All File Changes

v497_preview to v497_preview2 (2026-04-06 to 2026-04-13) v497

• confs/hgwdev.hg.conf
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    0f4c77d1456a3aef241cac69d76f4b734afba628 Sun Apr 12 01:11:17 2026 -0700
    Installing updated hg.conf files from UCSC servers
• docs/tutorials/gatewayTutorial.md
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    f704665435dca39ec3f9022bf2584553f3fddf00 Wed Apr 8 09:30:19 2026 -0700
    Updating the annotated screenshot without the phylo tree, no RM.
• src/CLAUDE.md
  • lines changed 14, context: html, text, full: html, text
    44a5fa24f9a25c1295107787bb6b8f41fc07831c Thu Apr 9 15:48:44 2026 -0700
    Add CLAUDE.md for AI assistant guidelines, no redmine Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    e05d5d771d71b63c84029df3e27266717548eaef Fri Apr 10 10:48:00 2026 -0700
    Add CSP inline handler rule to CLAUDE.md, no redmine Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    f28c94cca4b3080f1957751f998628c95eae9168 Sun Apr 12 12:17:17 2026 -0700
    Add rule to deploy static files via make, not manual copy Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/hgTables/filterFields.c
  • lines changed 46, context: html, text, full: html, text
    9a1687b6341af06ee8e0746a9a502ba09cee8284 Tue Apr 7 16:11:57 2026 -0700
    Add missing form labels and aria-labels across hgTables pages and main site search. refs #37343 Main page search bar (index.html): aria-label on search input. hgTables main page (mainPage.c): aria-label on Galaxy/GREAT checkboxes, fix Position label to target radio button instead of text input, aria-label on position text input. hgTables user regions (userRegions.c): aria-label on paste textarea and file upload input. hgTables filter page (filterFields.c): aria-label on all per-field filter dropdowns and text inputs across string, numeric, integer, and enum field types. hgTables intersect page (intersect.c): label elements on all 6 radio buttons and 2 complement checkboxes, aria-label on threshold text inputs.
• src/hg/hgTables/intersect.c
  • lines changed 23, context: html, text, full: html, text
    9a1687b6341af06ee8e0746a9a502ba09cee8284 Tue Apr 7 16:11:57 2026 -0700
    Add missing form labels and aria-labels across hgTables pages and main site search. refs #37343 Main page search bar (index.html): aria-label on search input. hgTables main page (mainPage.c): aria-label on Galaxy/GREAT checkboxes, fix Position label to target radio button instead of text input, aria-label on position text input. hgTables user regions (userRegions.c): aria-label on paste textarea and file upload input. hgTables filter page (filterFields.c): aria-label on all per-field filter dropdowns and text inputs across string, numeric, integer, and enum field types. hgTables intersect page (intersect.c): label elements on all 6 radio buttons and 2 complement checkboxes, aria-label on threshold text inputs.
• src/hg/hgTables/mainPage.c
  • lines changed 8, context: html, text, full: html, text
    9a1687b6341af06ee8e0746a9a502ba09cee8284 Tue Apr 7 16:11:57 2026 -0700
    Add missing form labels and aria-labels across hgTables pages and main site search. refs #37343 Main page search bar (index.html): aria-label on search input. hgTables main page (mainPage.c): aria-label on Galaxy/GREAT checkboxes, fix Position label to target radio button instead of text input, aria-label on position text input. hgTables user regions (userRegions.c): aria-label on paste textarea and file upload input. hgTables filter page (filterFields.c): aria-label on all per-field filter dropdowns and text inputs across string, numeric, integer, and enum field types. hgTables intersect page (intersect.c): label elements on all 6 radio buttons and 2 complement checkboxes, aria-label on threshold text inputs.
• src/hg/hgTables/userRegions.c
  • lines changed 5, context: html, text, full: html, text
    9a1687b6341af06ee8e0746a9a502ba09cee8284 Tue Apr 7 16:11:57 2026 -0700
    Add missing form labels and aria-labels across hgTables pages and main site search. refs #37343 Main page search bar (index.html): aria-label on search input. hgTables main page (mainPage.c): aria-label on Galaxy/GREAT checkboxes, fix Position label to target radio button instead of text input, aria-label on position text input. hgTables user regions (userRegions.c): aria-label on paste textarea and file upload input. hgTables filter page (filterFields.c): aria-label on all per-field filter dropdowns and text inputs across string, numeric, integer, and enum field types. hgTables intersect page (intersect.c): label elements on all 6 radio buttons and 2 complement checkboxes, aria-label on threshold text inputs.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 7, context: html, text, full: html, text
    8593c40cb74ab6ee9f2318056626305d9d9544d3 Fri Apr 10 12:54:44 2026 -0700
    Fix color picker from code review, refs #37329, refs #20460 - Replace Spectrum JS color picker with native HTML5 color input, matching existing Hi-C picker - Color saved on form submit, not immediately via AJAX - Add checkbox to enable/disable color override; auto-checks when user picks a color - Gate color picker behind hg.conf showColorPicker=on (off by default) - Only show picker for non-composite tracks that support it: bed, bigBed, genePred, bigGenePred, wig, bigWig, rmsk, interact, bigInteract, bigLolly, vcfTabix, vcf - Add colorFromCart calls to interact, lolly, vcf phased, and pgSnp drawing code - Revert hui.js Spectrum changes from cfeb4d4 (no longer needed) - Use htmlColorForCode()/htmlColorToRGB() from htmlColor.h instead of hand-rolled hex parsing in colorFromCart Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 10, context: html, text, full: html, text
    6239b81a7033f90749f836e73703c65eabd0de9c Fri Apr 10 15:56:31 2026 -0700
    Moved js and css includes for faceted composites into hgTrackUi for better detection of file changes. Dynamically change the track visibility based on selected subtracks (hiding it if everything is deselected, making it visible when something is selected). refs #36320
  • lines changed 48, context: html, text, full: html, text
    7d149b1935f8a1e5f11f31f3cb8da99d31b3a8e6 Fri Apr 10 16:34:48 2026 -0700
    Replaced handrolled JSON structure in faceted composite output from hgTrackUi with jsonWrite.h library-generated version, and added a defaultSortField trackDb setting to faceted composites to improve the subtrack presentation order, refs #36320
• src/hg/hgTracks/bedTrack.c
  • lines changed 8, context: html, text, full: html, text
    0c4b26c76ee09cadbe1a444016f2c41df33906f9 Thu Apr 9 15:48:53 2026 -0700
    Fix color picker and quickLift issues from code review, refs #37329 Color picker: fix [object Object] bug by calling .toHexString() on spectrum result, use htmlColor.h instead of hand-rolled hex parsing, show "color override active" status when override is set. quickLift: remove redundant quickLiftResolveTable call in genericBedClick, move hFindSplitTable into else branch where it's needed. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 8, context: html, text, full: html, text
    4905867d4df06d0c4cfe5769998334eaed96d6d6 Thu Apr 9 16:02:15 2026 -0700
    Revert "Fix color picker and quickLift issues from code review, refs #37329" This reverts commit 0c4b26c76ee09cadbe1a444016f2c41df33906f9.
  • lines changed 10, context: html, text, full: html, text
    8593c40cb74ab6ee9f2318056626305d9d9544d3 Fri Apr 10 12:54:44 2026 -0700
    Fix color picker from code review, refs #37329, refs #20460 - Replace Spectrum JS color picker with native HTML5 color input, matching existing Hi-C picker - Color saved on form submit, not immediately via AJAX - Add checkbox to enable/disable color override; auto-checks when user picks a color - Gate color picker behind hg.conf showColorPicker=on (off by default) - Only show picker for non-composite tracks that support it: bed, bigBed, genePred, bigGenePred, wig, bigWig, rmsk, interact, bigInteract, bigLolly, vcfTabix, vcf - Add colorFromCart calls to interact, lolly, vcf phased, and pgSnp drawing code - Revert hui.js Spectrum changes from cfeb4d4 (no longer needed) - Use htmlColorForCode()/htmlColorToRGB() from htmlColor.h instead of hand-rolled hex parsing in colorFromCart Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 14, context: html, text, full: html, text
    802ca99f5f06437c32db764bc8e01786ed395c21 Tue Apr 7 14:05:35 2026 -0700
    Fix mergeSpannedItems not working with quickLift For quickLifted tracks, bb->start/bb->end are in the source assembly coordinates while winStart/winEnd are in the target assembly, so the span check never matched. Use lf->start/lf->end (lifted coordinates) when quickLiftFile is set. Also use cloneBed(bedCopy) for building the merged item instead of re-parsing from source-assembly bedRow, refs #36048 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/hgTracks/config.c
  • lines changed 3, context: html, text, full: html, text
    acace5022c846865a6e449fe1973e94504394cde Tue Apr 7 16:33:34 2026 -0700
    Add aria-labels to Base Position and supertrack/container dropdowns on hgTracks. refs #37344 New hideShowDropDownWithClassExtraAndLabel() passes label through to the existing labeled dropdown function. superTrackDropDownWithExtra() now passes tdb->shortLabel. Ruler dropdown updated in both hgTracks.c and config.c. Brings hgTracks track dropdown label coverage from 69% to 100%.
• src/hg/hgTracks/hgTracks.c
  • lines changed 27, context: html, text, full: html, text
    16113a55a853321b5251989c64f6c995f8ed583b Mon Apr 6 14:05:40 2026 -0700
    restore the hg.conf switches to control the gcOnFly track - lost in later edits
  • lines changed 2, context: html, text, full: html, text
    acace5022c846865a6e449fe1973e94504394cde Tue Apr 7 16:33:34 2026 -0700
    Add aria-labels to Base Position and supertrack/container dropdowns on hgTracks. refs #37344 New hideShowDropDownWithClassExtraAndLabel() passes label through to the existing labeled dropdown function. superTrackDropDownWithExtra() now passes tdb->shortLabel. Ruler dropdown updated in both hgTracks.c and config.c. Brings hgTracks track dropdown label coverage from 69% to 100%.
