All File Changes

v500_preview2 to v500_base (2026-06-15 to 2026-06-29) v500

• docs/index.md
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    181787eb05d529cae4d743a10e3d161bd2be2f50 Wed Jun 24 13:47:25 2026 -0700
    adding link to slide decks, refs #37292
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 8, context: html, text, full: html, text
    447212628eb6b077565a5f4003acaeb09bec15f4 Wed Jun 24 09:37:05 2026 -0700
    Adding ADGC4 2027Q1 (end full year 2027-03-31) milestone updates
• src/hg/hgConvert/hgConvert.c
  • lines changed 4, context: html, text, full: html, text
    b3f4c2506806e4613e69903ff92c5d869bf9d832 Mon Jun 29 05:37:28 2026 -0700
    Removing the beta tag from QuickLift on hgConvert. refs #31986
• src/hg/hgGene/altSplice.c
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    3e922f07e4d8c51a3b989e3dc6748e33f8516e3b Mon Jun 22 09:10:05 2026 -0700
    Document two -O3 cleanup details raised in v500 code review Follow-up to code review #37767, addressing two points on commit f57fc11d951: - The else guards in sanger22gtf.c and bottleneck.c looked like leftovers from before errAbort was marked noreturn, but they are still required: removing either one reintroduces -Werror=format-overflow at -O3, because that warning runs before the noreturn-based dead-path pruning. Added a comment at each else saying so. - makeGrayShades (hgGene/altSplice.c and hgTracks/simpleTracks.c) writes shadesOfGray[maxShade+1] = MG_RED as an overflow sentinel. Spelled this out in both function descriptions so the maxShade+2 array sizing is documented at the function, not just at the caller. Comment-only; no behavior change. refs #37767 refs #37761
• src/hg/hgLogin/hgLogin.c
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    90246b77f01b5b5585ecc2d9bbaae55a92b9f3c1 Thu Jun 25 17:19:11 2026 -0700
    Adding bottleneck to hgLogin, refs #37699
• src/hg/hgTracks/bedTrack.c
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    abd7278ac7167ede325d8c144a35ea59a0798766 Wed Jun 17 03:55:47 2026 -0700
    Add a right click option to change color or background highlight color of individual track items. Only works for bed like items, refs #37778
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    48d45fa3cbdddcb62775f1fe01eef865407e035e Wed Jun 24 13:47:07 2026 -0700
    Revert "Add a right click option to change color or background highlight color of individual track items. Only works for bed like items, refs #37778" This reverts commit abd7278ac7167ede325d8c144a35ea59a0798766.
• src/hg/hgTracks/bigBedTrack.c
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    98572a57d651f8256c0d21e690f5df23fc1ce3c7 Tue Jun 23 16:05:31 2026 -0700
    hgTracks: show lifted (target) coordinates in quickLift bigBed mouseOvers, refs #37615 Under quickLift the bedRow used for mouseOver substitution is loaded from the source-assembly interval, so $chrom/${chromStart}/${chromEnd} reported the pre-lift position while the position bar showed the lifted position. Overwrite those three coordinate fields with the lifted bed's target coordinates before substituting, so the tooltip matches where the item is drawn. Replaces the earlier disclaimer note that flagged the discrepancy.
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    abd7278ac7167ede325d8c144a35ea59a0798766 Wed Jun 17 03:55:47 2026 -0700
    Add a right click option to change color or background highlight color of individual track items. Only works for bed like items, refs #37778
  • lines changed 15, context: html, text, full: html, text
    c3650b1ed157f95f90b5c486464d0fa430d13a99 Wed Jun 17 06:11:52 2026 -0700
    improved complement feature text, refs #37779
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    48d45fa3cbdddcb62775f1fe01eef865407e035e Wed Jun 24 13:47:07 2026 -0700
    Revert "Add a right click option to change color or background highlight color of individual track items. Only works for bed like items, refs #37778" This reverts commit abd7278ac7167ede325d8c144a35ea59a0798766.
• src/hg/hgTracks/hgTracks.h
  • lines changed 9, context: html, text, full: html, text
    abd7278ac7167ede325d8c144a35ea59a0798766 Wed Jun 17 03:55:47 2026 -0700
    Add a right click option to change color or background highlight color of individual track items. Only works for bed like items, refs #37778
  • lines changed 9, context: html, text, full: html, text
    48d45fa3cbdddcb62775f1fe01eef865407e035e Wed Jun 24 13:47:07 2026 -0700
    Revert "Add a right click option to change color or background highlight color of individual track items. Only works for bed like items, refs #37778" This reverts commit abd7278ac7167ede325d8c144a35ea59a0798766.
