File Changes for max

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

• src/hg/hgBlat/hgBlat.c
  • lines changed 454, context: html, text, full: html, text
    c683ecb63d721deb02fa8ab15bf66f70f1c3a326 Sat Jul 25 18:25:00 2026 -0700
    hgBlat/hgc: single-page BLAT results view with shareable alignment links Add a modern single-page BLAT results table (hgBlat.js) and a non-frameset alignment view (showSomeAlignmentModern in hgc, gated by the blatNewPage cart var). Share/reopen a result set from a durable bigPsl custom track pinned in the cart via a saved session (htcBlatAlign / loadBlatShareSessionIfAny). Factor the shared helpers into a new blatShare module (lib/blatShare.c, inc/blatShare.h).
  • lines changed 4, context: html, text, full: html, text
    6ae582f5103a8b27420c44a8f92f210969f65f4c Sat Jul 25 21:36:18 2026 -0700
    hgc BLAT alignment viewer: table-free page, share dialog, chromAlias, block-count fix refs #37893 Modern base-alignment page (showSomeAlignmentModern): - Switch page chrome to webStartGbNoBanner()/webEndGb() (menubar + <main>, no legacy nested section tables) and draw the gold title bar + grey Back/Share buttons in plain HTML instead of injecting them with JS. - Full-height "jump to" sidebar; its links are position:sticky so they stay visible while scrolling the long alignment. The per-block "Block N" links use the block count the renderer returns, not psl->blockCount. The DNA path (ffShAliPart) merges blocks separated by gaps <= 8 bases, so raw psl->blockCount over-counted and produced links to #N anchors that did not exist; the returned count matches the emitted anchors. - Show the genomic sequence's chromAlias names ("Genome sequence chr7 is also known as: ..."), de-duplicated. Friendly assembly label (organism + accession) for hub databases instead of the internal hub_NNN_ name. Durable "Share a link": - Opens the shared topLinks.js "Share a link" modal and hands it a durable hgc?g=htcBlatAlign link. The link carries only the hit selectors (c/o/i) plus u=l&s=; db and the browser window come from the saved session. htcBlatAlign rebuilds the one alignment from the session's durable bigPsl custom track (no BLAT re-run). - Restore the per-hit "Alignment" links on shared-session results tables (hgBlat.c). lib/cart.c: - cartWriteHeaderAndCont() is now idempotent (guards on cartDidContentType). hgc writes the CGI header early, so a later webStartGb* would otherwise write a second Set-Cookie/Content-Type into the page body.
• src/hg/hgTracks/cds.c
  • lines changed 134, context: html, text, full: html, text
    118634b1bb159357168a349dbf600f545e096f56 Fri Jul 24 08:17:41 2026 -0700
    Revert "hgTracks: strand-direction arrows on the zoomed-in codon/CDS and UTR display" This reverts commit ded41ea1968e30e2c248f65d1c9fec9793cb82fc.
  • lines changed 171, context: html, text, full: html, text
    43f042236ce180b8e0712d43c8baabc4ad8df1cd Sat Jul 25 18:21:54 2026 -0700
    hgTracks: add compactPack mode and codon strand-direction arrows When zoomed to codon-coloring level, draw strand-direction chevrons across the exons (white over coding codons when too small to label, contrasting color over UTRs), and a per-codon arrow between amino-acid letters via drawScaledBoxWithText. Add a compactPack trackDb setting for shorter pack/squish rows and a small squish-mode codon font. Adds mgFontForCellHeight() to memgfx and enables compactPack on the JASPAR track.
• src/hg/hgTracks/cds.h
  • lines changed 10, context: html, text, full: html, text
    118634b1bb159357168a349dbf600f545e096f56 Fri Jul 24 08:17:41 2026 -0700
    Revert "hgTracks: strand-direction arrows on the zoomed-in codon/CDS and UTR display" This reverts commit ded41ea1968e30e2c248f65d1c9fec9793cb82fc.
  • lines changed 10, context: html, text, full: html, text
    43f042236ce180b8e0712d43c8baabc4ad8df1cd Sat Jul 25 18:21:54 2026 -0700
    hgTracks: add compactPack mode and codon strand-direction arrows When zoomed to codon-coloring level, draw strand-direction chevrons across the exons (white over coding codons when too small to label, contrasting color over UTRs), and a per-codon arrow between amino-acid letters via drawScaledBoxWithText. Add a compactPack trackDb setting for shorter pack/squish rows and a small squish-mode codon font. Adds mgFontForCellHeight() to memgfx and enables compactPack on the JASPAR track.
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    43f042236ce180b8e0712d43c8baabc4ad8df1cd Sat Jul 25 18:21:54 2026 -0700
    hgTracks: add compactPack mode and codon strand-direction arrows When zoomed to codon-coloring level, draw strand-direction chevrons across the exons (white over coding codons when too small to label, contrasting color over UTRs), and a per-codon arrow between amino-acid letters via drawScaledBoxWithText. Add a compactPack trackDb setting for shorter pack/squish rows and a small squish-mode codon font. Adds mgFontForCellHeight() to memgfx and enables compactPack on the JASPAR track.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 19, context: html, text, full: html, text
    118634b1bb159357168a349dbf600f545e096f56 Fri Jul 24 08:17:41 2026 -0700
    Revert "hgTracks: strand-direction arrows on the zoomed-in codon/CDS and UTR display" This reverts commit ded41ea1968e30e2c248f65d1c9fec9793cb82fc.