  • lines changed 32, context: html, text, full: html, text
    b5cbbe9353e85ec653bb18eee381c6989f529289 Sun Apr 12 12:21:24 2026 -0700
    Show alternative chromosome names from chromAlias on hgTracks position line, refs #29201 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/hgTracks/interactTrack.c
  • lines changed 1, context: html, text, full: html, text
    8593c40cb74ab6ee9f2318056626305d9d9544d3 Fri Apr 10 12:54:44 2026 -0700
    Fix color picker from code review, refs #37329, refs #20460 - Replace Spectrum JS color picker with native HTML5 color input, matching existing Hi-C picker - Color saved on form submit, not immediately via AJAX - Add checkbox to enable/disable color override; auto-checks when user picks a color - Gate color picker behind hg.conf showColorPicker=on (off by default) - Only show picker for non-composite tracks that support it: bed, bigBed, genePred, bigGenePred, wig, bigWig, rmsk, interact, bigInteract, bigLolly, vcfTabix, vcf - Add colorFromCart calls to interact, lolly, vcf phased, and pgSnp drawing code - Revert hui.js Spectrum changes from cfeb4d4 (no longer needed) - Use htmlColorForCode()/htmlColorToRGB() from htmlColor.h instead of hand-rolled hex parsing in colorFromCart Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/hgTracks/lollyTrack.c
  • lines changed 2, context: html, text, full: html, text
    8593c40cb74ab6ee9f2318056626305d9d9544d3 Fri Apr 10 12:54:44 2026 -0700
    Fix color picker from code review, refs #37329, refs #20460 - Replace Spectrum JS color picker with native HTML5 color input, matching existing Hi-C picker - Color saved on form submit, not immediately via AJAX - Add checkbox to enable/disable color override; auto-checks when user picks a color - Gate color picker behind hg.conf showColorPicker=on (off by default) - Only show picker for non-composite tracks that support it: bed, bigBed, genePred, bigGenePred, wig, bigWig, rmsk, interact, bigInteract, bigLolly, vcfTabix, vcf - Add colorFromCart calls to interact, lolly, vcf phased, and pgSnp drawing code - Revert hui.js Spectrum changes from cfeb4d4 (no longer needed) - Use htmlColorForCode()/htmlColorToRGB() from htmlColor.h instead of hand-rolled hex parsing in colorFromCart Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    8593c40cb74ab6ee9f2318056626305d9d9544d3 Fri Apr 10 12:54:44 2026 -0700
    Fix color picker from code review, refs #37329, refs #20460 - Replace Spectrum JS color picker with native HTML5 color input, matching existing Hi-C picker - Color saved on form submit, not immediately via AJAX - Add checkbox to enable/disable color override; auto-checks when user picks a color - Gate color picker behind hg.conf showColorPicker=on (off by default) - Only show picker for non-composite tracks that support it: bed, bigBed, genePred, bigGenePred, wig, bigWig, rmsk, interact, bigInteract, bigLolly, vcfTabix, vcf - Add colorFromCart calls to interact, lolly, vcf phased, and pgSnp drawing code - Revert hui.js Spectrum changes from cfeb4d4 (no longer needed) - Use htmlColorForCode()/htmlColorToRGB() from htmlColor.h instead of hand-rolled hex parsing in colorFromCart Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/hgTracks/vcfTrack.c
  • lines changed 1, context: html, text, full: html, text
    8593c40cb74ab6ee9f2318056626305d9d9544d3 Fri Apr 10 12:54:44 2026 -0700
    Fix color picker from code review, refs #37329, refs #20460 - Replace Spectrum JS color picker with native HTML5 color input, matching existing Hi-C picker - Color saved on form submit, not immediately via AJAX - Add checkbox to enable/disable color override; auto-checks when user picks a color - Gate color picker behind hg.conf showColorPicker=on (off by default) - Only show picker for non-composite tracks that support it: bed, bigBed, genePred, bigGenePred, wig, bigWig, rmsk, interact, bigInteract, bigLolly, vcfTabix, vcf - Add colorFromCart calls to interact, lolly, vcf phased, and pgSnp drawing code - Revert hui.js Spectrum changes from cfeb4d4 (no longer needed) - Use htmlColorForCode()/htmlColorToRGB() from htmlColor.h instead of hand-rolled hex parsing in colorFromCart Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/hgc/hgc.c
  • lines changed 25, context: html, text, full: html, text
    b4538b995c8b87f8663861aa9cde4b8c68e83eb1 Tue Apr 7 12:52:56 2026 -0700
    Fix Get DNA position text box being ignored when table is specified, and accept single-base positions. refs #10316, #15336, #37325 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 15, context: html, text, full: html, text
    53621f3c5ef75891a7b04cf18d85180677a38f23 Wed Apr 8 11:38:53 2026 -0700
    Fix bug in hgc user defined table printing where we overwrote the variable that held the data for each custom table. Also fix a XSS vector with the table titles and some related code cleanup, refs #37340
  • lines changed 6, context: html, text, full: html, text
    54352b1c58abe76d6d8ea4404b4ffb9b00d294bf Wed Apr 8 12:23:43 2026 -0700
    don't output links to transcript or gene on quickLifted decipher SNV tracks #36061
  • lines changed 6, context: html, text, full: html, text
    1103e292ea1e3c3e1ac2daaa19f4752719ac5015 Thu Apr 9 14:52:32 2026 -0700
    fix quickLift DECIPHER SNV: add missing space after Transcript, show correct position for lifted assembly, refs #36061 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 15, context: html, text, full: html, text
    0c4b26c76ee09cadbe1a444016f2c41df33906f9 Thu Apr 9 15:48:53 2026 -0700
    Fix color picker and quickLift issues from code review, refs #37329 Color picker: fix [object Object] bug by calling .toHexString() on spectrum result, use htmlColor.h instead of hand-rolled hex parsing, show "color override active" status when override is set. quickLift: remove redundant quickLiftResolveTable call in genericBedClick, move hFindSplitTable into else branch where it's needed. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 15, context: html, text, full: html, text
    4905867d4df06d0c4cfe5769998334eaed96d6d6 Thu Apr 9 16:02:15 2026 -0700
    Revert "Fix color picker and quickLift issues from code review, refs #37329" This reverts commit 0c4b26c76ee09cadbe1a444016f2c41df33906f9.
• src/hg/hgc/vcfClick.c
  • lines changed 14, context: html, text, full: html, text
    412b01f1c0c78dd890c3d0d00fc121727e6085dd Fri Apr 10 05:59:34 2026 -0700
    warn on column count mismatch in sampleMetadataFile parsing, refs #37334 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/contribTracks.html
  • lines changed 1, context: html, text, full: html, text
    2059ffca9a9b74cd5ba9632a5835ae47d213b594 Tue Apr 7 11:04:02 2026 -0700
    Address CR feedback from #37315: fix broken color link, paraythroid typo, long lines, and incorrect #Supported anchor. Remove dead weng-lab.github.io color link in 12 ENCODE4 track HTML files. Fix "paraythroid" to "parathyroid" in 3 HTML files and wgEncodeReg4.ra labels. Break long lines in credits sections and availability paragraphs across hg38 and mm10 track HTML files. Replace nonexistent #Supported anchor with FAQ/FAQformat.html in contribTracks.html. refs #37315
• src/hg/htdocs/goldenPath/help/bigPsl.html
  • lines changed 6, context: html, text, full: html, text
    ca1f5d4b6f57481b8468c77dc40a65f9eb4ec029 Wed Apr 8 14:57:47 2026 -0700
    Fix bigPsl.as documentation: say "other sequence" not "other chromosome", add PSL field names, refs #37155 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/trackDb/changes.html
  • lines changed 8, context: html, text, full: html, text
    e6c80060e99101f891cea314cd796a82ed1055fd Wed Apr 8 02:24:44 2026 -0700
    Add detailsScript trackDb setting documentation, refs #37273 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 8, context: html, text, full: html, text
    089edf62bb8a818c89d8e696c8d1a09d53ecdb84 Fri Apr 10 05:49:40 2026 -0700
    document new sampleMetadataFile trackDb statement for VCF tracks, refs #37306 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 4, context: html, text, full: html, text
    e6c80060e99101f891cea314cd796a82ed1055fd Wed Apr 8 02:24:44 2026 -0700
    Add detailsScript trackDb setting documentation, refs #37273 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 3, context: html, text, full: html, text
    089edf62bb8a818c89d8e696c8d1a09d53ecdb84 Fri Apr 10 05:49:40 2026 -0700
    document new sampleMetadataFile trackDb statement for VCF tracks, refs #37306 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 4, context: html, text, full: html, text
    fbb29fc1a67f5e4c97e81bd1b7a2f85930bd8b74 Fri Apr 10 16:47:25 2026 -0700
    Adding trackDb docs for defaultSortField setting for faceted composites, refs #36320
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 4, context: html, text, full: html, text
    e6c80060e99101f891cea314cd796a82ed1055fd Wed Apr 8 02:24:44 2026 -0700
    Add detailsScript trackDb setting documentation, refs #37273 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 3, context: html, text, full: html, text
    089edf62bb8a818c89d8e696c8d1a09d53ecdb84 Fri Apr 10 05:49:40 2026 -0700
    document new sampleMetadataFile trackDb statement for VCF tracks, refs #37306 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 4, context: html, text, full: html, text
    fbb29fc1a67f5e4c97e81bd1b7a2f85930bd8b74 Fri Apr 10 16:47:25 2026 -0700
    Adding trackDb docs for defaultSortField setting for faceted composites, refs #36320
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 45, context: html, text, full: html, text
    e6c80060e99101f891cea314cd796a82ed1055fd Wed Apr 8 02:24:44 2026 -0700
    Add detailsScript trackDb setting documentation, refs #37273 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 28, context: html, text, full: html, text
    089edf62bb8a818c89d8e696c8d1a09d53ecdb84 Fri Apr 10 05:49:40 2026 -0700
    document new sampleMetadataFile trackDb statement for VCF tracks, refs #37306 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 15, context: html, text, full: html, text
    fbb29fc1a67f5e4c97e81bd1b7a2f85930bd8b74 Fri Apr 10 16:47:25 2026 -0700
    Adding trackDb docs for defaultSortField setting for faceted composites, refs #36320
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 75, context: html, text, full: html, text
    8caadf44150cd873343bb6af062f064cf039ce33 Fri Apr 10 16:04:39 2026 -0700
    Announing the STR superTrack and the gnomAD STR track, refs #36652 and #35420
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    ab4b62d2876e8ef84516ff751c2b8f90210563cb Fri Apr 10 16:35:02 2026 -0700
    Fixing some typos, refs #36652 #35420
• src/hg/htdocs/images/tutorialImages/gatewayPageAnnotated.png
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    f704665435dca39ec3f9022bf2584553f3fddf00 Wed Apr 8 09:30:19 2026 -0700
    Updating the annotated screenshot without the phylo tree, no RM.
• src/hg/htdocs/inc/globalNavBar.inc
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    3f380f0df2943e175eaf525a00178eb431da849c Tue Apr 7 13:47:16 2026 -0700
    Removing the April Fools menu link, no Redmine.
• src/hg/htdocs/index.html
  • lines changed 1, context: html, text, full: html, text
    9a1687b6341af06ee8e0746a9a502ba09cee8284 Tue Apr 7 16:11:57 2026 -0700
    Add missing form labels and aria-labels across hgTables pages and main site search. refs #37343 Main page search bar (index.html): aria-label on search input. hgTables main page (mainPage.c): aria-label on Galaxy/GREAT checkboxes, fix Position label to target radio button instead of text input, aria-label on position text input. hgTables user regions (userRegions.c): aria-label on paste textarea and file upload input. hgTables filter page (filterFields.c): aria-label on all per-field filter dropdowns and text inputs across string, numeric, integer, and enum field types. hgTables intersect page (intersect.c): label elements on all 6 radio buttons and 2 complement checkboxes, aria-label on threshold text inputs.
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    8caadf44150cd873343bb6af062f064cf039ce33 Fri Apr 10 16:04:39 2026 -0700
    Announing the STR superTrack and the gnomAD STR track, refs #36652 and #35420
• src/hg/htdocs/style/HGStyle.css
  • lines changed 12, context: html, text, full: html, text
    b5cbbe9353e85ec653bb18eee381c6989f529289 Sun Apr 12 12:21:24 2026 -0700
    Show alternative chromosome names from chromAlias on hgTracks position line, refs #29201 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/style/facetedComposite.css
  • lines changed 7, context: html, text, full: html, text
    d3841929bde0c503dd0aeda3b1efd1e61cd64ea7 Fri Apr 10 15:59:41 2026 -0700
    CSS changes to accompany logic disabling the 'show only selected' slider in the faceted composite UI when no tracks are selected, refs #36320
• src/hg/htdocs/style/jWest.css
  • lines changed 7, context: html, text, full: html, text
    f9fa02315060e80003f55f78c770dea0830d128c Tue Apr 7 15:33:47 2026 -0700
    Make Recent Genomes and Connected Hubs cards keyboard-accessible on hgGateway. refs #37342
• src/hg/hubApi/apiUtils.c
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    a62a60916a2ae4aebf9452d0f005f2ad2213ed94 Mon Apr 6 16:21:57 2026 -0700
    remove the gcOnFly track from consideration - do not see it at all anywhere refs #35958
• src/hg/inc/bigPsl.h
  • lines changed 7, context: html, text, full: html, text
    ca1f5d4b6f57481b8468c77dc40a65f9eb4ec029 Wed Apr 8 14:57:47 2026 -0700
    Fix bigPsl.as documentation: say "other sequence" not "other chromosome", add PSL field names, refs #37155 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/inc/bigTransMap.h
  • lines changed 6, context: html, text, full: html, text
    ca1f5d4b6f57481b8468c77dc40a65f9eb4ec029 Wed Apr 8 14:57:47 2026 -0700
    Fix bigPsl.as documentation: say "other sequence" not "other chromosome", add PSL field names, refs #37155 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/inc/hui.h
  • lines changed 2, context: html, text, full: html, text
    acace5022c846865a6e449fe1973e94504394cde Tue Apr 7 16:33:34 2026 -0700
    Add aria-labels to Base Position and supertrack/container dropdowns on hgTracks. refs #37344 New hideShowDropDownWithClassExtraAndLabel() passes label through to the existing labeled dropdown function. superTrackDropDownWithExtra() now passes tdb->shortLabel. Ruler dropdown updated in both hgTracks.c and config.c. Brings hgTracks track dropdown label coverage from 69% to 100%.