• src/hg/hgTracks/imageV2.c
  • lines changed 15, context: html, text, full: html, text
    7bed537d83b701bb4284080c2b634f1069417cae Thu Jun 18 12:07:03 2026 -0700
    fix squishyPack track stealing a neighboring track's center label when image orders collide A squishyPack track is split into a full-height part and a squished part that are stitched back together by smashSquish(), which assumes the squished clone is drawn immediately after its source. flatTracksCmp() broke an image-order tie involving a squink track purely by visibility, even against an unrelated track sharing the same order, so a colliding track (e.g. MANE vs GENCODE V49) could sort between the source and its squink. smashSquish() then merged the squished slice onto the wrong row, dragging the neighbor's center label with it. Keep a squink adjacent to its own source in flatTracksCmp(), and guard smashSquish() so it only merges a linked neighbor cloned from that track, refs #37785
• src/hg/hgTracks/simpleTracks.c
  • lines changed 124, context: html, text, full: html, text
    abd7278ac7167ede325d8c144a35ea59a0798766 Wed Jun 17 03:55:47 2026 -0700
    Add a right click option to change color or background highlight color of individual track items. Only works for bed like items, refs #37778
  • lines changed 3, context: html, text, full: html, text
    3e922f07e4d8c51a3b989e3dc6748e33f8516e3b Mon Jun 22 09:10:05 2026 -0700
    Document two -O3 cleanup details raised in v500 code review Follow-up to code review #37767, addressing two points on commit f57fc11d951: - The else guards in sanger22gtf.c and bottleneck.c looked like leftovers from before errAbort was marked noreturn, but they are still required: removing either one reintroduces -Werror=format-overflow at -O3, because that warning runs before the noreturn-based dead-path pruning. Added a comment at each else saying so. - makeGrayShades (hgGene/altSplice.c and hgTracks/simpleTracks.c) writes shadesOfGray[maxShade+1] = MG_RED as an overflow sentinel. Spelled this out in both function descriptions so the maxShade+2 array sizing is documented at the function, not just at the caller. Comment-only; no behavior change. refs #37767 refs #37761
  • lines changed 2, context: html, text, full: html, text
    6fe8c222be4d3cd6eee020f34d29984164e8626f Wed Jun 24 11:24:32 2026 -0700
    Fix exon length mouseOver on the codon-level path to match the other path: Length moved to the Exon line with a space before bp, refs #37439 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
  • lines changed 124, context: html, text, full: html, text
    48d45fa3cbdddcb62775f1fe01eef865407e035e Wed Jun 24 13:47:07 2026 -0700
    Revert "Add a right click option to change color or background highlight color of individual track items. Only works for bed like items, refs #37778" This reverts commit abd7278ac7167ede325d8c144a35ea59a0798766.
• src/hg/hgTracks/snake.c
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    ba2a019284cf8b41b243f3a8817763c23d870965 Mon Jun 15 14:54:55 2026 -0700
    prevent hgTracks crash when rearrangement and density graph are both enabled, refs #36668 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 63, context: html, text, full: html, text
    6cf524b43a05ac1bea2cfd20cd43a10d67e843c9 Thu Jun 25 17:29:43 2026 -0700
    Document how to add a new FreeType font to hgTracks in the mirror manual, and correct the default freeTypeDir path, refs #37698
  • lines changed 2, context: html, text, full: html, text
    a28c6b685f3bbe212c7bc14203cd01ae3b6a70dc Thu Jun 25 17:41:07 2026 -0700
    Fix mirror manual config.c link rendering as literal code tags in the generated HTML, refs #37698
  • lines changed 3, context: html, text, full: html, text
    767da6702e9bd053710e1b57cc4a7e2f2a9f5a17 Fri Jun 26 11:43:40 2026 -0700
    Link 'Building the kent source tree' reference to its section in the mirror manual, refs #37698