  • lines changed 72, context: html, text, full: html, text
    43f042236ce180b8e0712d43c8baabc4ad8df1cd Sat Jul 25 18:21:54 2026 -0700
    hgTracks: add compactPack mode and codon strand-direction arrows When zoomed to codon-coloring level, draw strand-direction chevrons across the exons (white over coding codons when too small to label, contrasting color over UTRs), and a per-codon arrow between amino-acid letters via drawScaledBoxWithText. Add a compactPack trackDb setting for shorter pack/squish rows and a small squish-mode codon font. Adds mgFontForCellHeight() to memgfx and enables compactPack on the JASPAR track.
• src/hg/hgTracks/vcfTrack.c
  • lines changed 44, context: html, text, full: html, text
    be36584718d57384b01657483422f51adf29f0bb Sat Jul 25 18:22:02 2026 -0700
    vcfTrack: add minimum alternate allele count (minAc) filter, refs #37927 When a VCF INFO column includes AC, offer a 'minimum allele count' filter in the track UI (e.g. 2 to hide singletons) and drop records whose largest alternate allele count is below the threshold.
• src/hg/hgc/hgc.c
  • lines changed 256, context: html, text, full: html, text
    c683ecb63d721deb02fa8ab15bf66f70f1c3a326 Sat Jul 25 18:25:00 2026 -0700
    hgBlat/hgc: single-page BLAT results view with shareable alignment links Add a modern single-page BLAT results table (hgBlat.js) and a non-frameset alignment view (showSomeAlignmentModern in hgc, gated by the blatNewPage cart var). Share/reopen a result set from a durable bigPsl custom track pinned in the cart via a saved session (htcBlatAlign / loadBlatShareSessionIfAny). Factor the shared helpers into a new blatShare module (lib/blatShare.c, inc/blatShare.h).
  • lines changed 208, context: html, text, full: html, text
    6ae582f5103a8b27420c44a8f92f210969f65f4c Sat Jul 25 21:36:18 2026 -0700
    hgc BLAT alignment viewer: table-free page, share dialog, chromAlias, block-count fix refs #37893 Modern base-alignment page (showSomeAlignmentModern): - Switch page chrome to webStartGbNoBanner()/webEndGb() (menubar + <main>, no legacy nested section tables) and draw the gold title bar + grey Back/Share buttons in plain HTML instead of injecting them with JS. - Full-height "jump to" sidebar; its links are position:sticky so they stay visible while scrolling the long alignment. The per-block "Block N" links use the block count the renderer returns, not psl->blockCount. The DNA path (ffShAliPart) merges blocks separated by gaps <= 8 bases, so raw psl->blockCount over-counted and produced links to #N anchors that did not exist; the returned count matches the emitted anchors. - Show the genomic sequence's chromAlias names ("Genome sequence chr7 is also known as: ..."), de-duplicated. Friendly assembly label (organism + accession) for hub databases instead of the internal hub_NNN_ name. Durable "Share a link": - Opens the shared topLinks.js "Share a link" modal and hands it a durable hgc?g=htcBlatAlign link. The link carries only the hit selectors (c/o/i) plus u=l&s=; db and the browser window come from the saved session. htcBlatAlign rebuilds the one alignment from the session's durable bigPsl custom track (no BLAT re-run). - Restore the per-hit "Alignment" links on shared-session results tables (hgBlat.c). lib/cart.c: - cartWriteHeaderAndCont() is now idempotent (guards on cartDidContentType). hgc writes the CGI header early, so a later webStartGb* would otherwise write a second Set-Cookie/Content-Type into the page body.
• src/hg/inc/blatShare.h
  • lines changed 34, context: html, text, full: html, text
    c683ecb63d721deb02fa8ab15bf66f70f1c3a326 Sat Jul 25 18:25:00 2026 -0700
    hgBlat/hgc: single-page BLAT results view with shareable alignment links Add a modern single-page BLAT results table (hgBlat.js) and a non-frameset alignment view (showSomeAlignmentModern in hgc, gated by the blatNewPage cart var). Share/reopen a result set from a durable bigPsl custom track pinned in the cart via a saved session (htcBlatAlign / loadBlatShareSessionIfAny). Factor the shared helpers into a new blatShare module (lib/blatShare.c, inc/blatShare.h).
• src/hg/inc/vcfUi.h
  • lines changed 4, context: html, text, full: html, text
    be36584718d57384b01657483422f51adf29f0bb Sat Jul 25 18:22:02 2026 -0700
    vcfTrack: add minimum alternate allele count (minAc) filter, refs #37927 When a VCF INFO column includes AC, offer a 'minimum allele count' filter in the track UI (e.g. 2 to hide singletons) and drop records whose largest alternate allele count is below the threshold.