• src/hg/js/facetedComposite.js
  • lines changed 75, context: html, text, full: html, text
    6239b81a7033f90749f836e73703c65eabd0de9c Fri Apr 10 15:56:31 2026 -0700
    Moved js and css includes for faceted composites into hgTrackUi for better detection of file changes. Dynamically change the track visibility based on selected subtracks (hiding it if everything is deselected, making it visible when something is selected). refs #36320
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    7d149b1935f8a1e5f11f31f3cb8da99d31b3a8e6 Fri Apr 10 16:34:48 2026 -0700
    Replaced handrolled JSON structure in faceted composite output from hgTrackUi with jsonWrite.h library-generated version, and added a defaultSortField trackDb setting to faceted composites to improve the subtrack presentation order, refs #36320
• src/hg/js/hgGateway.js
  • lines changed 15, context: html, text, full: html, text
    f9fa02315060e80003f55f78c770dea0830d128c Tue Apr 7 15:33:47 2026 -0700
    Make Recent Genomes and Connected Hubs cards keyboard-accessible on hgGateway. refs #37342
• src/hg/js/hgc.js
  • lines changed 5, context: html, text, full: html, text
    53621f3c5ef75891a7b04cf18d85180677a38f23 Wed Apr 8 11:38:53 2026 -0700
    Fix bug in hgc user defined table printing where we overwrote the variable that held the data for each custom table. Also fix a XSS vector with the table titles and some related code cleanup, refs #37340
• src/hg/js/hui.js
  • lines changed 28, context: html, text, full: html, text
    814472876eac4d004d61f0ed89bd2aaa07459d33 Thu Apr 9 06:42:24 2026 -0700
    Fix composite vis: prefer pack over full, fix [-] button hide, refs #37182 Two issues from QA (note-17): 1) exposeAll() and onUserCbChange() always set composite to "full" when re-enabling subtracks on tracks without a "pack" option. Now tries pack first, then dense, then full as last resort. 2) The matrix [-] button (btn_minus_all_left_top) did not hide the composite. _matSetMatrixCheckBoxes() called hideAll() which triggered propagateVis, and propagateVis re-checked all subCBs when checkedCount===0, undoing the hide. Fix: set composite to hide directly via prop('selectedIndex', 0) without triggering propagateVis. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 9, context: html, text, full: html, text
    0c4b26c76ee09cadbe1a444016f2c41df33906f9 Thu Apr 9 15:48:53 2026 -0700
    Fix color picker and quickLift issues from code review, refs #37329 Color picker: fix [object Object] bug by calling .toHexString() on spectrum result, use htmlColor.h instead of hand-rolled hex parsing, show "color override active" status when override is set. quickLift: remove redundant quickLiftResolveTable call in genericBedClick, move hFindSplitTable into else branch where it's needed. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 9, context: html, text, full: html, text
    4905867d4df06d0c4cfe5769998334eaed96d6d6 Thu Apr 9 16:02:15 2026 -0700
    Revert "Fix color picker and quickLift issues from code review, refs #37329" This reverts commit 0c4b26c76ee09cadbe1a444016f2c41df33906f9.
  • lines changed 12, context: html, text, full: html, text
    f1f04f7cc152203f17d587f10b1bc176e45e9eae Fri Apr 10 01:52:03 2026 -0700
    fixing up after claude
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    8593c40cb74ab6ee9f2318056626305d9d9544d3 Fri Apr 10 12:54:44 2026 -0700
    Fix color picker from code review, refs #37329, refs #20460 - Replace Spectrum JS color picker with native HTML5 color input, matching existing Hi-C picker - Color saved on form submit, not immediately via AJAX - Add checkbox to enable/disable color override; auto-checks when user picks a color - Gate color picker behind hg.conf showColorPicker=on (off by default) - Only show picker for non-composite tracks that support it: bed, bigBed, genePred, bigGenePred, wig, bigWig, rmsk, interact, bigInteract, bigLolly, vcfTabix, vcf - Add colorFromCart calls to interact, lolly, vcf phased, and pgSnp drawing code - Revert hui.js Spectrum changes from cfeb4d4 (no longer needed) - Use htmlColorForCode()/htmlColorToRGB() from htmlColor.h instead of hand-rolled hex parsing in colorFromCart Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/js/subCfg.js
  • lines changed 8, context: html, text, full: html, text
    814472876eac4d004d61f0ed89bd2aaa07459d33 Thu Apr 9 06:42:24 2026 -0700
    Fix composite vis: prefer pack over full, fix [-] button hide, refs #37182 Two issues from QA (note-17): 1) exposeAll() and onUserCbChange() always set composite to "full" when re-enabling subtracks on tracks without a "pack" option. Now tries pack first, then dense, then full as last resort. 2) The matrix [-] button (btn_minus_all_left_top) did not hide the composite. _matSetMatrixCheckBoxes() called hideAll() which triggered propagateVis, and propagateVis re-checked all subCBs when checkedCount===0, undoing the hide. Fix: set composite to hide directly via prop('selectedIndex', 0) without triggering propagateVis. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/lib/bigBedFind.c
  • lines changed 10, context: html, text, full: html, text
    8637af0782efc3d9d13ae865e3e8e0a4f1f1545d Fri Apr 10 14:18:16 2026 -0700
    When doing bigBed searches, the hgPos->browserName needs to match tg->mapItemName so item highlights work. Typically this works because we expect to search for things by item name, but with multiple indexes if we get a match on a non-name index then we need to be sure the name field is set as browserName (and thus hgFind.matches on the URL) rather than the searched term, refs #34866
• src/hg/lib/bigPsl.as
  • lines changed 6, context: html, text, full: html, text
    ca1f5d4b6f57481b8468c77dc40a65f9eb4ec029 Wed Apr 8 14:57:47 2026 -0700
    Fix bigPsl.as documentation: say "other sequence" not "other chromosome", add PSL field names, refs #37155 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/lib/bigTransMap.as
  • lines changed 6, context: html, text, full: html, text
    ca1f5d4b6f57481b8468c77dc40a65f9eb4ec029 Wed Apr 8 14:57:47 2026 -0700
    Fix bigPsl.as documentation: say "other sequence" not "other chromosome", add PSL field names, refs #37155 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/lib/hui.c
  • lines changed 14, context: html, text, full: html, text
    acace5022c846865a6e449fe1973e94504394cde Tue Apr 7 16:33:34 2026 -0700
    Add aria-labels to Base Position and supertrack/container dropdowns on hgTracks. refs #37344 New hideShowDropDownWithClassExtraAndLabel() passes label through to the existing labeled dropdown function. superTrackDropDownWithExtra() now passes tdb->shortLabel. Ruler dropdown updated in both hgTracks.c and config.c. Brings hgTracks track dropdown label coverage from 69% to 100%.
  • lines changed 4, context: html, text, full: html, text
    a37d4ffb473b6ebf6c66545f2b7d5f7eef35ef4b Fri Apr 10 03:00:33 2026 -0700
    Color strVar subtracks by expected heterozygosity instead of motif period, fix hgTrackUi filter label truncation, refs #36652 Change all four strVar subtracks (webstr, tommoStr, trexplorer, viennaVntr) from motif-period-based coloring to expected heterozygosity (het = 1 - sum(p_i^2)), using a blue-to-red heat map: dark blue (het<0.1) through medium blue, light purple, salmon, to dark red (het>=0.7). Add het as a filterable bigBed field with scoreFilter and filterByRange on each track. Update mouseOver, track docs, and makedoc. Also fix hgTrackUi to strip the "|..." suffix from autoSql comments when displaying numeric filter labels. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 16, context: html, text, full: html, text
    8593c40cb74ab6ee9f2318056626305d9d9544d3 Fri Apr 10 12:54:44 2026 -0700
    Fix color picker from code review, refs #37329, refs #20460 - Replace Spectrum JS color picker with native HTML5 color input, matching existing Hi-C picker - Color saved on form submit, not immediately via AJAX - Add checkbox to enable/disable color override; auto-checks when user picks a color - Gate color picker behind hg.conf showColorPicker=on (off by default) - Only show picker for non-composite tracks that support it: bed, bigBed, genePred, bigGenePred, wig, bigWig, rmsk, interact, bigInteract, bigLolly, vcfTabix, vcf - Add colorFromCart calls to interact, lolly, vcf phased, and pgSnp drawing code - Revert hui.js Spectrum changes from cfeb4d4 (no longer needed) - Use htmlColorForCode()/htmlColorToRGB() from htmlColor.h instead of hand-rolled hex parsing in colorFromCart Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/evaSnp8.txt
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    d02449d1394960b2bc3e6f0de73ad6ae32458456 Wed Apr 8 14:09:17 2026 -0700
    minor issues noted from claude code review refs #36957
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    908132d6c2e74753a8c44df8d97a8557fbb331d0 Wed Apr 8 14:19:21 2026 -0700
    correct spelling Andian -> Andean correction found by claude code review
• src/hg/makeDb/doc/hg38/encode4.regulation.txt
  • lines changed 145, context: html, text, full: html, text
    5b55849bed022137ad7f399d96f6458dc7509a7e Fri Apr 10 11:51:52 2026 -0700
    Update ENCODE4 Regulation makedocs for hg38 and mm10. refs #34923 Updated to reflect all work through Weng lab feedback round 2: tp/ave fix, tissue default subtracks, color fixes, credits audit, biosample cleanup, ENCODE3 rename, relatedTracks, and current file/disk counts.
  • lines changed 1, context: html, text, full: html, text
    2762a10400229116f476c3f526712c2d0126ed0c Mon Apr 13 09:40:34 2026 -0700
    Fix gray organ count in hg38 makedoc per CR feedback. refs #34923
• src/hg/makeDb/doc/hg38/strVar.txt
  • lines changed 59, context: html, text, full: html, text
    a37d4ffb473b6ebf6c66545f2b7d5f7eef35ef4b Fri Apr 10 03:00:33 2026 -0700
    Color strVar subtracks by expected heterozygosity instead of motif period, fix hgTrackUi filter label truncation, refs #36652 Change all four strVar subtracks (webstr, tommoStr, trexplorer, viennaVntr) from motif-period-based coloring to expected heterozygosity (het = 1 - sum(p_i^2)), using a blue-to-red heat map: dark blue (het<0.1) through medium blue, light purple, salmon, to dark red (het>=0.7). Add het as a filterable bigBed field with scoreFilter and filterByRange on each track. Update mouseOver, track docs, and makedoc. Also fix hgTrackUi to strip the "|..." suffix from autoSql comments when displaying numeric filter labels. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    92d94309df312d21e49178f9b682bfb7147582d6 Mon Apr 6 21:31:26 2026 -0700
    differentiate between great and intermediate fruit-eating bat refs #29545
• src/hg/makeDb/doc/mm10.encode4.regulation.txt
  • lines changed 76, context: html, text, full: html, text
    5b55849bed022137ad7f399d96f6458dc7509a7e Fri Apr 10 11:51:52 2026 -0700
    Update ENCODE4 Regulation makedocs for hg38 and mm10. refs #34923 Updated to reflect all work through Weng lab feedback round 2: tp/ave fix, tissue default subtracks, color fixes, credits audit, biosample cleanup, ENCODE3 rename, relatedTracks, and current file/disk counts.