  • lines changed 5, context: html, text, full: html, text
    71339ec8afb5bbcaac8922ef4538f1c9ac944e5a Fri Jun 26 11:58:46 2026 -0700
    Reword the intro to the add-a-font steps in the mirror manual, refs #37698
  • lines changed 4, context: html, text, full: html, text
    5d0ada09248607057deba841ace59fd4d1f766ec Fri Jun 26 12:49:54 2026 -0700
    Use e.g. for font examples and make configure page's Font menu wording consistent in the mirror manual, refs #37698
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 2, context: html, text, full: html, text
    b9e05f0d81f3b1c3dc37942fdec403f1bd40156d Sun Jun 28 08:32:33 2026 -0700
    Adding link from trackDb docs to faceted composite page, refs #36320
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 97, context: html, text, full: html, text
    e9f1b6e4a64d031a574ec74e19b37b2309fd019c Tue Jun 23 14:00:08 2026 -0700
    Announcing the non-canonical ORFs track for hg38, refs #35101
  • lines changed 4, context: html, text, full: html, text
    73c73e23cc52a603a2c6536d6f063af17cbf14c5 Tue Jun 23 14:17:05 2026 -0700
    Making grammar edits to the Non-canonical news post, refs #35101
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    6dec8ee413485b5cd696cabbfdb528582d3b82c3 Wed Jun 24 13:59:25 2026 -0700
    fixing link for g2p track, refs #35054
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    c9a757f239030036c1f4c4a01ff757c27037a341 Thu Jun 25 05:27:40 2026 -0700
    Announcing the Varaico release 3 tracks, refs #37658
• src/hg/htdocs/index.html
  • lines changed 12, context: html, text, full: html, text
    46ab0e5e990c43db43a4982475eae69dc8358a16 Tue Jun 23 15:39:24 2026 -0700
    Removing 3 meetings that already happened, and removing the banner box which was meant to be temporary. No RM.
• src/hg/htdocs/indexMeetings.html
  • lines changed 31, context: html, text, full: html, text
    46ab0e5e990c43db43a4982475eae69dc8358a16 Tue Jun 23 15:39:24 2026 -0700
    Removing 3 meetings that already happened, and removing the banner box which was meant to be temporary. No RM.
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    e9f1b6e4a64d031a574ec74e19b37b2309fd019c Tue Jun 23 14:00:08 2026 -0700
    Announcing the non-canonical ORFs track for hg38, refs #35101
  • lines changed 12, context: html, text, full: html, text
    c9a757f239030036c1f4c4a01ff757c27037a341 Thu Jun 25 05:27:40 2026 -0700
    Announcing the Varaico release 3 tracks, refs #37658
• src/hg/js/hgTracks.js
  • lines changed 284, context: html, text, full: html, text
    abd7278ac7167ede325d8c144a35ea59a0798766 Wed Jun 17 03:55:47 2026 -0700
    Add a right click option to change color or background highlight color of individual track items. Only works for bed like items, refs #37778
  • lines changed 284, context: html, text, full: html, text
    48d45fa3cbdddcb62775f1fe01eef865407e035e Wed Jun 24 13:47:07 2026 -0700
    Revert "Add a right click option to change color or background highlight color of individual track items. Only works for bed like items, refs #37778" This reverts commit abd7278ac7167ede325d8c144a35ea59a0798766.
  • lines changed 1, context: html, text, full: html, text
    36b9de7c24cba2dfabb7fccb49abf496c5835e5c Thu Jun 25 08:57:23 2026 -0700
    Fix single-click on ruler track to zoom regardless of the highlight-dialog setting, refs #27113 A single click on the base position ruler updated the displayed position text but did not zoom when the Enable highlight with drag-and-select option was on (the default). selectEnd computed the zoom window and wrote it to the position display, then called selectionEndDialog, which returns early on a single click (startTime null), so nothing navigated. The dialog branch never checked for a ruler click even though its comment said it should. Add that check so a ruler click always falls through to the zoom path.