• src/hg/js/hgBlat.js
  • lines changed 455, context: html, text, full: html, text
    c683ecb63d721deb02fa8ab15bf66f70f1c3a326 Sat Jul 25 18:25:00 2026 -0700
    hgBlat/hgc: single-page BLAT results view with shareable alignment links Add a modern single-page BLAT results table (hgBlat.js) and a non-frameset alignment view (showSomeAlignmentModern in hgc, gated by the blatNewPage cart var). Share/reopen a result set from a durable bigPsl custom track pinned in the cart via a saved session (htcBlatAlign / loadBlatShareSessionIfAny). Factor the shared helpers into a new blatShare module (lib/blatShare.c, inc/blatShare.h).
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    c683ecb63d721deb02fa8ab15bf66f70f1c3a326 Sat Jul 25 18:25:00 2026 -0700
    hgBlat/hgc: single-page BLAT results view with shareable alignment links Add a modern single-page BLAT results table (hgBlat.js) and a non-frameset alignment view (showSomeAlignmentModern in hgc, gated by the blatNewPage cart var). Share/reopen a result set from a durable bigPsl custom track pinned in the cart via a saved session (htcBlatAlign / loadBlatShareSessionIfAny). Factor the shared helpers into a new blatShare module (lib/blatShare.c, inc/blatShare.h).
• src/hg/lib/blatShare.c
  • lines changed 114, context: html, text, full: html, text
    c683ecb63d721deb02fa8ab15bf66f70f1c3a326 Sat Jul 25 18:25:00 2026 -0700
    hgBlat/hgc: single-page BLAT results view with shareable alignment links Add a modern single-page BLAT results table (hgBlat.js) and a non-frameset alignment view (showSomeAlignmentModern in hgc, gated by the blatNewPage cart var). Share/reopen a result set from a durable bigPsl custom track pinned in the cart via a saved session (htcBlatAlign / loadBlatShareSessionIfAny). Factor the shared helpers into a new blatShare module (lib/blatShare.c, inc/blatShare.h).
• src/hg/lib/cart.c
  • lines changed 5, context: html, text, full: html, text
    6ae582f5103a8b27420c44a8f92f210969f65f4c Sat Jul 25 21:36:18 2026 -0700
    hgc BLAT alignment viewer: table-free page, share dialog, chromAlias, block-count fix refs #37893 Modern base-alignment page (showSomeAlignmentModern): - Switch page chrome to webStartGbNoBanner()/webEndGb() (menubar + <main>, no legacy nested section tables) and draw the gold title bar + grey Back/Share buttons in plain HTML instead of injecting them with JS. - Full-height "jump to" sidebar; its links are position:sticky so they stay visible while scrolling the long alignment. The per-block "Block N" links use the block count the renderer returns, not psl->blockCount. The DNA path (ffShAliPart) merges blocks separated by gaps <= 8 bases, so raw psl->blockCount over-counted and produced links to #N anchors that did not exist; the returned count matches the emitted anchors. - Show the genomic sequence's chromAlias names ("Genome sequence chr7 is also known as: ..."), de-duplicated. Friendly assembly label (organism + accession) for hub databases instead of the internal hub_NNN_ name. Durable "Share a link": - Opens the shared topLinks.js "Share a link" modal and hands it a durable hgc?g=htcBlatAlign link. The link carries only the hit selectors (c/o/i) plus u=l&s=; db and the browser window come from the saved session. htcBlatAlign rebuilds the one alignment from the session's durable bigPsl custom track (no BLAT re-run). - Restore the per-hit "Alignment" links on shared-session results tables (hgBlat.c). lib/cart.c: - cartWriteHeaderAndCont() is now idempotent (guards on cartDidContentType). hgc writes the CGI header early, so a later webStartGb* would otherwise write a second Set-Cookie/Content-Type into the page body.
• src/hg/lib/hui.c
  • lines changed 40, context: html, text, full: html, text
    329cebf37d4a04c2a490121e21d166cab69e8562 Sat Jul 25 18:22:02 2026 -0700
    hui: warn when a numeric filter setting has no matching filter.<field>, refs #37927 A numeric range filter is only discovered from a filter.<field> (or <field>Filter) setting. Emit a warning for orphaned filter settings that will otherwise be silently ignored.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    c683ecb63d721deb02fa8ab15bf66f70f1c3a326 Sat Jul 25 18:25:00 2026 -0700
    hgBlat/hgc: single-page BLAT results view with shareable alignment links Add a modern single-page BLAT results table (hgBlat.js) and a non-frameset alignment view (showSomeAlignmentModern in hgc, gated by the blatNewPage cart var). Share/reopen a result set from a durable bigPsl custom track pinned in the cart via a saved session (htcBlatAlign / loadBlatShareSessionIfAny). Factor the shared helpers into a new blatShare module (lib/blatShare.c, inc/blatShare.h).
• src/hg/lib/vcfUi.c
  • lines changed 17, context: html, text, full: html, text
    be36584718d57384b01657483422f51adf29f0bb Sat Jul 25 18:22:02 2026 -0700
    vcfTrack: add minimum alternate allele count (minAc) filter, refs #37927 When a VCF INFO column includes AC, offer a 'minimum allele count' filter in the track UI (e.g. 2 to hide singletons) and drop records whose largest alternate allele count is below the threshold.