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 0, context: html, text, full: html, text
    0a566da9105da8a5434482c3b5df14e983a8073f Wed Apr 8 14:14:59 2026 -0700
    fixup minor errors found by claude review
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 7, context: html, text, full: html, text
    0a566da9105da8a5434482c3b5df14e983a8073f Wed Apr 8 14:14:59 2026 -0700
    fixup minor errors found by claude review
• src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    908132d6c2e74753a8c44df8d97a8557fbb331d0 Wed Apr 8 14:19:21 2026 -0700
    correct spelling Andian -> Andean correction found by claude code review
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    92d94309df312d21e49178f9b682bfb7147582d6 Mon Apr 6 21:31:26 2026 -0700
    differentiate between great and intermediate fruit-eating bat refs #29545
  • lines changed 1, context: html, text, full: html, text
    908132d6c2e74753a8c44df8d97a8557fbb331d0 Wed Apr 8 14:19:21 2026 -0700
    correct spelling Andian -> Andean correction found by claude code review
• src/hg/makeDb/scripts/tommoStr/tommoStr.as
  • lines changed 21, context: html, text, full: html, text
    a37d4ffb473b6ebf6c66545f2b7d5f7eef35ef4b Fri Apr 10 03:00:33 2026 -0700
    Color strVar subtracks by expected heterozygosity instead of motif period, fix hgTrackUi filter label truncation, refs #36652 Change all four strVar subtracks (webstr, tommoStr, trexplorer, viennaVntr) from motif-period-based coloring to expected heterozygosity (het = 1 - sum(p_i^2)), using a blue-to-red heat map: dark blue (het<0.1) through medium blue, light purple, salmon, to dark red (het>=0.7). Add het as a filterable bigBed field with scoreFilter and filterByRange on each track. Update mouseOver, track docs, and makedoc. Also fix hgTrackUi to strip the "|..." suffix from autoSql comments when displaying numeric filter labels. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/tommoStr/tommoStrToBed.py
  • lines changed 172, context: html, text, full: html, text
    a37d4ffb473b6ebf6c66545f2b7d5f7eef35ef4b Fri Apr 10 03:00:33 2026 -0700
    Color strVar subtracks by expected heterozygosity instead of motif period, fix hgTrackUi filter label truncation, refs #36652 Change all four strVar subtracks (webstr, tommoStr, trexplorer, viennaVntr) from motif-period-based coloring to expected heterozygosity (het = 1 - sum(p_i^2)), using a blue-to-red heat map: dark blue (het<0.1) through medium blue, light purple, salmon, to dark red (het>=0.7). Add het as a filterable bigBed field with scoreFilter and filterByRange on each track. Update mouseOver, track docs, and makedoc. Also fix hgTrackUi to strip the "|..." suffix from autoSql comments when displaying numeric filter labels. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/trexplorer/trexplorer.as
  • lines changed 1, context: html, text, full: html, text
    a37d4ffb473b6ebf6c66545f2b7d5f7eef35ef4b Fri Apr 10 03:00:33 2026 -0700
    Color strVar subtracks by expected heterozygosity instead of motif period, fix hgTrackUi filter label truncation, refs #36652 Change all four strVar subtracks (webstr, tommoStr, trexplorer, viennaVntr) from motif-period-based coloring to expected heterozygosity (het = 1 - sum(p_i^2)), using a blue-to-red heat map: dark blue (het<0.1) through medium blue, light purple, salmon, to dark red (het>=0.7). Add het as a filterable bigBed field with scoreFilter and filterByRange on each track. Update mouseOver, track docs, and makedoc. Also fix hgTrackUi to strip the "|..." suffix from autoSql comments when displaying numeric filter labels. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/trexplorer/trexplorerToBed.py
  • lines changed 53, context: html, text, full: html, text
    a37d4ffb473b6ebf6c66545f2b7d5f7eef35ef4b Fri Apr 10 03:00:33 2026 -0700
    Color strVar subtracks by expected heterozygosity instead of motif period, fix hgTrackUi filter label truncation, refs #36652 Change all four strVar subtracks (webstr, tommoStr, trexplorer, viennaVntr) from motif-period-based coloring to expected heterozygosity (het = 1 - sum(p_i^2)), using a blue-to-red heat map: dark blue (het<0.1) through medium blue, light purple, salmon, to dark red (het>=0.7). Add het as a filterable bigBed field with scoreFilter and filterByRange on each track. Update mouseOver, track docs, and makedoc. Also fix hgTrackUi to strip the "|..." suffix from autoSql comments when displaying numeric filter labels. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/viennaVntr/viennaVntr.as
  • lines changed 26, context: html, text, full: html, text
    a37d4ffb473b6ebf6c66545f2b7d5f7eef35ef4b Fri Apr 10 03:00:33 2026 -0700
    Color strVar subtracks by expected heterozygosity instead of motif period, fix hgTrackUi filter label truncation, refs #36652 Change all four strVar subtracks (webstr, tommoStr, trexplorer, viennaVntr) from motif-period-based coloring to expected heterozygosity (het = 1 - sum(p_i^2)), using a blue-to-red heat map: dark blue (het<0.1) through medium blue, light purple, salmon, to dark red (het>=0.7). Add het as a filterable bigBed field with scoreFilter and filterByRange on each track. Update mouseOver, track docs, and makedoc. Also fix hgTrackUi to strip the "|..." suffix from autoSql comments when displaying numeric filter labels. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/viennaVntr/viennaVntrHet.py
  • lines changed 62, context: html, text, full: html, text
    a37d4ffb473b6ebf6c66545f2b7d5f7eef35ef4b Fri Apr 10 03:00:33 2026 -0700
    Color strVar subtracks by expected heterozygosity instead of motif period, fix hgTrackUi filter label truncation, refs #36652 Change all four strVar subtracks (webstr, tommoStr, trexplorer, viennaVntr) from motif-period-based coloring to expected heterozygosity (het = 1 - sum(p_i^2)), using a blue-to-red heat map: dark blue (het<0.1) through medium blue, light purple, salmon, to dark red (het>=0.7). Add het as a filterable bigBed field with scoreFilter and filterByRange on each track. Update mouseOver, track docs, and makedoc. Also fix hgTrackUi to strip the "|..." suffix from autoSql comments when displaying numeric filter labels. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/viennaVntr/viennaVntrToBed.py
  • lines changed 126, context: html, text, full: html, text
    a37d4ffb473b6ebf6c66545f2b7d5f7eef35ef4b Fri Apr 10 03:00:33 2026 -0700
    Color strVar subtracks by expected heterozygosity instead of motif period, fix hgTrackUi filter label truncation, refs #36652 Change all four strVar subtracks (webstr, tommoStr, trexplorer, viennaVntr) from motif-period-based coloring to expected heterozygosity (het = 1 - sum(p_i^2)), using a blue-to-red heat map: dark blue (het<0.1) through medium blue, light purple, salmon, to dark red (het>=0.7). Add het as a filterable bigBed field with scoreFilter and filterByRange on each track. Update mouseOver, track docs, and makedoc. Also fix hgTrackUi to strip the "|..." suffix from autoSql comments when displaying numeric filter labels. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/webstr/webstr.as
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    ed005215c7fdd3e97c61edb41931c89805d9566b Thu Apr 9 03:06:48 2026 -0700
    Add repeatId field to webstr bigBed for outlinks, update webstr and strVar docs, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    a37d4ffb473b6ebf6c66545f2b7d5f7eef35ef4b Fri Apr 10 03:00:33 2026 -0700
    Color strVar subtracks by expected heterozygosity instead of motif period, fix hgTrackUi filter label truncation, refs #36652 Change all four strVar subtracks (webstr, tommoStr, trexplorer, viennaVntr) from motif-period-based coloring to expected heterozygosity (het = 1 - sum(p_i^2)), using a blue-to-red heat map: dark blue (het<0.1) through medium blue, light purple, salmon, to dark red (het>=0.7). Add het as a filterable bigBed field with scoreFilter and filterByRange on each track. Update mouseOver, track docs, and makedoc. Also fix hgTrackUi to strip the "|..." suffix from autoSql comments when displaying numeric filter labels. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/webstr/webstrToBed.py
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    ed005215c7fdd3e97c61edb41931c89805d9566b Thu Apr 9 03:06:48 2026 -0700
    Add repeatId field to webstr bigBed for outlinks, update webstr and strVar docs, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 57, context: html, text, full: html, text
    a37d4ffb473b6ebf6c66545f2b7d5f7eef35ef4b Fri Apr 10 03:00:33 2026 -0700
    Color strVar subtracks by expected heterozygosity instead of motif period, fix hgTrackUi filter label truncation, refs #36652 Change all four strVar subtracks (webstr, tommoStr, trexplorer, viennaVntr) from motif-period-based coloring to expected heterozygosity (het = 1 - sum(p_i^2)), using a blue-to-red heat map: dark blue (het<0.1) through medium blue, light purple, salmon, to dark red (het>=0.7). Add het as a filterable bigBed field with scoreFilter and filterByRange on each track. Update mouseOver, track docs, and makedoc. Also fix hgTrackUi to strip the "|..." suffix from autoSql comments when displaying numeric filter labels. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/affy.html
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    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/affyAllExonProbes.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/affyTranscriptome.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/allenBrainAli.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/bacteria/staAur2/cons369way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/betaGenArk.txt
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    e36763d9058bbd555e6c0be3987c4dbdf8ca8c31 Mon Apr 6 23:40:46 2026 -0700
    begin experiment with vgp577way alignment first on on GCF_037176765.1
• src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/bushbaby/otoGar3/cons3way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/cat/felCat3/multiz4way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/cat/felCat4/cons6way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/ccdsGene.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/chicken/galGal2/multiz7way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/chicken/galGal3/multiz7way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/chicken/galGal6/cons77way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/chicken/galGal6/refSeqComposite.ra
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/chicken/galGal7b/genArk.trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/chicken/galGal7w/genArk.trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/cow/bosTau4/multiz5way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/criGri/criGriChoV1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/criGri/criGriChoV2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/criGri/regenCho1/cons7way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/dog/canFam1/mzHg17Mm5_phast.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/dog/canFam2/multiz4way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/bdgpGene.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/bdgpNonCoding.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dm1/cytoBand.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dm1/description.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dm2/cytoBand.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dm2/description.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dm2/flyBaseGene.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dm2/flyBaseNoncoding.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dm2/multiz12way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dm2/multiz15way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dm2/multiz8way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dm2/multiz9way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dm3/cytoBand.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dm3/description.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dm3/flyBaseGene.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dm3/flyBaseNoncoding.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dm3/multiz15way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dm6/cons124way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dm6/cons27way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dm6/cytoBand.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dm6/refGene.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dp3/description.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dp3/flyBaseGene.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dp3/genewise.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/dp3/twinscan.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/mzDy1Dp2Ag1_phast.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/drosophila/netDp3.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbPred.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbPred1.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbPredClassIMac.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/ebola/eboVir3/iedbSupp3.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/ensEst.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/ensEstGene.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/ensGene.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/ensemblGeneScaffold.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/fugu/ensGene.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/fugu/fr2/multiz5way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/fugu/fr2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/fugu/fr3/cons8way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/galVar/galVar1/cons4way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/galVar/galVar1/cons5way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/galVar/galVar1/cons6way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/genieAlt.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/genieBounds.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/gorilla/gorGor3/cons11way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/guineaPig/cavPor3/cons5way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/guineaPig/cavPor3/cons6way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/horse/equCab2/multiz6way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/TFrPeakClusters.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/affy10K.html