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 25, context: html, text, full: html, text
    7d3781f58bee4e535a2f11341d9b419c06adff4e Mon Jun 22 15:50:10 2026 -0700
    VGP update
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 52, context: html, text, full: html, text
    6e0dbcea330c6b906ea717efd1a97166255e0de7 Mon Jun 22 15:49:50 2026 -0700
    birdsAsmHub/birds.orderList.tsv
• src/hg/makeDb/doc/hg19.txt
  • lines changed 39, context: html, text, full: html, text
    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/doc/hg38/tad.txt
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
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    6e0dbcea330c6b906ea717efd1a97166255e0de7 Mon Jun 22 15:49:50 2026 -0700
    birdsAsmHub/birds.orderList.tsv
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 32, context: html, text, full: html, text
    6e0dbcea330c6b906ea717efd1a97166255e0de7 Mon Jun 22 15:49:50 2026 -0700
    birdsAsmHub/birds.orderList.tsv
• src/hg/makeDb/doc/mm10/tad.txt
  • lines changed 105, context: html, text, full: html, text
    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/doc/mm39/tad.txt
  • lines changed 1, context: html, text, full: html, text
    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
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    6e0dbcea330c6b906ea717efd1a97166255e0de7 Mon Jun 22 15:49:50 2026 -0700
    birdsAsmHub/birds.orderList.tsv
• src/hg/makeDb/outside/sanger22gtf/sanger22gtf.c
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    3e922f07e4d8c51a3b989e3dc6748e33f8516e3b Mon Jun 22 09:10:05 2026 -0700
    Document two -O3 cleanup details raised in v500 code review Follow-up to code review #37767, addressing two points on commit f57fc11d951: - The else guards in sanger22gtf.c and bottleneck.c looked like leftovers from before errAbort was marked noreturn, but they are still required: removing either one reintroduces -Werror=format-overflow at -O3, because that warning runs before the noreturn-based dead-path pruning. Added a comment at each else saying so. - makeGrayShades (hgGene/altSplice.c and hgTracks/simpleTracks.c) writes shadesOfGray[maxShade+1] = MG_RED as an overflow sentinel. Spelled this out in both function descriptions so the maxShade+2 array sizing is documented at the function, not just at the caller. Comment-only; no behavior change. refs #37767 refs #37761
• src/hg/makeDb/scripts/tad/buildDixonMouse.sh
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/scripts/tad/buildTads3dgb.py
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/scripts/tad/buildTadsEncode.py
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/scripts/tad/liftEncodeMouse.sh
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/scripts/tad/liftTads3dgbMouse.sh
  • lines changed 27, context: html, text, full: html, text
    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/scripts/tad/tadBoundary.as
  • lines changed 8, context: html, text, full: html, text
    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/scripts/tad/tadDomain.as
  • lines changed 8, context: html, text, full: html, text
    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/scripts/tad/tadDomainEncode.as
  • lines changed 13, context: html, text, full: html, text
    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/scripts/tad/tadStability.as
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/scripts/varFreqs/vcfToBigBed.py
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    533cc89eb4febc78c9f8f104aed4523de06bf85b Fri Jun 19 08:58:02 2026 -0700
    varFreqs: fix numeric filter rendering and trim per-cohort filters #Preview2 week - bugs introduced now will need a build patch to fix The Affected/Background track config pages showed none of the AF/AC/AN filters. hgTrackUi only discovers a numeric filter from a filter.<field> (or <field>Filter) setting (FILTER_NUMBER_WILDCARD in bigBedFilter.h); the generated fragment had only filterByRange.<field>/filterLimits.<field> for those fields, so they were silently dropped. vcfToBigBed.py now emits filter.<field> (a full-range default, so nothing is filtered by default) plus filterLimits for every numeric filter. That made ~140 filters appear, which overwhelmed the config page, so the per-database and per-population AF/AC filters are emitted commented out (range_filter enabled=False) and can be re-enabled individually by removing the leading "# ". Only the global filters remain active: variant type, consequence, the affected/case and background AF/AC/AN summaries, the affected/case-cohort and background-source selectors, the in-affected flag, and the length filters. The per-cohort data columns are unchanged in the bigBed and still show on the details page. No bigBed rebuild needed; this is trackDb-only. refs #36642
• src/hg/makeDb/trackDb/human/hg19/tad.ra
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/human/hg19/tads.html
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/human/hg19/tadsDixon.html
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/human/hg19/tadsMcArthur.html
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/human/hg19/tadsSchmitt.html
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/human/hg38/encode4.ccres.ra
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    21fd9312696790cba374e2ae8d8f8d74ab63d5dd Sun Jun 21 10:01:27 2026 -0700
    Adding a cCRE_class filter to the coreCcres composite on hg38 and mm10. The filter lives on the cCREs_view so it is inherited by all biosample cCRE subtracks, matching the filter style of the cCREregistry track. Values and order follow the registry as closely as the sample-specific class vocabulary allows. No RM.