• src/hg/makeDb/doc/hg38/clinvarMapped.txt
  • lines changed 66, context: html, text, full: html, text
    c9446936b026a803d97e7f5128404a327829fe2e Sun Jul 19 00:01:22 2026 -0700
    ClinVar Mapped: add Pfam-domain mapping method Maps ClinVar coding variants through Pfam protein domains as a second method under the clinvarMapped container. Each Pfam family's profile HMM gives a shared coordinate, so a variant inside a domain is projected to the residue in the same HMM match-state column in every other MANE Select gene carrying that domain, then mapped back to that gene's genomic codon. This links genes that share a domain without being paralogs (e.g. the SCN sodium channels and the CACNA1 calcium channels via Ion_trans). Each variant is shown at its 25 most conserved equivalents. Uses Pfam-A 38.2. Adds two alpha subtracks (Pfam Domain Variants, Pfam Domains), the hmmsearch/hmmalign build scripts, autoSql, makeDoc and description page, refs #37883
• src/hg/makeDb/doc/hg38/lrSv.txt
  • lines changed 32, context: html, text, full: html, text
    cc6ef4c74d072de9c22e8bb88ab0e0983e6f2f47 Wed Jul 22 18:09:16 2026 -0700
    lrSv cardSv: switch CARD count fields from carrier counts to allele counts The NIH CARD provider republished the display bigBed with the count columns changed to diploid allele counts (alleleCount = nabecAlleleCount + hbccAlleleCount). Re-downloaded and rebuilt; renamed the schema fields to AC / nabecAc / hbccAc, updated filter ranges (0:702, 0:410, 0:292) and labels to allele counts, and reworded cardSv.html and the lrSv.html summary. Also noted there are no Alzheimer's cases in these cohorts. Re-ran the merge so lrSvAll carries CARD's allele counts. refs #36258
  • lines changed 13, context: html, text, full: html, text
    0656b0a9ad98986ef3944b6ceaf305ab08ca4e39 Fri Jul 24 01:10:13 2026 -0700
    noyvertSv: swap UK Biobank r2 filter for leave-one-out metrics, revise description Per author (Boris Noyvert) request, replace the r2Ukb (UK Biobank imputation r2) filter with r2Loo and concordanceLoo, the primary SV imputation quality measures for the multi-ancestry reference panel (r2Ukb mainly reflects European-ancestry performance). Both fields already exist in noyvert.bb, so this is a trackDb-only change. Also update the description page with the author's revised text, including a comparison with the 1KG ONT Vienna dataset. refs #37888
  • lines changed 13, context: html, text, full: html, text
    7bdcd030cdf434c72f3f6a492ee8f84372c752c7 Sat Jul 25 19:22:57 2026 -0700
    noyvertSv: note the Boehringer/Vienna relationship and call-level overlap The Noyvert panel is an independent reprocessing of the same ONT reads as the 1KG ONT Vienna track (Schloissnig et al. 2025). Add a description sentence with the deletion counts (~38k vs ~58k, ~12k shared at 50% reciprocal overlap) and the concordance both ways (about a third of this track's deletions and a fifth of Vienna's at 50%, a quarter and a sixth at 90%; ~a quarter of insertions match within 100 bp). Overlap analysis recorded in the makeDoc. refs #37888
• src/hg/makeDb/hgLoadMaf/hgLoadMafSummary.c
  • lines changed 54, context: html, text, full: html, text
    2db6bab8db05291ff90bbc867784be7f7c9177f6 Sat Jul 25 21:48:14 2026 -0700
    hgLoadMafSummary: robustly split MAF sequence names into assembly and chrom Handle a pipe separator, no-dot names, GenArk accession dbs (GCA_/GCF_, which carry an accession.version dot), and a dotted chrom, without aborting on an ordinary assembly.chrom name that sits next to dotted query names. Fixes a regression from ae63ce5 (refs #36592). refs #37928
• src/hg/makeDb/scripts/clinvarMapped/clinvarMappedPfam.as
  • lines changed 32, context: html, text, full: html, text
    c9446936b026a803d97e7f5128404a327829fe2e Sun Jul 19 00:01:22 2026 -0700
    ClinVar Mapped: add Pfam-domain mapping method Maps ClinVar coding variants through Pfam protein domains as a second method under the clinvarMapped container. Each Pfam family's profile HMM gives a shared coordinate, so a variant inside a domain is projected to the residue in the same HMM match-state column in every other MANE Select gene carrying that domain, then mapped back to that gene's genomic codon. This links genes that share a domain without being paralogs (e.g. the SCN sodium channels and the CACNA1 calcium channels via Ion_trans). Each variant is shown at its 25 most conserved equivalents. Uses Pfam-A 38.2. Adds two alpha subtracks (Pfam Domain Variants, Pfam Domains), the hmmsearch/hmmalign build scripts, autoSql, makeDoc and description page, refs #37883
• src/hg/makeDb/scripts/clinvarMapped/clinvarMappedPfamAlign.py
  • lines changed 159, context: html, text, full: html, text
    c9446936b026a803d97e7f5128404a327829fe2e Sun Jul 19 00:01:22 2026 -0700