  • lines changed 3, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/affy120K.html
  • lines changed 3, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/affy500K.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/affyHuEx1.html
  • lines changed 3, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/affyTranscription.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/affyTransfrags.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/chm13/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/colorsDb.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/encodeEgaspFull.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/encodeEgaspSuper.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/encodeRikenCage.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/encodeRikenCageMappedTags.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/encodeUvaDnaRep.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/encodeUvaDnaRepSuper.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/encodeUvaDnaRepTr50.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/geneHancer.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg16/encodeMlaganAlign.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg16/exoniphy.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg16/tfbsCons.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg17/encodeDless.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg17/encodeEvoFold.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg17/encodeMlaganAlign.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg17/encodeMsaElements.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg17/exoniphy.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg17/exoniphyHMR.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg17/seg.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg17/snpArray.html
  • lines changed 4, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg17/tfbsConsSites.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg18/encodeEvoFold.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg18/exoniphy.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg18/multiz28way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg18/multizPrimate.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg18/pgSnp.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg18/phyloPCons28way.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg18/phyloPConsLs44way.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg18/snpArrayBeta.html
  • lines changed 3, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg18/snpArrayWith1M.html
  • lines changed 3, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg18/tfbsConsSites.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeExonArraySuper.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHelicosRnaSeq.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeSangerGencode.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg18/wgRna.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg18/wgRnaJun09.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/dhcBamDenisova.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/dhcHumDerDenAnc.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/dhcVcfDenisovaPinky.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/exoniphy.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/pgSnp.html
  • lines changed 4, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/refSeqComposite.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/tfbsConsSites.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencode.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.ra
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.ra
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV12.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV12.ra
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV13.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV14.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV15.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV16.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV17.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV18.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.ra
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.ra
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.ra
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegDnaseClusteredV2.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClusteredV3.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.patch.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release3.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg38/ancient.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg38/cons17way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg38/cons20way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg38/cons27way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg38/cons30way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg38/cons4way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg38/cons5way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg38/cons7way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg38/gnomad.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 1, context: html, text, full: html, text
    8caadf44150cd873343bb6af062f064cf039ce33 Fri Apr 10 16:04:39 2026 -0700
    Announing the STR superTrack and the gnomAD STR track, refs #36652 and #35420
• src/hg/makeDb/trackDb/human/hg38/gnomadStr.html
  • lines changed 21, context: html, text, full: html, text
    38bff13d35b43e9213a8de21d0288f990a333572 Fri Apr 10 14:51:35 2026 -0700
    Making each line less than 100 characters and updating the references section after using getTrackReferences for formatting, refs #36652
  • lines changed 2, context: html, text, full: html, text
    171b2f3bfaa163f1db7a84d97eebff266d99ea04 Fri Apr 10 15:03:25 2026 -0700
    QA fixes for STR track description pages: fix line lengths, references, link prefixes, missing target="_blank", and section ordering, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/gnomadV3.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg38/gnomadV3_1.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg38/gnomadV3_1_1.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg38/gnomadV4.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hg38/hprcV2.trackDb.txt
  • lines changed 44, context: html, text, full: html, text
    cd2739b2490649fcaab39f8acb015c815e8945d2 Fri Apr 10 11:11:18 2026 -0700
    initial test of two HPRC V2 chain tracks refs #35415
• src/hg/makeDb/trackDb/human/hg38/mb2.html
  • lines changed 39, context: html, text, full: html, text
    8c6db4c392b96c9dbe33b27b8bf415885a5e9d06 Fri Apr 10 10:26:18 2026 -0700
    Initial commit of MethBase 2 track set using the faceted composite UI, refs #36320
• src/hg/makeDb/trackDb/human/hg38/mb2.ra
  • lines changed 74984, context: html, text, full: html, text
    8c6db4c392b96c9dbe33b27b8bf415885a5e9d06 Fri Apr 10 10:26:18 2026 -0700
    Initial commit of MethBase 2 track set using the faceted composite UI, refs #36320
  • lines changed 10, context: html, text, full: html, text
    47a44abb479f73d38ba1b037a1d0b70c26c3792e Fri Apr 10 14:41:17 2026 -0700
    Set up a custom supertrack for MethBase2 during development to work around trackDb issues when adding an alpha release child of a released parent supertrack. Also turned on a couple of subtracks by default. refs #36320
  • lines changed 3, context: html, text, full: html, text
    643fda00ff35f42b06250b88481d5e52eec7edd4 Fri Apr 10 17:13:52 2026 -0700
    Removing old trackDb comments, refs #36320
  • lines changed 16274, context: html, text, full: html, text
    ad97ee85604aae9372160649a0b82c3e7c88c799 Fri Apr 10 17:38:29 2026 -0700
    Added a bit more contextual info to the MethBase 2 subtrack short and long labels, refs #36320
• src/hg/makeDb/trackDb/human/hg38/mb2_2.ra
  • lines changed 73296, context: html, text, full: html, text
    8c6db4c392b96c9dbe33b27b8bf415885a5e9d06 Fri Apr 10 10:26:18 2026 -0700
    Initial commit of MethBase 2 track set using the faceted composite UI, refs #36320
  • lines changed 2, context: html, text, full: html, text
    47a44abb479f73d38ba1b037a1d0b70c26c3792e Fri Apr 10 14:41:17 2026 -0700
    Set up a custom supertrack for MethBase2 during development to work around trackDb issues when adding an alpha release child of a released parent supertrack. Also turned on a couple of subtracks by default. refs #36320
  • lines changed 15748, context: html, text, full: html, text
    ad97ee85604aae9372160649a0b82c3e7c88c799 Fri Apr 10 17:38:29 2026 -0700
    Added a bit more contextual info to the MethBase 2 subtrack short and long labels, refs #36320
• src/hg/makeDb/trackDb/human/hg38/mpra.ra
  • lines changed 1, context: html, text, full: html, text
    ff128a6ed0d1f03aa6ca3808669f4109e1d05542 Fri Apr 10 20:29:24 2026 -0700
    moving mpra back into regulation, typo, refs #34284
• src/hg/makeDb/trackDb/human/hg38/strVar.html
  • lines changed 10, context: html, text, full: html, text
    ed005215c7fdd3e97c61edb41931c89805d9566b Thu Apr 9 03:06:48 2026 -0700
    Add repeatId field to webstr bigBed for outlinks, update webstr and strVar docs, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 7, context: html, text, full: html, text
    38bff13d35b43e9213a8de21d0288f990a333572 Fri Apr 10 14:51:35 2026 -0700
    Making each line less than 100 characters and updating the references section after using getTrackReferences for formatting, refs #36652
• src/hg/makeDb/trackDb/human/hg38/strVar.ra
  • lines changed 29, context: html, text, full: html, text
    ed005215c7fdd3e97c61edb41931c89805d9566b Thu Apr 9 03:06:48 2026 -0700
    Add repeatId field to webstr bigBed for outlinks, update webstr and strVar docs, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 19, context: html, text, full: html, text
    a37d4ffb473b6ebf6c66545f2b7d5f7eef35ef4b Fri Apr 10 03:00:33 2026 -0700
    Color strVar subtracks by expected heterozygosity instead of motif period, fix hgTrackUi filter label truncation, refs #36652 Change all four strVar subtracks (webstr, tommoStr, trexplorer, viennaVntr) from motif-period-based coloring to expected heterozygosity (het = 1 - sum(p_i^2)), using a blue-to-red heat map: dark blue (het<0.1) through medium blue, light purple, salmon, to dark red (het>=0.7). Add het as a filterable bigBed field with scoreFilter and filterByRange on each track. Update mouseOver, track docs, and makedoc. Also fix hgTrackUi to strip the "|..." suffix from autoSql comments when displaying numeric filter labels. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    8caadf44150cd873343bb6af062f064cf039ce33 Fri Apr 10 16:04:39 2026 -0700
    Announing the STR superTrack and the gnomAD STR track, refs #36652 and #35420
• src/hg/makeDb/trackDb/human/hg38/strchive.html
  • lines changed 11, context: html, text, full: html, text
    38bff13d35b43e9213a8de21d0288f990a333572 Fri Apr 10 14:51:35 2026 -0700
    Making each line less than 100 characters and updating the references section after using getTrackReferences for formatting, refs #36652
  • lines changed 2, context: html, text, full: html, text
    171b2f3bfaa163f1db7a84d97eebff266d99ea04 Fri Apr 10 15:03:25 2026 -0700
    QA fixes for STR track description pages: fix line lengths, references, link prefixes, missing target="_blank", and section ordering, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    05116be7da93f94110fa0653ed916ba29d96285c Fri Apr 10 15:26:05 2026 -0700
    Fixing download links with the correct path, refs #36652
• src/hg/makeDb/trackDb/human/hg38/tommoStr.html
  • lines changed 118, context: html, text, full: html, text
    a37d4ffb473b6ebf6c66545f2b7d5f7eef35ef4b Fri Apr 10 03:00:33 2026 -0700
    Color strVar subtracks by expected heterozygosity instead of motif period, fix hgTrackUi filter label truncation, refs #36652 Change all four strVar subtracks (webstr, tommoStr, trexplorer, viennaVntr) from motif-period-based coloring to expected heterozygosity (het = 1 - sum(p_i^2)), using a blue-to-red heat map: dark blue (het<0.1) through medium blue, light purple, salmon, to dark red (het>=0.7). Add het as a filterable bigBed field with scoreFilter and filterByRange on each track. Update mouseOver, track docs, and makedoc. Also fix hgTrackUi to strip the "|..." suffix from autoSql comments when displaying numeric filter labels. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 24, context: html, text, full: html, text
    38bff13d35b43e9213a8de21d0288f990a333572 Fri Apr 10 14:51:35 2026 -0700
    Making each line less than 100 characters and updating the references section after using getTrackReferences for formatting, refs #36652
  • lines changed 43, context: html, text, full: html, text
    171b2f3bfaa163f1db7a84d97eebff266d99ea04 Fri Apr 10 15:03:25 2026 -0700
    QA fixes for STR track description pages: fix line lengths, references, link prefixes, missing target="_blank", and section ordering, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    9087a84ab83ac09ae5f543aeb08e0cbc88f35d9e Tue Apr 7 15:12:46 2026 -0700
    Releasing the STR tracks for hg38, refs #36652
  • lines changed 4, context: html, text, full: html, text
    8c6db4c392b96c9dbe33b27b8bf415885a5e9d06 Fri Apr 10 10:26:18 2026 -0700
    Initial commit of MethBase 2 track set using the faceted composite UI, refs #36320
  • lines changed 3, context: html, text, full: html, text