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
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    385e276fdc97704f20505310cbd0bbd8f3734a3c Tue Jun 23 16:09:44 2026 -0700
    Removing a stray '}' in the position mouseOver, refs #37805
• src/hg/makeDb/trackDb/human/hg38/tad.ra
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/human/hg38/tads.html
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/human/hg38/tads3dgb.html
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/human/hg38/tads3dgb.ra
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/human/hg38/tadsDixon.html
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/human/hg38/tadsEncode.html
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/human/hg38/tadsEncode.ra
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/human/hg38/tadsMcArthur.html
  • lines changed 62, context: html, text, full: html, text
    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/human/hg38/tadsSchmitt.html
  • lines changed 44, context: html, text, full: html, text
    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/human/hs1/LCRs.html
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    493239164214cc39a342541ebb30dd0afa188593 Fri Jun 26 09:35:52 2026 -0700
    tweaking capitalization in title at top of desc page, no refs
• src/hg/makeDb/trackDb/human/hs1/hs1PrimateChainNet.html
  • lines changed 27, context: html, text, full: html, text
    7072384d5e6f4228bec4186d3d677527be0c9bc5 Fri Jun 26 09:37:20 2026 -0700
    Adding data access to hs1 pages on the RR, refs #
• src/hg/makeDb/trackDb/human/hs1/html/catLiftOffGenesV1.html
  • lines changed 25, context: html, text, full: html, text
    7072384d5e6f4228bec4186d3d677527be0c9bc5 Fri Jun 26 09:37:20 2026 -0700
    Adding data access to hs1 pages on the RR, refs #
• src/hg/makeDb/trackDb/human/hs1/html/censat.html
  • lines changed 24, context: html, text, full: html, text
    7072384d5e6f4228bec4186d3d677527be0c9bc5 Fri Jun 26 09:37:20 2026 -0700
    Adding data access to hs1 pages on the RR, refs #
• src/hg/makeDb/trackDb/human/hs1/html/clinVar20220313.html
  • lines changed 18, context: html, text, full: html, text
    7072384d5e6f4228bec4186d3d677527be0c9bc5 Fri Jun 26 09:37:20 2026 -0700
    Adding data access to hs1 pages on the RR, refs #
• src/hg/makeDb/trackDb/human/hs1/html/dbSNP155.html
  • lines changed 18, context: html, text, full: html, text
    7072384d5e6f4228bec4186d3d677527be0c9bc5 Fri Jun 26 09:37:20 2026 -0700
    Adding data access to hs1 pages on the RR, refs #
• src/hg/makeDb/trackDb/human/hs1/html/encode.html
  • lines changed 25, context: html, text, full: html, text
    7072384d5e6f4228bec4186d3d677527be0c9bc5 Fri Jun 26 09:37:20 2026 -0700
    Adding data access to hs1 pages on the RR, refs #
• src/hg/makeDb/trackDb/human/hs1/html/gwasSNPs2022-03-08.html
  • lines changed 18, context: html, text, full: html, text
    7072384d5e6f4228bec4186d3d677527be0c9bc5 Fri Jun 26 09:37:20 2026 -0700
    Adding data access to hs1 pages on the RR, refs #
• src/hg/makeDb/trackDb/human/hs1/html/hgCactus.html
  • lines changed 17, context: html, text, full: html, text
    7072384d5e6f4228bec4186d3d677527be0c9bc5 Fri Jun 26 09:37:20 2026 -0700
    Adding data access to hs1 pages on the RR, refs #
• src/hg/makeDb/trackDb/human/hs1/html/hgLiftOver.html
  • lines changed 16, context: html, text, full: html, text
    7072384d5e6f4228bec4186d3d677527be0c9bc5 Fri Jun 26 09:37:20 2026 -0700
    Adding data access to hs1 pages on the RR, refs #
• src/hg/makeDb/trackDb/human/hs1/html/hgUnique.html
  • lines changed 24, context: html, text, full: html, text
    7072384d5e6f4228bec4186d3d677527be0c9bc5 Fri Jun 26 09:37:20 2026 -0700
    Adding data access to hs1 pages on the RR, refs #
• src/hg/makeDb/trackDb/human/hs1/html/microsatellites.html
  • lines changed 24, context: html, text, full: html, text
    7072384d5e6f4228bec4186d3d677527be0c9bc5 Fri Jun 26 09:37:20 2026 -0700
    Adding data access to hs1 pages on the RR, refs #
• src/hg/makeDb/trackDb/human/hs1/html/rdnaModel.html
  • lines changed 24, context: html, text, full: html, text
    7072384d5e6f4228bec4186d3d677527be0c9bc5 Fri Jun 26 09:37:20 2026 -0700
    Adding data access to hs1 pages on the RR, refs #