    ClinVar Mapped: add Pfam-domain mapping method Maps ClinVar coding variants through Pfam protein domains as a second method under the clinvarMapped container. Each Pfam family's profile HMM gives a shared coordinate, so a variant inside a domain is projected to the residue in the same HMM match-state column in every other MANE Select gene carrying that domain, then mapped back to that gene's genomic codon. This links genes that share a domain without being paralogs (e.g. the SCN sodium channels and the CACNA1 calcium channels via Ion_trans). Each variant is shown at its 25 most conserved equivalents. Uses Pfam-A 38.2. Adds two alpha subtracks (Pfam Domain Variants, Pfam Domains), the hmmsearch/hmmalign build scripts, autoSql, makeDoc and description page, refs #37883
• src/hg/makeDb/scripts/clinvarMapped/clinvarMappedPfamAln.as
  • lines changed 24, context: html, text, full: html, text
    c9446936b026a803d97e7f5128404a327829fe2e Sun Jul 19 00:01:22 2026 -0700
    ClinVar Mapped: add Pfam-domain mapping method Maps ClinVar coding variants through Pfam protein domains as a second method under the clinvarMapped container. Each Pfam family's profile HMM gives a shared coordinate, so a variant inside a domain is projected to the residue in the same HMM match-state column in every other MANE Select gene carrying that domain, then mapped back to that gene's genomic codon. This links genes that share a domain without being paralogs (e.g. the SCN sodium channels and the CACNA1 calcium channels via Ion_trans). Each variant is shown at its 25 most conserved equivalents. Uses Pfam-A 38.2. Adds two alpha subtracks (Pfam Domain Variants, Pfam Domains), the hmmsearch/hmmalign build scripts, autoSql, makeDoc and description page, refs #37883
• src/hg/makeDb/scripts/clinvarMapped/clinvarMappedPfamAln.py
  • lines changed 99, context: html, text, full: html, text
    c9446936b026a803d97e7f5128404a327829fe2e Sun Jul 19 00:01:22 2026 -0700
    ClinVar Mapped: add Pfam-domain mapping method Maps ClinVar coding variants through Pfam protein domains as a second method under the clinvarMapped container. Each Pfam family's profile HMM gives a shared coordinate, so a variant inside a domain is projected to the residue in the same HMM match-state column in every other MANE Select gene carrying that domain, then mapped back to that gene's genomic codon. This links genes that share a domain without being paralogs (e.g. the SCN sodium channels and the CACNA1 calcium channels via Ion_trans). Each variant is shown at its 25 most conserved equivalents. Uses Pfam-A 38.2. Adds two alpha subtracks (Pfam Domain Variants, Pfam Domains), the hmmsearch/hmmalign build scripts, autoSql, makeDoc and description page, refs #37883
• src/hg/makeDb/scripts/clinvarMapped/clinvarMappedPfamProject.py
  • lines changed 198, context: html, text, full: html, text
    c9446936b026a803d97e7f5128404a327829fe2e Sun Jul 19 00:01:22 2026 -0700
    ClinVar Mapped: add Pfam-domain mapping method Maps ClinVar coding variants through Pfam protein domains as a second method under the clinvarMapped container. Each Pfam family's profile HMM gives a shared coordinate, so a variant inside a domain is projected to the residue in the same HMM match-state column in every other MANE Select gene carrying that domain, then mapped back to that gene's genomic codon. This links genes that share a domain without being paralogs (e.g. the SCN sodium channels and the CACNA1 calcium channels via Ion_trans). Each variant is shown at its 25 most conserved equivalents. Uses Pfam-A 38.2. Adds two alpha subtracks (Pfam Domain Variants, Pfam Domains), the hmmsearch/hmmalign build scripts, autoSql, makeDoc and description page, refs #37883
• src/hg/makeDb/scripts/lrSv/lrSvCard.as
  • lines changed 4, context: html, text, full: html, text
    cc6ef4c74d072de9c22e8bb88ab0e0983e6f2f47 Wed Jul 22 18:09:16 2026 -0700
    lrSv cardSv: switch CARD count fields from carrier counts to allele counts The NIH CARD provider republished the display bigBed with the count columns changed to diploid allele counts (alleleCount = nabecAlleleCount + hbccAlleleCount). Re-downloaded and rebuilt; renamed the schema fields to AC / nabecAc / hbccAc, updated filter ranges (0:702, 0:410, 0:292) and labels to allele counts, and reworded cardSv.html and the lrSv.html summary. Also noted there are no Alzheimer's cases in these cohorts. Re-ran the merge so lrSvAll carries CARD's allele counts. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvCardBbToBed.py
  • lines changed 13, context: html, text, full: html, text
    cc6ef4c74d072de9c22e8bb88ab0e0983e6f2f47 Wed Jul 22 18:09:16 2026 -0700