    cd2739b2490649fcaab39f8acb015c815e8945d2 Fri Apr 10 11:11:18 2026 -0700
    initial test of two HPRC V2 chain tracks refs #35415
  • lines changed 1, context: html, text, full: html, text
    77a40437a3d14dfc86d46500b0c3efbd5640aba1 Fri Apr 10 11:19:12 2026 -0700
    initial test of two HPRC V2 chain tracks refs #35415
• src/hg/makeDb/trackDb/human/hg38/trexplorer.html
  • lines changed 10, context: html, text, full: html, text
    a37d4ffb473b6ebf6c66545f2b7d5f7eef35ef4b Fri Apr 10 03:00:33 2026 -0700
    Color strVar subtracks by expected heterozygosity instead of motif period, fix hgTrackUi filter label truncation, refs #36652 Change all four strVar subtracks (webstr, tommoStr, trexplorer, viennaVntr) from motif-period-based coloring to expected heterozygosity (het = 1 - sum(p_i^2)), using a blue-to-red heat map: dark blue (het<0.1) through medium blue, light purple, salmon, to dark red (het>=0.7). Add het as a filterable bigBed field with scoreFilter and filterByRange on each track. Update mouseOver, track docs, and makedoc. Also fix hgTrackUi to strip the "|..." suffix from autoSql comments when displaying numeric filter labels. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 14, context: html, text, full: html, text
    38bff13d35b43e9213a8de21d0288f990a333572 Fri Apr 10 14:51:35 2026 -0700
    Making each line less than 100 characters and updating the references section after using getTrackReferences for formatting, refs #36652
  • lines changed 2, context: html, text, full: html, text
    171b2f3bfaa163f1db7a84d97eebff266d99ea04 Fri Apr 10 15:03:25 2026 -0700
    QA fixes for STR track description pages: fix line lengths, references, link prefixes, missing target="_blank", and section ordering, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    15b33dcb00334648b1673bcf56dbd80258193d2f Fri Apr 10 16:11:54 2026 -0700
    Fix color scheme description in trexplorer.html Methods section, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/viennaVntr.html
  • lines changed 108, context: html, text, full: html, text
    a37d4ffb473b6ebf6c66545f2b7d5f7eef35ef4b Fri Apr 10 03:00:33 2026 -0700
    Color strVar subtracks by expected heterozygosity instead of motif period, fix hgTrackUi filter label truncation, refs #36652 Change all four strVar subtracks (webstr, tommoStr, trexplorer, viennaVntr) from motif-period-based coloring to expected heterozygosity (het = 1 - sum(p_i^2)), using a blue-to-red heat map: dark blue (het<0.1) through medium blue, light purple, salmon, to dark red (het>=0.7). Add het as a filterable bigBed field with scoreFilter and filterByRange on each track. Update mouseOver, track docs, and makedoc. Also fix hgTrackUi to strip the "|..." suffix from autoSql comments when displaying numeric filter labels. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 4, context: html, text, full: html, text
    38bff13d35b43e9213a8de21d0288f990a333572 Fri Apr 10 14:51:35 2026 -0700
    Making each line less than 100 characters and updating the references section after using getTrackReferences for formatting, refs #36652
  • lines changed 41, context: html, text, full: html, text
    171b2f3bfaa163f1db7a84d97eebff266d99ea04 Fri Apr 10 15:03:25 2026 -0700
    QA fixes for STR track description pages: fix line lengths, references, link prefixes, missing target="_blank", and section ordering, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/webstr.html
  • lines changed 22, context: html, text, full: html, text
    ed005215c7fdd3e97c61edb41931c89805d9566b Thu Apr 9 03:06:48 2026 -0700
    Add repeatId field to webstr bigBed for outlinks, update webstr and strVar docs, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 12, context: html, text, full: html, text
    a37d4ffb473b6ebf6c66545f2b7d5f7eef35ef4b Fri Apr 10 03:00:33 2026 -0700
    Color strVar subtracks by expected heterozygosity instead of motif period, fix hgTrackUi filter label truncation, refs #36652 Change all four strVar subtracks (webstr, tommoStr, trexplorer, viennaVntr) from motif-period-based coloring to expected heterozygosity (het = 1 - sum(p_i^2)), using a blue-to-red heat map: dark blue (het<0.1) through medium blue, light purple, salmon, to dark red (het>=0.7). Add het as a filterable bigBed field with scoreFilter and filterByRange on each track. Update mouseOver, track docs, and makedoc. Also fix hgTrackUi to strip the "|..." suffix from autoSql comments when displaying numeric filter labels. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 17, context: html, text, full: html, text
    38bff13d35b43e9213a8de21d0288f990a333572 Fri Apr 10 14:51:35 2026 -0700
    Making each line less than 100 characters and updating the references section after using getTrackReferences for formatting, refs #36652
  • lines changed 2, context: html, text, full: html, text
    171b2f3bfaa163f1db7a84d97eebff266d99ea04 Fri Apr 10 15:03:25 2026 -0700
    QA fixes for STR track description pages: fix line lengths, references, link prefixes, missing target="_blank", and section ordering, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    05116be7da93f94110fa0653ed916ba29d96285c Fri Apr 10 15:26:05 2026 -0700
    Fixing download links with the correct path, refs #36652
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.alpha.ra
  • lines changed 2, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.ra
  • lines changed 6, context: html, text, full: html, text
    2059ffca9a9b74cd5ba9632a5835ae47d213b594 Tue Apr 7 11:04:02 2026 -0700
    Address CR feedback from #37315: fix broken color link, paraythroid typo, long lines, and incorrect #Supported anchor. Remove dead weng-lab.github.io color link in 12 ENCODE4 track HTML files. Fix "paraythroid" to "parathyroid" in 3 HTML files and wgEncodeReg4.ra labels. Break long lines in credits sections and availability paragraphs across hg38 and mm10 track HTML files. Replace nonexistent #Supported anchor with FAQ/FAQformat.html in contribTracks.html. refs #37315
  • lines changed 137, context: html, text, full: html, text
    dd40846f55b0cb21d346f2edbe51936f04007bb2 Tue Apr 7 11:07:15 2026 -0700
    Adding peak+signal data and new organ subtracks to hg38 ENCODE4 Regulation. refs #34923 Epigenetics composite: added 3,154 bigBed peak subtracks (was signal-only), composite type changed from bigWig to bed 3, Data Type facet added. TF ChIP composite: added 2,462 bigWig signal subtracks (was peak-only), composite type changed from bigBed 5 to bed 3, Data Type facet added. MultiWig organ-averaged tracks: added 15 new organ subtracks across ATAC (+2), H3K4me3 (+3), H3K27ac (+4), CTCF (+6). Updated bone marrow tissue-only subtracks for H3K4me3 and H3K27ac to use new separate tp. data files.
  • lines changed 967, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
  • lines changed 22, context: html, text, full: html, text
    7a4b3c8ae0be8a7a0f1df90dab1b606b0d9af10b Fri Apr 10 10:59:18 2026 -0700
    Fix duplicate priority in hg38 DNase multiWig all-biosamples section. refs #34923 DnaseAllOvary and DnaseAllSmallIntestine both had priority 33, and there was a gap at priority 55 (leftover from nose insertion/lymphoid tissue removal). Renumbered all DNase all-biosamples subtracks to be contiguous (25-64). Feedback from code review.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Atac.html
  • lines changed 10, context: html, text, full: html, text
    2059ffca9a9b74cd5ba9632a5835ae47d213b594 Tue Apr 7 11:04:02 2026 -0700
    Address CR feedback from #37315: fix broken color link, paraythroid typo, long lines, and incorrect #Supported anchor. Remove dead weng-lab.github.io color link in 12 ENCODE4 track HTML files. Fix "paraythroid" to "parathyroid" in 3 HTML files and wgEncodeReg4.ra labels. Break long lines in credits sections and availability paragraphs across hg38 and mm10 track HTML files. Replace nonexistent #Supported anchor with FAQ/FAQformat.html in contribTracks.html. refs #37315
  • lines changed 5, context: html, text, full: html, text
    a1e8bd10892f1d84b1a9a16ddadc3a6ee3f01038 Tue Apr 7 11:22:52 2026 -0700
    Fix production lab credits to be assay-specific for ENCODE4 multiWig tracks. refs #34923 Each multiWig HTML page was using the full 13-lab Epigenetics list instead of the assay-specific production labs from the hub. Updated DNase, ATAC, H3K4me3, H3K27ac, and CTCF credits for hg38, and ATAC, H3K4me3, H3K27ac, and CTCF for mm10 to match the hub's per-assay credits.
  • lines changed 3, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Dnase.html
  • lines changed 10, context: html, text, full: html, text
    2059ffca9a9b74cd5ba9632a5835ae47d213b594 Tue Apr 7 11:04:02 2026 -0700
    Address CR feedback from #37315: fix broken color link, paraythroid typo, long lines, and incorrect #Supported anchor. Remove dead weng-lab.github.io color link in 12 ENCODE4 track HTML files. Fix "paraythroid" to "parathyroid" in 3 HTML files and wgEncodeReg4.ra labels. Break long lines in credits sections and availability paragraphs across hg38 and mm10 track HTML files. Replace nonexistent #Supported anchor with FAQ/FAQformat.html in contribTracks.html. refs #37315
  • lines changed 5, context: html, text, full: html, text
    a1e8bd10892f1d84b1a9a16ddadc3a6ee3f01038 Tue Apr 7 11:22:52 2026 -0700
    Fix production lab credits to be assay-specific for ENCODE4 multiWig tracks. refs #34923 Each multiWig HTML page was using the full 13-lab Epigenetics list instead of the assay-specific production labs from the hub. Updated DNase, ATAC, H3K4me3, H3K27ac, and CTCF credits for hg38, and ATAC, H3K4me3, H3K27ac, and CTCF for mm10 to match the hub's per-assay credits.
  • lines changed 3, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra
  • lines changed 28388, context: html, text, full: html, text
    dd40846f55b0cb21d346f2edbe51936f04007bb2 Tue Apr 7 11:07:15 2026 -0700
    Adding peak+signal data and new organ subtracks to hg38 ENCODE4 Regulation. refs #34923 Epigenetics composite: added 3,154 bigBed peak subtracks (was signal-only), composite type changed from bigWig to bed 3, Data Type facet added. TF ChIP composite: added 2,462 bigWig signal subtracks (was peak-only), composite type changed from bigBed 5 to bed 3, Data Type facet added. MultiWig organ-averaged tracks: added 15 new organ subtracks across ATAC (+2), H3K4me3 (+3), H3K27ac (+4), CTCF (+6). Updated bone marrow tissue-only subtracks for H3K4me3 and H3K27ac to use new separate tp. data files.
  • lines changed 38, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkCtcf.html
  • lines changed 11, context: html, text, full: html, text
    2059ffca9a9b74cd5ba9632a5835ae47d213b594 Tue Apr 7 11:04:02 2026 -0700
    Address CR feedback from #37315: fix broken color link, paraythroid typo, long lines, and incorrect #Supported anchor. Remove dead weng-lab.github.io color link in 12 ENCODE4 track HTML files. Fix "paraythroid" to "parathyroid" in 3 HTML files and wgEncodeReg4.ra labels. Break long lines in credits sections and availability paragraphs across hg38 and mm10 track HTML files. Replace nonexistent #Supported anchor with FAQ/FAQformat.html in contribTracks.html. refs #37315
  • lines changed 6, context: html, text, full: html, text
    a1e8bd10892f1d84b1a9a16ddadc3a6ee3f01038 Tue Apr 7 11:22:52 2026 -0700
    Fix production lab credits to be assay-specific for ENCODE4 multiWig tracks. refs #34923 Each multiWig HTML page was using the full 13-lab Epigenetics list instead of the assay-specific production labs from the hub. Updated DNase, ATAC, H3K4me3, H3K27ac, and CTCF credits for hg38, and ATAC, H3K4me3, H3K27ac, and CTCF for mm10 to match the hub's per-assay credits.
  • lines changed 3, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k27ac.html
  • lines changed 11, context: html, text, full: html, text
    2059ffca9a9b74cd5ba9632a5835ae47d213b594 Tue Apr 7 11:04:02 2026 -0700
    Address CR feedback from #37315: fix broken color link, paraythroid typo, long lines, and incorrect #Supported anchor. Remove dead weng-lab.github.io color link in 12 ENCODE4 track HTML files. Fix "paraythroid" to "parathyroid" in 3 HTML files and wgEncodeReg4.ra labels. Break long lines in credits sections and availability paragraphs across hg38 and mm10 track HTML files. Replace nonexistent #Supported anchor with FAQ/FAQformat.html in contribTracks.html. refs #37315
  • lines changed 6, context: html, text, full: html, text
    a1e8bd10892f1d84b1a9a16ddadc3a6ee3f01038 Tue Apr 7 11:22:52 2026 -0700
    Fix production lab credits to be assay-specific for ENCODE4 multiWig tracks. refs #34923 Each multiWig HTML page was using the full 13-lab Epigenetics list instead of the assay-specific production labs from the hub. Updated DNase, ATAC, H3K4me3, H3K27ac, and CTCF credits for hg38, and ATAC, H3K4me3, H3K27ac, and CTCF for mm10 to match the hub's per-assay credits.
  • lines changed 3, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k4me3.html
  • lines changed 11, context: html, text, full: html, text
    2059ffca9a9b74cd5ba9632a5835ae47d213b594 Tue Apr 7 11:04:02 2026 -0700
    Address CR feedback from #37315: fix broken color link, paraythroid typo, long lines, and incorrect #Supported anchor. Remove dead weng-lab.github.io color link in 12 ENCODE4 track HTML files. Fix "paraythroid" to "parathyroid" in 3 HTML files and wgEncodeReg4.ra labels. Break long lines in credits sections and availability paragraphs across hg38 and mm10 track HTML files. Replace nonexistent #Supported anchor with FAQ/FAQformat.html in contribTracks.html. refs #37315
  • lines changed 6, context: html, text, full: html, text
    a1e8bd10892f1d84b1a9a16ddadc3a6ee3f01038 Tue Apr 7 11:22:52 2026 -0700
    Fix production lab credits to be assay-specific for ENCODE4 multiWig tracks. refs #34923 Each multiWig HTML page was using the full 13-lab Epigenetics list instead of the assay-specific production labs from the hub. Updated DNase, ATAC, H3K4me3, H3K27ac, and CTCF credits for hg38, and ATAC, H3K4me3, H3K27ac, and CTCF for mm10 to match the hub's per-assay credits.