• src/hg/makeDb/trackDb/human/hs1/html/sedefSegDups.html
  • lines changed 24, context: html, text, full: html, text
    7072384d5e6f4228bec4186d3d677527be0c9bc5 Fri Jun 26 09:37:20 2026 -0700
    Adding data access to hs1 pages on the RR, refs #
• src/hg/makeDb/trackDb/human/hs1/html/sgdpCopyNumber.html
  • lines changed 24, context: html, text, full: html, text
    7072384d5e6f4228bec4186d3d677527be0c9bc5 Fri Jun 26 09:37:20 2026 -0700
    Adding data access to hs1 pages on the RR, refs #
• src/hg/makeDb/trackDb/human/hs1/html/t2tRepeatMasker.html
  • lines changed 24, context: html, text, full: html, text
    7072384d5e6f4228bec4186d3d677527be0c9bc5 Fri Jun 26 09:37:20 2026 -0700
    Adding data access to hs1 pages on the RR, refs #
• src/hg/makeDb/trackDb/human/hs1/problematic.html
  • lines changed 24, context: html, text, full: html, text
    7072384d5e6f4228bec4186d3d677527be0c9bc5 Fri Jun 26 09:37:20 2026 -0700
    Adding data access to hs1 pages on the RR, refs #
• src/hg/makeDb/trackDb/human/longReadVariants.ra
  • lines changed 2, context: html, text, full: html, text
    3785c3e424471815dbeab245fb48b22df7ffaa19 Wed Jun 24 09:58:50 2026 -0700
    Fixing the track description pages for the ColorsDb tracks, refs #36258
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    98193faa598cf04b4dbd2cdb0007e712d3d845cf Thu Jun 25 06:11:04 2026 -0700
    Updating the pennantIcons for the Variants in Papers superTrack and Varaico tracks, refs #37658
• src/hg/makeDb/trackDb/human/varFreqs.html
  • lines changed 1, context: html, text, full: html, text
    1259dcfba3a263d92d2602665fd866dc44b47996 Sun Jun 21 11:17:10 2026 -0700
    Clarify varFreqs description page wording per code review feedback. refs #37733 Reword the default_an sentence in the Pooled allele frequency sections of varFreqsAffected.html and varFreqsBackground.html to explain that cohorts publishing only AF are pooled via an assigned default_an, with per-arm AC derived as round(AF * default_an). Change "tokens" to "terms" in the Consequence filter section of varFreqs.html.
• src/hg/makeDb/trackDb/human/varFreqs.ra
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    533cc89eb4febc78c9f8f104aed4523de06bf85b Fri Jun 19 08:58:02 2026 -0700
    varFreqs: fix numeric filter rendering and trim per-cohort filters #Preview2 week - bugs introduced now will need a build patch to fix The Affected/Background track config pages showed none of the AF/AC/AN filters. hgTrackUi only discovers a numeric filter from a filter.<field> (or <field>Filter) setting (FILTER_NUMBER_WILDCARD in bigBedFilter.h); the generated fragment had only filterByRange.<field>/filterLimits.<field> for those fields, so they were silently dropped. vcfToBigBed.py now emits filter.<field> (a full-range default, so nothing is filtered by default) plus filterLimits for every numeric filter. That made ~140 filters appear, which overwhelmed the config page, so the per-database and per-population AF/AC filters are emitted commented out (range_filter enabled=False) and can be re-enabled individually by removing the leading "# ". Only the global filters remain active: variant type, consequence, the affected/case and background AF/AC/AN summaries, the affected/case-cohort and background-source selectors, the in-affected flag, and the length filters. The per-cohort data columns are unchanged in the bigBed and still show on the details page. No bigBed rebuild needed; this is trackDb-only. refs #36642
• src/hg/makeDb/trackDb/human/varFreqsAffected.html
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    f57e872b724de4bb82b14f07db837aeed4f5174a Wed Jun 17 03:55:08 2026 -0700
    Fix commas and update wording in varFreqs description pages. refs #37733
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    1259dcfba3a263d92d2602665fd866dc44b47996 Sun Jun 21 11:17:10 2026 -0700
    Clarify varFreqs description page wording per code review feedback. refs #37733 Reword the default_an sentence in the Pooled allele frequency sections of varFreqsAffected.html and varFreqsBackground.html to explain that cohorts publishing only AF are pooled via an assigned default_an, with per-arm AC derived as round(AF * default_an). Change "tokens" to "terms" in the Consequence filter section of varFreqs.html.
