superpopulation allele frequencies, imputation-accuracy metrics and UK Biobank SV-WAS associations. Converter approximates AC/AN from AF and the genotype missing rate (source has no allele count), stores BND mate breakends, and follows the shared lrSv svType/svLen/insLen/AC field convention so the container-level filters apply. refs #36258
• src/hg/makeDb/trackDb/human/popEve.html
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    3d194de4d74f67c1a453035e20c4769d88bec4c4 Mon Jul 13 12:52:57 2026 -0700
    Order popEVE heatmap amino acid rows by class to match the MaveDB track. refs #37791 Change the heatmap row order from alphabetical to physicochemical-amino-acid-class order (A V L I M F Y W R H K D E S T N Q G C P), matching the MaveDB Experiments heatmap so the tracks can be compared row-for-row. Rebuilds popEve.bb; updates the makedoc, the AutoSql row label comment, and the description page.
• src/hg/makeDb/trackDb/human/varFreqs.ra
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    99764ad55bb121d285e9734de955bba41802ad06 Wed Jul 15 23:35:19 2026 -0700
    varFreqs: add gnomAD-Canada HostSeq SNV frequencies and fold into combined tracks, refs #36642 #Preview2 week - bugs introduced now will need a build patch to fix New "hostseq" vcfTabix subtrack of the SNV Frequencies container: gnomAD-Canada v1.0 / HostSeq, 10,487 Canadian COVID-19 WGS genomes on hg38. The release ships only as a ~104 GB Hail table, so hostseqHtToVcf.py reads it with Hail and flattens the freq array into a sites-only VCF with overall + 9 gnomAD ancestry-group AC/AN/AF, nhomalt, grpmax, dbSNP rsID and the variant filter status. 232,028,491 release rows -> 213,382,086 written (18,646,405 AC0 sites dropped). Registered HostSeq (is_disease=0) in databases.tsv and its 9 ancestry groups in populations.tsv, and rebuilt varFreqsAffected/varFreqsBackground so HostSeq feeds the background side (29 cohorts, 185 fields; merged set 1,374,129,993 variants). Added HostSeq to filterValues.backgroundSources.
• src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html
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    1f43db197e0e58c47901a1d9f00531ecb08cacf0 Wed Jul 15 23:40:36 2026 -0700
    Updating hg38 ENCODE4 cCREs description pages to match mm10 (max-Z threshold, ATAC caveat, Core Collection link, Low-DNase/CA-only classes), fixing a filterValues typo and a few broken links along the way, and restoring the mm10 ENCODE4 Regulation links since ENCODE4 is on the RR. refs #37845 refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/coreCollection.html
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    1f43db197e0e58c47901a1d9f00531ecb08cacf0 Wed Jul 15 23:40:36 2026 -0700
    Updating hg38 ENCODE4 cCREs description pages to match mm10 (max-Z threshold, ATAC caveat, Core Collection link, Low-DNase/CA-only classes), fixing a filterValues typo and a few broken links along the way, and restoring the mm10 ENCODE4 Regulation links since ENCODE4 is on the RR. refs #37845 refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/developmentTimecourseSignalMm10.html
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    e6bafe04b348ec643f503c1600ab336c56870214 Tue Jul 14 18:01:27 2026 -0700
    Adding the mouseDevTimecourse bigWig signal composite for mm10, including its track description page, build scripts, and makedoc documentation, using Claude, refs #37001
• src/hg/makeDb/trackDb/mouse/mm10/developmentTimecourseSignalMm10.ra
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    e6bafe04b348ec643f503c1600ab336c56870214 Tue Jul 14 18:01:27 2026 -0700
    Adding the mouseDevTimecourse bigWig signal composite for mm10, including its track description page, build scripts, and makedoc documentation, using Claude, refs #37001
• src/hg/makeDb/trackDb/mouse/mm10/mouseDevTimecourse.html
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    e6bafe04b348ec643f503c1600ab336c56870214 Tue Jul 14 18:01:27 2026 -0700
    Adding the mouseDevTimecourse bigWig signal composite for mm10, including its track description page, build scripts, and makedoc documentation, using Claude, refs #37001
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    e6bafe04b348ec643f503c1600ab336c56870214 Tue Jul 14 18:01:27 2026 -0700
    Adding the mouseDevTimecourse bigWig signal composite for mm10, including its track description page, build scripts, and makedoc documentation, using Claude, refs #37001
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.alpha.ra
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    10fb7902ebfda7cdddb0b410d506bf2f571b4ec6 Wed Jul 15 21:20:24 2026 -0700
    TrackDb and makedoc for UCSC Genes version of GENCODE VM39, refs #37391
• src/hg/makeDb/trackDb/mouse/mm39/knownGeneArchive.ra
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    10fb7902ebfda7cdddb0b410d506bf2f571b4ec6 Wed Jul 15 21:20:24 2026 -0700
    TrackDb and makedoc for UCSC Genes version of GENCODE VM39, refs #37391
• src/hg/makeDb/trackDb/mouse/mm39/knownGeneVM39.html
  • lines changed 124, context: html, text, full: html, text
    10fb7902ebfda7cdddb0b410d506bf2f571b4ec6 Wed Jul 15 21:20:24 2026 -0700
    TrackDb and makedoc for UCSC Genes version of GENCODE VM39, refs #37391
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