    lrSv cardSv: switch CARD count fields from carrier counts to allele counts The NIH CARD provider republished the display bigBed with the count columns changed to diploid allele counts (alleleCount = nabecAlleleCount + hbccAlleleCount). Re-downloaded and rebuilt; renamed the schema fields to AC / nabecAc / hbccAc, updated filter ranges (0:702, 0:410, 0:292) and labels to allele counts, and reworded cardSv.html and the lrSv.html summary. Also noted there are no Alzheimer's cases in these cohorts. Re-ran the merge so lrSvAll carries CARD's allele counts. refs #36258
• src/hg/makeDb/scripts/mei/meiDeepmei1kgVcfToBed.py
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    cff06e342525a24806d958cf8af28e9f54f1503c Sat Jul 25 18:25:07 2026 -0700
    mei: change item name format to <class>-<svLen>:<carrierCount>
• src/hg/makeDb/scripts/mei/meiHgsvc3CsvToBed.py
  • lines changed 2, context: html, text, full: html, text
    cff06e342525a24806d958cf8af28e9f54f1503c Sat Jul 25 18:25:07 2026 -0700
    mei: change item name format to <class>-<svLen>:<carrierCount>
• src/hg/makeDb/trackDb/human/cardSv.html
  • lines changed 6, context: html, text, full: html, text
    cc6ef4c74d072de9c22e8bb88ab0e0983e6f2f47 Wed Jul 22 18:09:16 2026 -0700
    lrSv cardSv: switch CARD count fields from carrier counts to allele counts The NIH CARD provider republished the display bigBed with the count columns changed to diploid allele counts (alleleCount = nabecAlleleCount + hbccAlleleCount). Re-downloaded and rebuilt; renamed the schema fields to AC / nabecAc / hbccAc, updated filter ranges (0:702, 0:410, 0:292) and labels to allele counts, and reworded cardSv.html and the lrSv.html summary. Also noted there are no Alzheimer's cases in these cohorts. Re-ran the merge so lrSvAll carries CARD's allele counts. refs #36258
• src/hg/makeDb/trackDb/human/gustafsonSv.html
  • lines changed 6, context: html, text, full: html, text
    3870b9e5e1b3fc67b0638fa77f6644bf5f133c9f Mon Jul 20 10:52:55 2026 -0700
    lrSv: relabel lrSv1kLin and gustafsonSv, write lrSv1kLin description Per Eichler lab request: relabel lrSv1kLin to 'Structural Variants from 1218 1KG individuals (HiFi, ONT & assembly)' and write its description page (drawn from HPRC year 2, HGSVC3, Vienna 1KG-ONT and UW 1KG-ONT). Relabel gustafsonSv as the University of Washington 1KG-ONT effort. Track names unchanged; no data rebuilt, counts kept honest at the current 100-sample Gustafson data. refs #36258
• src/hg/makeDb/trackDb/human/hg38/clinvarMapped.html
  • lines changed 71, context: html, text, full: html, text
    c9446936b026a803d97e7f5128404a327829fe2e Sun Jul 19 00:01:22 2026 -0700
    ClinVar Mapped: add Pfam-domain mapping method Maps ClinVar coding variants through Pfam protein domains as a second method under the clinvarMapped container. Each Pfam family's profile HMM gives a shared coordinate, so a variant inside a domain is projected to the residue in the same HMM match-state column in every other MANE Select gene carrying that domain, then mapped back to that gene's genomic codon. This links genes that share a domain without being paralogs (e.g. the SCN sodium channels and the CACNA1 calcium channels via Ion_trans). Each variant is shown at its 25 most conserved equivalents. Uses Pfam-A 38.2. Adds two alpha subtracks (Pfam Domain Variants, Pfam Domains), the hmmsearch/hmmalign build scripts, autoSql, makeDoc and description page, refs #37883
• src/hg/makeDb/trackDb/human/hg38/clinvarMapped.ra
  • lines changed 47, context: html, text, full: html, text
    c9446936b026a803d97e7f5128404a327829fe2e Sun Jul 19 00:01:22 2026 -0700
    ClinVar Mapped: add Pfam-domain mapping method Maps ClinVar coding variants through Pfam protein domains as a second method under the clinvarMapped container. Each Pfam family's profile HMM gives a shared coordinate, so a variant inside a domain is projected to the residue in the same HMM match-state column in every other MANE Select gene carrying that domain, then mapped back to that gene's genomic codon. This links genes that share a domain without being paralogs (e.g. the SCN sodium channels and the CACNA1 calcium channels via Ion_trans). Each variant is shown at its 25 most conserved equivalents. Uses Pfam-A 38.2. Adds two alpha subtracks (Pfam Domain Variants, Pfam Domains), the hmmsearch/hmmalign build scripts, autoSql, makeDoc and description page, refs #37883
• src/hg/makeDb/trackDb/human/jaspar.ra
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    43f042236ce180b8e0712d43c8baabc4ad8df1cd Sat Jul 25 18:21:54 2026 -0700
    hgTracks: add compactPack mode and codon strand-direction arrows When zoomed to codon-coloring level, draw strand-direction chevrons across the exons (white over coding codons when too small to label, contrasting color over UTRs), and a per-codon arrow between amino-acid letters via drawScaledBoxWithText. Add a compactPack trackDb setting for shorter pack/squish rows and a small squish-mode codon font. Adds mgFontForCellHeight() to memgfx and enables compactPack on the JASPAR track.