• src/hg/makeDb/trackDb/human/varFreqsArray.html
  • lines changed 4, context: html, text, full: html, text
    f57e872b724de4bb82b14f07db837aeed4f5174a Wed Jun 17 03:55:08 2026 -0700
    Fix commas and update wording in varFreqs description pages. refs #37733
• src/hg/makeDb/trackDb/human/varFreqsBackground.html
  • lines changed 1, context: html, text, full: html, text
    f57e872b724de4bb82b14f07db837aeed4f5174a Wed Jun 17 03:55:08 2026 -0700
    Fix commas and update wording in varFreqs description pages. refs #37733
  • lines changed 4, context: html, text, full: html, text
    1259dcfba3a263d92d2602665fd866dc44b47996 Sun Jun 21 11:17:10 2026 -0700
    Clarify varFreqs description page wording per code review feedback. refs #37733 Reword the default_an sentence in the Pooled allele frequency sections of varFreqsAffected.html and varFreqsBackground.html to explain that cohorts publishing only AF are pooled via an assigned default_an, with per-arm AC derived as round(AF * default_an). Change "tokens" to "terms" in the Consequence filter section of varFreqs.html.
• src/hg/makeDb/trackDb/human/varaico.html
  • lines changed 1, context: html, text, full: html, text
    7295ac9e32f256e136f762bbc0b4b39ce78cc108 Wed Jun 24 08:56:52 2026 -0700
    fixing link to varaico terms of use, no refs
• src/hg/makeDb/trackDb/mouse/mm10/encode4.ccres.ra
  • lines changed 3, context: html, text, full: html, text
    21fd9312696790cba374e2ae8d8f8d74ab63d5dd Sun Jun 21 10:01:27 2026 -0700
    Adding a cCRE_class filter to the coreCcres composite on hg38 and mm10. The filter lives on the cCREs_view so it is inherited by all biosample cCRE subtracks, matching the filter style of the cCREregistry track. Values and order follow the registry as closely as the sample-specific class vocabulary allows. No RM.
• src/hg/makeDb/trackDb/mouse/mm10/tad.ra
  • lines changed 39, context: html, text, full: html, text
    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/mouse/mm10/tads.html
  • lines changed 78, context: html, text, full: html, text
    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/mouse/mm10/tads3dgb.html
  • lines changed 66, context: html, text, full: html, text
    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/mouse/mm10/tads3dgb.ra
  • lines changed 315, context: html, text, full: html, text
    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/mouse/mm10/tadsDixon.html
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/mouse/mm10/tadsEncode.html
  • lines changed 68, context: html, text, full: html, text
    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/mouse/mm10/tadsEncode.ra
  • lines changed 176, context: html, text, full: html, text
    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/mouse/mm39/tad.ra
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/mouse/mm39/tads.html
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/mouse/mm39/tads3dgb.html
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/mouse/mm39/tads3dgb.ra
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/mouse/mm39/tadsDixon.html
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/mouse/mm39/tadsEncode.html
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/mouse/mm39/tadsEncode.ra
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
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    17b7d3c37be41135afaf8e91e365e3847af96ca5 Mon Jun 22 10:56:56 2026 -0700
    Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).
• src/hg/utils/otto/chainTables/toFromCounts.sh
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    55524dfee524fdfa2b9fbea92093984c55f89e06 Tue Jun 23 16:22:29 2026 -0700
    verify liftOverChain and quickLiftChain have identical fromDb,toDb pairs refs #36233
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    ffea9fcf11c914d47c78c86bf4f2fb808094d1b2 Thu Jun 25 09:30:04 2026 -0700
    correct name of script refs #36233
• src/hg/utils/otto/otto.crontab
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    e412ddfeae024619e58d55cc39835372c41b1622 Tue Jun 23 16:24:35 2026 -0700
    verify liftOverChain and quickLiftChain have identical fromDb,toDb pairs refs #36233
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    ffea9fcf11c914d47c78c86bf4f2fb808094d1b2 Thu Jun 25 09:30:04 2026 -0700
    correct name of script refs #36233
• src/inc/common.mk
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    0939cd926f6ff4d587eafff011363540d2b05b53 Mon Jun 22 10:50:23 2026 -0700
    Add -g to the default COPT so production -O3 builds keep debug symbols Default COPT becomes "-O3 -g". -g only emits DWARF debug sections; it does not change code generation, so optimization is unaffected and the binary keeps gdb symbols and meaningful apache stack traces. An explicit COPT on the command line or in the environment still overrides it. Validated on hgwbeta by rendering a heavy Recommended Track Set session (Non_Coding_SNVs hg38) at two ranges with -O3 vs -O3 -g binaries, 12 interleaved iterations each: the two straddle each other within run-to-run noise (O3g 2.5% faster on one range, 0.9% slower on the other), i.e. no measurable slowdown. refs #37767 refs #37761
• src/product/README.txt
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    e6e1368336e28a3d336405cc8bd2cdc5480c1a9d Thu Jun 25 17:34:02 2026 -0700
    Fix typos in mirror README markdown that had drifted from the generated HTML, No RM.