  • lines changed 3, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.ra
  • lines changed 11, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.html
  • lines changed 4, context: html, text, full: html, text
    2059ffca9a9b74cd5ba9632a5835ae47d213b594 Tue Apr 7 11:04:02 2026 -0700
    Address CR feedback from #37315: fix broken color link, paraythroid typo, long lines, and incorrect #Supported anchor. Remove dead weng-lab.github.io color link in 12 ENCODE4 track HTML files. Fix "paraythroid" to "parathyroid" in 3 HTML files and wgEncodeReg4.ra labels. Break long lines in credits sections and availability paragraphs across hg38 and mm10 track HTML files. Replace nonexistent #Supported anchor with FAQ/FAQformat.html in contribTracks.html. refs #37315
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.ra
  • lines changed 24622, context: html, text, full: html, text
    dd40846f55b0cb21d346f2edbe51936f04007bb2 Tue Apr 7 11:07:15 2026 -0700
    Adding peak+signal data and new organ subtracks to hg38 ENCODE4 Regulation. refs #34923 Epigenetics composite: added 3,154 bigBed peak subtracks (was signal-only), composite type changed from bigWig to bed 3, Data Type facet added. TF ChIP composite: added 2,462 bigWig signal subtracks (was peak-only), composite type changed from bigBed 5 to bed 3, Data Type facet added. MultiWig organ-averaged tracks: added 15 new organ subtracks across ATAC (+2), H3K4me3 (+3), H3K27ac (+4), CTCF (+6). Updated bone marrow tissue-only subtracks for H3K4me3 and H3K27ac to use new separate tp. data files.
  • lines changed 18, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfPeaks.html
  • lines changed 5, context: html, text, full: html, text
    2059ffca9a9b74cd5ba9632a5835ae47d213b594 Tue Apr 7 11:04:02 2026 -0700
    Address CR feedback from #37315: fix broken color link, paraythroid typo, long lines, and incorrect #Supported anchor. Remove dead weng-lab.github.io color link in 12 ENCODE4 track HTML files. Fix "paraythroid" to "parathyroid" in 3 HTML files and wgEncodeReg4.ra labels. Break long lines in credits sections and availability paragraphs across hg38 and mm10 track HTML files. Replace nonexistent #Supported anchor with FAQ/FAQformat.html in contribTracks.html. refs #37315
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Txn.html
  • lines changed 6, context: html, text, full: html, text
    2059ffca9a9b74cd5ba9632a5835ae47d213b594 Tue Apr 7 11:04:02 2026 -0700
    Address CR feedback from #37315: fix broken color link, paraythroid typo, long lines, and incorrect #Supported anchor. Remove dead weng-lab.github.io color link in 12 ENCODE4 track HTML files. Fix "paraythroid" to "parathyroid" in 3 HTML files and wgEncodeReg4.ra labels. Break long lines in credits sections and availability paragraphs across hg38 and mm10 track HTML files. Replace nonexistent #Supported anchor with FAQ/FAQformat.html in contribTracks.html. refs #37315
  • lines changed 3, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/human/hg7/affyTranscriptome.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hgIkmc.html
  • lines changed 3, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/hs1/ncbiRefSeq.trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/refSeqComposite.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/snpArray.html
  • lines changed 3, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/snpMap.html
  • lines changed 3, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/human/wgRnaOld.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/joinedRmsk.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/lamprey/petMar1/multiz6way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/lancelet/braFlo1/multiz5way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/lizard/anoCar2/cons7way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/marmoset/calJac4/customRefSeqComposite.ra
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/medaka/oryLat2/multiz5way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mgcOrfeomeMrna.html
  • lines changed 4, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/moleRat/hetGla1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/moleRat/hetGla2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/igtc.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/ikmc.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html
  • lines changed 6, context: html, text, full: html, text
    c1e2ffdb7a237a98ecf0816d2f0a7572da953410 Wed Apr 8 17:10:49 2026 -0700
    Updating the mm10 ENCODE4 cCREs track description page: added Core Collection link and add score threshold description. Updated max-Z mouseOver casing. refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/cons4way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/mm10/encode.cCREs.override.ra
  • lines changed 1, context: html, text, full: html, text
    c1e2ffdb7a237a98ecf0816d2f0a7572da953410 Wed Apr 8 17:10:49 2026 -0700
    Updating the mm10 ENCODE4 cCREs track description page: added Core Collection link and add score threshold description. Updated max-Z mouseOver casing. refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/encode3RenAtac.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/mm10/encode3RenChromHmm.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.html
  • lines changed 1, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.ra
  • lines changed 7, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegAtac.html
  • lines changed 9, context: html, text, full: html, text
    2059ffca9a9b74cd5ba9632a5835ae47d213b594 Tue Apr 7 11:04:02 2026 -0700
    Address CR feedback from #37315: fix broken color link, paraythroid typo, long lines, and incorrect #Supported anchor. Remove dead weng-lab.github.io color link in 12 ENCODE4 track HTML files. Fix "paraythroid" to "parathyroid" in 3 HTML files and wgEncodeReg4.ra labels. Break long lines in credits sections and availability paragraphs across hg38 and mm10 track HTML files. Replace nonexistent #Supported anchor with FAQ/FAQformat.html in contribTracks.html. refs #37315
  • lines changed 1, context: html, text, full: html, text
    a1e8bd10892f1d84b1a9a16ddadc3a6ee3f01038 Tue Apr 7 11:22:52 2026 -0700
    Fix production lab credits to be assay-specific for ENCODE4 multiWig tracks. refs #34923 Each multiWig HTML page was using the full 13-lab Epigenetics list instead of the assay-specific production labs from the hub. Updated DNase, ATAC, H3K4me3, H3K27ac, and CTCF credits for hg38, and ATAC, H3K4me3, H3K27ac, and CTCF for mm10 to match the hub's per-assay credits.
  • lines changed 3, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegDnase.html
  • lines changed 8, context: html, text, full: html, text
    2059ffca9a9b74cd5ba9632a5835ae47d213b594 Tue Apr 7 11:04:02 2026 -0700
    Address CR feedback from #37315: fix broken color link, paraythroid typo, long lines, and incorrect #Supported anchor. Remove dead weng-lab.github.io color link in 12 ENCODE4 track HTML files. Fix "paraythroid" to "parathyroid" in 3 HTML files and wgEncodeReg4.ra labels. Break long lines in credits sections and availability paragraphs across hg38 and mm10 track HTML files. Replace nonexistent #Supported anchor with FAQ/FAQformat.html in contribTracks.html. refs #37315
  • lines changed 6, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra
  • lines changed 40, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkCtcf.html
  • lines changed 8, context: html, text, full: html, text
    2059ffca9a9b74cd5ba9632a5835ae47d213b594 Tue Apr 7 11:04:02 2026 -0700
    Address CR feedback from #37315: fix broken color link, paraythroid typo, long lines, and incorrect #Supported anchor. Remove dead weng-lab.github.io color link in 12 ENCODE4 track HTML files. Fix "paraythroid" to "parathyroid" in 3 HTML files and wgEncodeReg4.ra labels. Break long lines in credits sections and availability paragraphs across hg38 and mm10 track HTML files. Replace nonexistent #Supported anchor with FAQ/FAQformat.html in contribTracks.html. refs #37315
  • lines changed 3, context: html, text, full: html, text
    a1e8bd10892f1d84b1a9a16ddadc3a6ee3f01038 Tue Apr 7 11:22:52 2026 -0700
    Fix production lab credits to be assay-specific for ENCODE4 multiWig tracks. refs #34923 Each multiWig HTML page was using the full 13-lab Epigenetics list instead of the assay-specific production labs from the hub. Updated DNase, ATAC, H3K4me3, H3K27ac, and CTCF credits for hg38, and ATAC, H3K4me3, H3K27ac, and CTCF for mm10 to match the hub's per-assay credits.
  • lines changed 3, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k27ac.html
  • lines changed 8, context: html, text, full: html, text
    2059ffca9a9b74cd5ba9632a5835ae47d213b594 Tue Apr 7 11:04:02 2026 -0700
    Address CR feedback from #37315: fix broken color link, paraythroid typo, long lines, and incorrect #Supported anchor. Remove dead weng-lab.github.io color link in 12 ENCODE4 track HTML files. Fix "paraythroid" to "parathyroid" in 3 HTML files and wgEncodeReg4.ra labels. Break long lines in credits sections and availability paragraphs across hg38 and mm10 track HTML files. Replace nonexistent #Supported anchor with FAQ/FAQformat.html in contribTracks.html. refs #37315
  • lines changed 4, context: html, text, full: html, text
    a1e8bd10892f1d84b1a9a16ddadc3a6ee3f01038 Tue Apr 7 11:22:52 2026 -0700
    Fix production lab credits to be assay-specific for ENCODE4 multiWig tracks. refs #34923 Each multiWig HTML page was using the full 13-lab Epigenetics list instead of the assay-specific production labs from the hub. Updated DNase, ATAC, H3K4me3, H3K27ac, and CTCF credits for hg38, and ATAC, H3K4me3, H3K27ac, and CTCF for mm10 to match the hub's per-assay credits.
  • lines changed 3, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k4me3.html
  • lines changed 8, context: html, text, full: html, text
    2059ffca9a9b74cd5ba9632a5835ae47d213b594 Tue Apr 7 11:04:02 2026 -0700
    Address CR feedback from #37315: fix broken color link, paraythroid typo, long lines, and incorrect #Supported anchor. Remove dead weng-lab.github.io color link in 12 ENCODE4 track HTML files. Fix "paraythroid" to "parathyroid" in 3 HTML files and wgEncodeReg4.ra labels. Break long lines in credits sections and availability paragraphs across hg38 and mm10 track HTML files. Replace nonexistent #Supported anchor with FAQ/FAQformat.html in contribTracks.html. refs #37315
  • lines changed 4, context: html, text, full: html, text
    a1e8bd10892f1d84b1a9a16ddadc3a6ee3f01038 Tue Apr 7 11:22:52 2026 -0700
    Fix production lab credits to be assay-specific for ENCODE4 multiWig tracks. refs #34923 Each multiWig HTML page was using the full 13-lab Epigenetics list instead of the assay-specific production labs from the hub. Updated DNase, ATAC, H3K4me3, H3K27ac, and CTCF credits for hg38, and ATAC, H3K4me3, H3K27ac, and CTCF for mm10 to match the hub's per-assay credits.