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    10fb7902ebfda7cdddb0b410d506bf2f571b4ec6 Wed Jul 15 21:20:24 2026 -0700
    TrackDb and makedoc for UCSC Genes version of GENCODE VM39, refs #37391
• src/hg/makeDb/trackDb/pig/susScr11/susScr11.canFam6.chainNet.ra
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    9788869c3604b98837101f727d872cdb8f32590a Tue Jul 14 19:53:18 2026 -0700
    chainNet trackDb for susScr11 canFam6, otto liftOver
• src/hg/makeDb/trackDb/pig/susScr11/trackDb.ra
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    9788869c3604b98837101f727d872cdb8f32590a Tue Jul 14 19:53:18 2026 -0700
    chainNet trackDb for susScr11 canFam6, otto liftOver
• src/hg/utils/automation/importTrackHub
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    943fd670e29550dee31d37fcfecd9bdfd0e53d50 Tue Jul 14 12:18:25 2026 -0700
    Remove unused importTrackHub script. It was a one-off used once in 2017 to import the Hoffman lab mappability hub (recorded in hg38.txt), is not installed by any makefile, has no callers, and even that single use fell back to a manual fetch. History retains it (added in 22740c40dcb) if it is ever needed again. refs #19154
• src/hg/utils/chainInDel/chainInDel.c
  • lines changed 103, context: html, text, full: html, text
    f977ac0a76489eb506045886eb1a1343af94818b Fri Jul 17 12:44:43 2026 -0700
    chainInDel: add optional left-normalization of indels, refs #35415 Add -t2bit and -q2bit options to left-normalize indels to their leftmost equivalent position within a repeat or homopolymer. -t2bit normalizes pure deletions using the target sequence; -q2bit additionally normalizes pure insertions and requires -t2bit. Complex indels are left untouched, and minus-strand queries are reverse-complemented into chain orientation. Without these options the output is byte-for-byte identical to before, so the existing HPRC indel build is unaffected until the options are added to it. Left-normalizing makes indel calls line up across HPRC releases even when the chain builder places the same event a few bases apart inside a repeat, which is a prerequisite for stable cross-release IDs.
• src/hg/utils/otto/genArk/pushRR.sh
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    fa90223f31c18b4c8afab1b0fff499bbdb46f707 Thu Jul 16 08:06:37 2026 -0700
    creating listings of contrib files in the outside/genark/listings/ directory refs #34917
• src/hg/utils/otto/userRequests/chainNetTrackDb.pl
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    e987e68d1cb3af2af122c809ecf35053f6baabd1 Tue Jul 14 19:38:49 2026 -0700
    do not bother about uncommited log files in the kent source tree used to update the hubs refs #31811
• src/inc/userAppMulti.mk
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    40de350c7aff82babf54c7a7eea41ff5c354bafc Tue Jul 14 11:15:31 2026 -0700
    Build shared objects once before parallel sub-makes in userAppMulti.mk. refs #37809 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/utils/codeReviewAi.py
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    3a5f01ff264521fd46312b8ada68f3b9c7708d64 Tue Jul 14 07:57:07 2026 -0700
    Add --since/--until window options to codeReviewAi.py --daily mode. refs #36890 Let --daily review an explicit date window instead of only the last N hours, so a missed period can be backfilled in digestible chunks (e.g. one week at a time) rather than one large bundle. --since (with optional --until) is passed straight to git log; --hours behavior is unchanged when --since is absent, so the cron is unaffected. The window is reflected in the review prompt, progress output, and the failure-alert email, and is included in saved review filenames so same-day backfill runs do not overwrite each other.
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    8b1cdafd019d4adcad11a6712f48549b0460f1fa Tue Jul 14 10:31:16 2026 -0700
    Fix codeReviewAi.py false auth-failure on reviews that quote error strings. refs #36890 detect_cli_failure scanned the whole CLI response for auth-error markers before validating, so a well-formed review whose text legitimately quotes strings like "authentication_error" or "API Error: 401" (e.g. a review of the auth-handling code itself) was misflagged as a Claude CLI authentication failure - skipping the author email and firing a spurious alert. Validate the response first and only scan for auth markers when it is not a valid review.
• src/utils/qa/qaTestScript.py
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    b539e4e9e97af625cc089cc79c1800d03f28e2a6 Fri Jul 17 09:55:46 2026 -0700
    Updating the hgPcr test to click the first PCR result link due to GENCODE transcript accessions and positions changing after a new version release, No RM
• src/utils/redmineCli
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    8600f5319ad0670e63cdee1f17fe2872224bd89d Sat Jul 18 14:00:49 2026 -0700
    redmineCli: support --assemblies and --custom-field on create Trackers with required custom fields (e.g. Track requires Assemblies) 422'd on a bare create. Add a named --assemblies flag (custom field 2) and a generic repeatable --custom-field ID=VALUE, reusing the same parsing/validation as update. refs #37281 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

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• files changed: 173