• src/hg/makeDb/trackDb/human/lrSv.html
  • lines changed 6, context: html, text, full: html, text
    3870b9e5e1b3fc67b0638fa77f6644bf5f133c9f Mon Jul 20 10:52:55 2026 -0700
    lrSv: relabel lrSv1kLin and gustafsonSv, write lrSv1kLin description Per Eichler lab request: relabel lrSv1kLin to 'Structural Variants from 1218 1KG individuals (HiFi, ONT & assembly)' and write its description page (drawn from HPRC year 2, HGSVC3, Vienna 1KG-ONT and UW 1KG-ONT). Relabel gustafsonSv as the University of Washington 1KG-ONT effort. Track names unchanged; no data rebuilt, counts kept honest at the current 100-sample Gustafson data. refs #36258
  • lines changed 10, context: html, text, full: html, text
    cc6ef4c74d072de9c22e8bb88ab0e0983e6f2f47 Wed Jul 22 18:09:16 2026 -0700
    lrSv cardSv: switch CARD count fields from carrier counts to allele counts The NIH CARD provider republished the display bigBed with the count columns changed to diploid allele counts (alleleCount = nabecAlleleCount + hbccAlleleCount). Re-downloaded and rebuilt; renamed the schema fields to AC / nabecAc / hbccAc, updated filter ranges (0:702, 0:410, 0:292) and labels to allele counts, and reworded cardSv.html and the lrSv.html summary. Also noted there are no Alzheimer's cases in these cohorts. Re-ran the merge so lrSvAll carries CARD's allele counts. refs #36258
• src/hg/makeDb/trackDb/human/lrSv.ra
  • lines changed 4, context: html, text, full: html, text
    3870b9e5e1b3fc67b0638fa77f6644bf5f133c9f Mon Jul 20 10:52:55 2026 -0700
    lrSv: relabel lrSv1kLin and gustafsonSv, write lrSv1kLin description Per Eichler lab request: relabel lrSv1kLin to 'Structural Variants from 1218 1KG individuals (HiFi, ONT & assembly)' and write its description page (drawn from HPRC year 2, HGSVC3, Vienna 1KG-ONT and UW 1KG-ONT). Relabel gustafsonSv as the University of Washington 1KG-ONT effort. Track names unchanged; no data rebuilt, counts kept honest at the current 100-sample Gustafson data. refs #36258
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    23f68df8fb0481fd1bd4351f4adbf913f039f237 Mon Jul 20 11:49:57 2026 -0700
    lrSv1kLin: add per-population AF filter defaults and full Data Access section Add missing filter.afAfr/afAmr/afEas/afEur/afSas default ranges so the per-population allele-frequency filters render. Expand the description page's Data Access section to the standard form with bigBed download URLs for both the hg38 and hs1 native builds. refs #36258
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    cc6ef4c74d072de9c22e8bb88ab0e0983e6f2f47 Wed Jul 22 18:09:16 2026 -0700
    lrSv cardSv: switch CARD count fields from carrier counts to allele counts The NIH CARD provider republished the display bigBed with the count columns changed to diploid allele counts (alleleCount = nabecAlleleCount + hbccAlleleCount). Re-downloaded and rebuilt; renamed the schema fields to AC / nabecAc / hbccAc, updated filter ranges (0:702, 0:410, 0:292) and labels to allele counts, and reworded cardSv.html and the lrSv.html summary. Also noted there are no Alzheimer's cases in these cohorts. Re-ran the merge so lrSvAll carries CARD's allele counts. refs #36258
  • lines changed 7, context: html, text, full: html, text
    27c2565b448892d69bbb365459b8b5dfe682b505 Fri Jul 24 00:31:50 2026 -0700
    changing lrSv labels, email from Evan Eichler
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    5a84070bbe697b8ebee5ab44903a67d0a2e642b0 Fri Jul 24 01:06:00 2026 -0700
    label changes after email from boris.noyvert@boehringer-ingelheim.com
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    0656b0a9ad98986ef3944b6ceaf305ab08ca4e39 Fri Jul 24 01:10:13 2026 -0700
    noyvertSv: swap UK Biobank r2 filter for leave-one-out metrics, revise description Per author (Boris Noyvert) request, replace the r2Ukb (UK Biobank imputation r2) filter with r2Loo and concordanceLoo, the primary SV imputation quality measures for the multi-ancestry reference panel (r2Ukb mainly reflects European-ancestry performance). Both fields already exist in noyvert.bb, so this is a trackDb-only change. Also update the description page with the author's revised text, including a comparison with the 1KG ONT Vienna dataset. refs #37888
• src/hg/makeDb/trackDb/human/lrSv1kLin.html
  • lines changed 95, context: html, text, full: html, text
    3870b9e5e1b3fc67b0638fa77f6644bf5f133c9f Mon Jul 20 10:52:55 2026 -0700
    lrSv: relabel lrSv1kLin and gustafsonSv, write lrSv1kLin description Per Eichler lab request: relabel lrSv1kLin to 'Structural Variants from 1218 1KG individuals (HiFi, ONT & assembly)' and write its description page (drawn from HPRC year 2, HGSVC3, Vienna 1KG-ONT and UW 1KG-ONT). Relabel gustafsonSv as the University of Washington 1KG-ONT effort. Track names unchanged; no data rebuilt, counts kept honest at the current 100-sample Gustafson data. refs #36258
  • lines changed 22, context: html, text, full: html, text
    23f68df8fb0481fd1bd4351f4adbf913f039f237 Mon Jul 20 11:49:57 2026 -0700