  • lines changed 3, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.ra
  • lines changed 7, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra
  • lines changed 20, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegTxn.html
  • lines changed 9, context: html, text, full: html, text
    2059ffca9a9b74cd5ba9632a5835ae47d213b594 Tue Apr 7 11:04:02 2026 -0700
    Address CR feedback from #37315: fix broken color link, paraythroid typo, long lines, and incorrect #Supported anchor. Remove dead weng-lab.github.io color link in 12 ENCODE4 track HTML files. Fix "paraythroid" to "parathyroid" in 3 HTML files and wgEncodeReg4.ra labels. Break long lines in credits sections and availability paragraphs across hg38 and mm10 track HTML files. Replace nonexistent #Supported anchor with FAQ/FAQformat.html in contribTracks.html. refs #37315
  • lines changed 3, context: html, text, full: html, text
    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/mouse/mm10/refSeqComposite.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/mm10/strainSNPs.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.alpha.ra
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    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/mouse/mm2/genieAlt.html
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    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/mm39/cons35way.html
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    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/mm39/refSeqComposite.html
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    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/mm4/description.html
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    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/mm7/multiz17way.html
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    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/mm8/multiz17way.html
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    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
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    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/mm9/exoniphy.html
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    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/mm9/miRNAMay2008.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/mm9/multiz30way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/refSeqComposite.mm10.mm39.ra
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    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/rikenCageCtss.html
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    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouse/rikenCageTc.html
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    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/mouseLemur/micMur3/cons3way.html
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    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/opossum/monDom4/multiz7way.html
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    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/opossum/monDom5/multiz9way.html
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    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/opossum/multiz5way.html
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    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/orangutan/ponAbe2/multiz8way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/orfeomeMrna.html
  • lines changed 4, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/other/repeats2/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/platypus/ornAna1/multiz6way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/rat/regenRn1/cons7way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/rat/rn1/ensRatMusHom.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/rat/rn4/multiz9way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/rat/rn5/cons13way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/rat/rn6/cons20way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/rat/rn8/genArk.trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/refSeqComposite.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/refSeqComposite.ra
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/relatedTracks.ra
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    0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
    Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923 hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data. The Weng lab fixed a bug where both variants pointed to the same file. Now 83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files, 80 former fake tissue-only subtracks converted to all-biosamples, and the DNase nose organ added / lymphoid tissue all-biosamples removed to match hub. Default subtracks changed from cell lines to tissue samples per Weng lab request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks. Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166), mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added ENCODE color mapping wiki link to all 12 multiWig HTML description pages. Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison). mm10 supertrack developer list corrected (removed Greg Andrews per hub). ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
• src/hg/makeDb/trackDb/rhesus/rheMac10/rhesusSNVs.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/sacCer/multizYeast.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/sacCer/sacCer2/multiz7way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/sacCer/sacCer3/multiz7way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/saiBol/saiBol1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/snp.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/stickleback/gasAcu1/multiz8way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    7d149b1935f8a1e5f11f31f3cb8da99d31b3a8e6 Fri Apr 10 16:34:48 2026 -0700
    Replaced handrolled JSON structure in faceted composite output from hgTrackUi with jsonWrite.h library-generated version, and added a defaultSortField trackDb setting to faceted composites to improve the subtrack presentation order, refs #36320
• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons17way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons20way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/treeShrew/tupChi1/cons4way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/treeShrew/tupChi1/cons5way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/virus/wuhCor1/cons119way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/virus/wuhCor1/cons44way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/virus/wuhCor1/cons7way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/virus/wuhCor1/sarsCov2Phylo.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/virus/wuhCor1/sarsCov2PhyloPub.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/worm/ce10/cons7way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/worm/ce10/cons9way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/worm/ce11/cons135way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/worm/ce11/cons26way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/worm/ce2/c_briggsae_pwMaf.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/worm/ce4/multiz5way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/worm/ce6/multiz6way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/xenTro/xenTro2/multiz7way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/xenTro/xenTro9/cons11way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/zebrafish/danRer1/affyZebrafish.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/zebrafish/danRer10/cons12way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/zebrafish/danRer12/genArk.trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/zebrafish/danRer2/affyZebrafish.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/zebrafish/danRer3/multiz5way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/zebrafish/danRer4/ensGeneNonCoding.html
  • lines changed 1, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/zebrafish/danRer4/multiz7way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/zebrafish/danRer4/rhMap.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/zebrafish/danRer5/affyConsensusAndTargetZonWildType.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/makeDb/trackDb/zebrafish/danRer7/cons8way.html
  • lines changed 2, context: html, text, full: html, text
    089c09e98db52e92da694ab1a0c8891c1a7fd3e8 Thu Apr 2 15:50:07 2026 -0700
    Fix broken external links in trackDb HTML docs found by uiLinks cron (2026-03-23 run). Updated 261 trackDb HTML and .ra files: - Fixed 404s: replaced dead URLs (sequenceontology.org wiki, compgen.cshl.edu PDFs, chori.org, PolyPhen v1, uswest.ensembl.org, RIKEN GSC) with current locations; removed links for defunct sites (snpdata.cshl.edu, zfrhmaps, renlab encode3 download, oia.gachon.ac.kr, phylohmm.pdf across 92 conservation track docs). - Fixed 301s: updated http→https (encodeproject.org, flybase.org, gene-regulation.com, drive5.com/muscle, microbesonline.org/fasttree, brain-map.org); updated moved domains (blackwell-synergy→wiley, genome.cshlp.org path fix, sanger.ac.uk path fix); removed hijacked domains (seqll.com, orfeomecollaboration.org, farnhamlab.com). - Fixed 302s: updated http→https (ensembl.org, affymetrix.com, asntech.org, cdna.eva.mpg.de, arcseqhub.com); updated moved domains (dfam.janelia.org→dfam.org, hmmer.janelia.org→hmmer.org, immuneepitope.org→iedb.org, ensembl variation path). No RM.
• src/hg/ratStuff/mafAddIRows/makefile
  • lines changed 3, context: html, text, full: html, text
    e8258c11259af202782b3c2bb62198cc55a3e2f1 Tue Apr 7 12:59:16 2026 -0700
    add testing in preparation for a new program to replace this one - these tests are the same for the new command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRows/tests/expected/expected.maf
  • lines changed 31, context: html, text, full: html, text
    e8258c11259af202782b3c2bb62198cc55a3e2f1 Tue Apr 7 12:59:16 2026 -0700
    add testing in preparation for a new program to replace this one - these tests are the same for the new command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRows/tests/expected/expectedGC.maf
  • lines changed 31, context: html, text, full: html, text
    e8258c11259af202782b3c2bb62198cc55a3e2f1 Tue Apr 7 12:59:16 2026 -0700
    add testing in preparation for a new program to replace this one - these tests are the same for the new command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRows/tests/input/input.2bit
  • lines changed 0, context: html, text, full: html, text
    e8258c11259af202782b3c2bb62198cc55a3e2f1 Tue Apr 7 12:59:16 2026 -0700
    add testing in preparation for a new program to replace this one - these tests are the same for the new command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRows/tests/input/input.maf
  • lines changed 16, context: html, text, full: html, text
    e8258c11259af202782b3c2bb62198cc55a3e2f1 Tue Apr 7 12:59:16 2026 -0700
    add testing in preparation for a new program to replace this one - these tests are the same for the new command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRows/tests/input/inputGC.maf
  • lines changed 16, context: html, text, full: html, text
    e8258c11259af202782b3c2bb62198cc55a3e2f1 Tue Apr 7 12:59:16 2026 -0700
    add testing in preparation for a new program to replace this one - these tests are the same for the new command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRows/tests/makefile
  • lines changed 20, context: html, text, full: html, text
    e8258c11259af202782b3c2bb62198cc55a3e2f1 Tue Apr 7 12:59:16 2026 -0700
    add testing in preparation for a new program to replace this one - these tests are the same for the new command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRowsStream/makefile
  • lines changed 3, context: html, text, full: html, text
    1b7d4ae05dffff0eeb67deac21f445816ad4e21d Tue Apr 7 13:02:32 2026 -0700
    add testing for this new program to replace mafAddIRows - this has been exhaustedly tested with full runs on hs1 and hg38 Tb of data input and output, identical to mafAddIRows - these tests are the same for the new and previous command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRowsStream/tests/expected/expected.maf
  • lines changed 31, context: html, text, full: html, text
    1b7d4ae05dffff0eeb67deac21f445816ad4e21d Tue Apr 7 13:02:32 2026 -0700
    add testing for this new program to replace mafAddIRows - this has been exhaustedly tested with full runs on hs1 and hg38 Tb of data input and output, identical to mafAddIRows - these tests are the same for the new and previous command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRowsStream/tests/expected/expectedGC.maf
  • lines changed 31, context: html, text, full: html, text
    1b7d4ae05dffff0eeb67deac21f445816ad4e21d Tue Apr 7 13:02:32 2026 -0700
    add testing for this new program to replace mafAddIRows - this has been exhaustedly tested with full runs on hs1 and hg38 Tb of data input and output, identical to mafAddIRows - these tests are the same for the new and previous command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRowsStream/tests/input/input.2bit
  • lines changed 0, context: html, text, full: html, text
    1b7d4ae05dffff0eeb67deac21f445816ad4e21d Tue Apr 7 13:02:32 2026 -0700
    add testing for this new program to replace mafAddIRows - this has been exhaustedly tested with full runs on hs1 and hg38 Tb of data input and output, identical to mafAddIRows - these tests are the same for the new and previous command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRowsStream/tests/input/input.maf
  • lines changed 16, context: html, text, full: html, text
    1b7d4ae05dffff0eeb67deac21f445816ad4e21d Tue Apr 7 13:02:32 2026 -0700
    add testing for this new program to replace mafAddIRows - this has been exhaustedly tested with full runs on hs1 and hg38 Tb of data input and output, identical to mafAddIRows - these tests are the same for the new and previous command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRowsStream/tests/input/inputGC.maf
  • lines changed 16, context: html, text, full: html, text
    1b7d4ae05dffff0eeb67deac21f445816ad4e21d Tue Apr 7 13:02:32 2026 -0700
    add testing for this new program to replace mafAddIRows - this has been exhaustedly tested with full runs on hs1 and hg38 Tb of data input and output, identical to mafAddIRows - these tests are the same for the new and previous command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRowsStream/tests/makefile
  • lines changed 20, context: html, text, full: html, text
    1b7d4ae05dffff0eeb67deac21f445816ad4e21d Tue Apr 7 13:02:32 2026 -0700
    add testing for this new program to replace mafAddIRows - this has been exhaustedly tested with full runs on hs1 and hg38 Tb of data input and output, identical to mafAddIRows - these tests are the same for the new and previous command, as suggested by claude refs #34370
• src/hg/ratStuff/makefile
  • lines changed 1, context: html, text, full: html, text
    94b4f059748ac6676cac1a7c9096b4d9cc138142 Tue Apr 7 13:04:32 2026 -0700
    adding mafAddIRowsStream to the utils output - more efficient version of mafAddIRows - refs #34370
• src/hg/utils/otto/lrg/bigPsl+6.as
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    ca1f5d4b6f57481b8468c77dc40a65f9eb4ec029 Wed Apr 8 14:57:47 2026 -0700
    Fix bigPsl.as documentation: say "other sequence" not "other chromosome", add PSL field names, refs #37155 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/utils/otto/uniprot/bigPslUniprot.as
  • lines changed 6, context: html, text, full: html, text
    ca1f5d4b6f57481b8468c77dc40a65f9eb4ec029 Wed Apr 8 14:57:47 2026 -0700
    Fix bigPsl.as documentation: say "other sequence" not "other chromosome", add PSL field names, refs #37155 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/product/installer/browserSetup.sh
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    b65520b87b2f80ac7fd537e8c361223d0a9dc72d Thu Apr 9 01:42:08 2026 -0700
    fixing various gbic issues found by Theo/Jorge and Claude code review, no redmine
  • lines changed 1, context: html, text, full: html, text
    fdded708bc8405da6d0ff43d42f0092a872a0a97 Fri Apr 10 01:51:06 2026 -0700
    fixing dumb bug in install script, no redmine
• src/utils/qa/mlqAutomate.py
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    833be021d3df3caba9a3ef6e2a6ceb9d41e2162b Sat Apr 11 12:45:32 2026 -0700
    Increase Anthropic API retry resilience in mlqAutomate. Retries now wait longer (5s/15s/45s/135s instead of 2s/4s/8s) to ride out transient 529 overload errors. If retries are still exhausted, the script logs a clear error message and skips the affected emails instead of crashing, so the next cron run picks them up. refs #36801
• src/utils/redmineCli
  • lines changed 187, context: html, text, full: html, text
    9745b5b84a513b8fc527081b47f416884a0aad5f Tue Apr 7 14:57:14 2026 -0700
    Add relate, watch, and users subcommands to redmineCli, refs #37339 - `relate`: create relations between two or more tickets - `watch`: add watchers to a ticket by name - `users`: list project members with short names and IDs - Expand user ID table from 5 hardcoded MLQ members to all 42 project members Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 36, context: html, text, full: html, text
    427905a00dc6799d3c8d750de5d9376bccc3c972 Thu Apr 9 15:49:33 2026 -0700
    Add tracker name resolution to redmineCli list command, refs #37339 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

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• files changed: 475