• src/product/installer/browserSetup.sh
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    36fbb0bc581f5189dddc2c2a68aea11a378ad8fc Wed Jun 17 06:54:40 2026 -0700
    prevent docker image build failure when one mirror is down by adding curl timeouts and || true to the genome vs genome-euro latency check in browserSetup.sh, refs #37780 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/product/mirrorManual.txt
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    6cf524b43a05ac1bea2cfd20cd43a10d67e843c9 Thu Jun 25 17:29:43 2026 -0700
    Document how to add a new FreeType font to hgTracks in the mirror manual, and correct the default freeTypeDir path, refs #37698
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    a28c6b685f3bbe212c7bc14203cd01ae3b6a70dc Thu Jun 25 17:41:07 2026 -0700
    Fix mirror manual config.c link rendering as literal code tags in the generated HTML, refs #37698
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    767da6702e9bd053710e1b57cc4a7e2f2a9f5a17 Fri Jun 26 11:43:40 2026 -0700
    Link 'Building the kent source tree' reference to its section in the mirror manual, refs #37698
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    71339ec8afb5bbcaac8922ef4538f1c9ac944e5a Fri Jun 26 11:58:46 2026 -0700
    Reword the intro to the add-a-font steps in the mirror manual, refs #37698
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    5d0ada09248607057deba841ace59fd4d1f766ec Fri Jun 26 12:49:54 2026 -0700
    Use e.g. for font examples and make configure page's Font menu wording consistent in the mirror manual, refs #37698
• src/utils/qa/checkUiLinks.py
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    22339e5f262e1e9ed004c5fb2f9ea54a45648418 Tue Jun 23 14:45:09 2026 -0700
    New --errors-only option outputs only errors from checkTrackUiLinks.csh, ignoring No errors found messages, refs #37379
• src/utils/qa/copyHgcentral
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    b9589bd31f984863f6b7ae48e322859f3c66c7ee Tue Jun 23 16:00:21 2026 -0700
    porting script to python3, refs #37573
• src/utils/qa/mlqAutomate.py
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    09cd6de009c6de84beecd8c388f5c96a7ddf7060 Sun Jun 21 10:10:58 2026 -0700
    Strip numbered reply prefixes (Re[2]:, Re(2):, Re^2:) in MLQ subject normalization so mail.ru-style replies match their existing ticket instead of creating a duplicate. refs #37759 refs #37758
• src/utils/qa/runBits
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    aa145ac73643ba31fab4dadd0e2d65996ae90349 Wed Jun 24 07:30:04 2026 -0700
    porting runBits to python3, no refs
• src/weblet/bottleneck/bottleneck.c
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    3e922f07e4d8c51a3b989e3dc6748e33f8516e3b Mon Jun 22 09:10:05 2026 -0700
    Document two -O3 cleanup details raised in v500 code review Follow-up to code review #37767, addressing two points on commit f57fc11d951: - The else guards in sanger22gtf.c and bottleneck.c looked like leftovers from before errAbort was marked noreturn, but they are still required: removing either one reintroduces -Werror=format-overflow at -O3, because that warning runs before the noreturn-based dead-path pruning. Added a comment at each else saying so. - makeGrayShades (hgGene/altSplice.c and hgTracks/simpleTracks.c) writes shadesOfGray[maxShade+1] = MG_RED as an overflow sentinel. Spelled this out in both function descriptions so the maxShade+2 array sizing is documented at the function, not just at the caller. Comment-only; no behavior change. refs #37767 refs #37761

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