    lrSv1kLin: add per-population AF filter defaults and full Data Access section Add missing filter.afAfr/afAmr/afEas/afEur/afSas default ranges so the per-population allele-frequency filters render. Expand the description page's Data Access section to the standard form with bigBed download URLs for both the hg38 and hs1 native builds. refs #36258
• src/hg/makeDb/trackDb/human/noyvertSv.html
  • lines changed 28, context: html, text, full: html, text
    0656b0a9ad98986ef3944b6ceaf305ab08ca4e39 Fri Jul 24 01:10:13 2026 -0700
    noyvertSv: swap UK Biobank r2 filter for leave-one-out metrics, revise description Per author (Boris Noyvert) request, replace the r2Ukb (UK Biobank imputation r2) filter with r2Loo and concordanceLoo, the primary SV imputation quality measures for the multi-ancestry reference panel (r2Ukb mainly reflects European-ancestry performance). Both fields already exist in noyvert.bb, so this is a trackDb-only change. Also update the description page with the author's revised text, including a comparison with the 1KG ONT Vienna dataset. refs #37888
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    d2dff1a21b65cf37a89f2701c326e1dabf1a1272 Sat Jul 25 18:25:07 2026 -0700
    noyvertSv: clarify that the dataset is an independent reprocessing of the 1KG ONT Vienna reads
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    7bdcd030cdf434c72f3f6a492ee8f84372c752c7 Sat Jul 25 19:22:57 2026 -0700
    noyvertSv: note the Boehringer/Vienna relationship and call-level overlap The Noyvert panel is an independent reprocessing of the same ONT reads as the 1KG ONT Vienna track (Schloissnig et al. 2025). Add a description sentence with the deletion counts (~38k vs ~58k, ~12k shared at 50% reciprocal overlap) and the concordance both ways (about a third of this track's deletions and a fifth of Vienna's at 50%, a quarter and a sixth at 90%; ~a quarter of insertions match within 100 bp). Overlap analysis recorded in the makeDoc. refs #37888
• src/hg/makeDb/trackDb/human/sfariSparkExomes.html
  • lines changed 22, context: html, text, full: html, text
    8d5759442b9034d07823c7c57ad4c53f7fc2d6bc Sat Jul 25 18:25:07 2026 -0700
    sfariSparkExomes: update track description
• src/inc/memgfx.h
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    43f042236ce180b8e0712d43c8baabc4ad8df1cd Sat Jul 25 18:21:54 2026 -0700
    hgTracks: add compactPack mode and codon strand-direction arrows When zoomed to codon-coloring level, draw strand-direction chevrons across the exons (white over coding codons when too small to label, contrasting color over UTRs), and a per-codon arrow between amino-acid letters via drawScaledBoxWithText. Add a compactPack trackDb setting for shorter pack/squish rows and a small squish-mode codon font. Adds mgFontForCellHeight() to memgfx and enables compactPack on the JASPAR track.
• src/lib/memgfx.c
  • lines changed 16, context: html, text, full: html, text
    43f042236ce180b8e0712d43c8baabc4ad8df1cd Sat Jul 25 18:21:54 2026 -0700
    hgTracks: add compactPack mode and codon strand-direction arrows When zoomed to codon-coloring level, draw strand-direction chevrons across the exons (white over coding codons when too small to label, contrasting color over UTRs), and a per-codon arrow between amino-acid letters via drawScaledBoxWithText. Add a compactPack trackDb setting for shorter pack/squish rows and a small squish-mode codon font. Adds mgFontForCellHeight() to memgfx and enables compactPack on the JASPAR track.
• src/utils/genark/genark
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    4c4c0b323e2b979d9b0b3dbe1b6fd66abd920584 Sat Jul 25 19:35:32 2026 -0700
    Add genark tool for managing GenArk assembly hubs New subcommand-based utility in src/utils/genark: - addContrib <name>: install a contributed track collection into the GenArk assembly hubs (symlink the .bb/.bw data files and doc pages into each assembly's contrib/<name>/ dir, write a per-assembly trackDb with hub-root relative paths, and wire that block into the assembly's useOneFile hub.txt; --remove uninstalls). - checkContrib <name>: run hubCheck across the assemblies carrying the collection and separate contrib-specific problems from the assemblies' own pre-existing hub warnings. refs #35415
• src/utils/genark/makefile
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    4c4c0b323e2b979d9b0b3dbe1b6fd66abd920584 Sat Jul 25 19:35:32 2026 -0700
    Add genark tool for managing GenArk assembly hubs New subcommand-based utility in src/utils/genark: - addContrib <name>: install a contributed track collection into the GenArk assembly hubs (symlink the .bb/.bw data files and doc pages into each assembly's contrib/<name>/ dir, write a per-assembly trackDb with hub-root relative paths, and wire that block into the assembly's useOneFile hub.txt; --remove uninstalls). - checkContrib <name>: run hubCheck across the assemblies carrying the collection and separate contrib-specific problems from the assemblies' own pre-existing hub warnings. refs #35415