All File Changes

v496_preview2 to v496_base (2026-03-23 to 2026-03-30) v496

• docs/genomeBrowserGlossary.md
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    e76b0018bb4c574f92f691f1594e85cbf7a7b3f0 Tue Mar 24 08:31:10 2026 -0700
    minor tweaks based on CR, refs #37250
• docs/index.md
  • lines changed 118, context: html, text, full: html, text
    3b9272e66fdac648a90baf02dc5eb696a286fdf1 Sat Mar 28 16:06:45 2026 -0700
    revamping page, refs #36894
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 18, context: html, text, full: html, text
    a7d3d4f35aebfbbc6d974796fb107cd3e64c1470 Wed Mar 25 11:34:26 2026 -0700
    Standardizing end Q2 to June 30th rather than July 1st 07-01 -> 06-30
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    862aa45f4c9d8dd0703955b3ab7d94e7476e5cbc Wed Mar 25 12:07:54 2026 -0700
    Adding Yale Year 4 updates (may change) up until 2027Q2 end (03-31)
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    8336f592bdb0158573034c2e4432f3a5548528cf Wed Mar 25 12:26:08 2026 -0700
    Adding 27 Q2 - 28 Q1 Yale Budget Year 5 plans - %% to surpress timeline impact
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    9ab37a5c7846963ba7f24a36d5b4c7f49e306fda Thu Mar 26 07:46:38 2026 -0700
    Code Review changes per browser-code-reviews-group
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    db1a018d321ef17cfadb24ed5f990f30135efc0d Thu Mar 26 07:50:02 2026 -0700
    Fixing source 20026 typo from ADGCs (directly copied from their milestones) -found in code review.
• src/hg/hgConvert/hgConvert.c
  • lines changed 11, context: html, text, full: html, text
    b5820fe28821425cd0703ba4d92bfb36d7abb8e6 Wed Mar 25 13:43:40 2026 -0700
    Fix hgConvert for genark toDb selections. Previously the toDb cgi variable was in a <select>, and so choosing a genark search result that wasn't in the pre-existing select submits the form with the old value. Now the <select> gets a separate variable name, and on choosing a result the toDb variable is updated appropriately. Also fix weird default chain selection, if the toDb is explicitly provided, then choose that chain if it exists rather than scoring all of them to find a 'default' choice, refs Braney email
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    3b7a323713edb0adefb48de6a5fc81e8265e4067 Sat Mar 28 11:22:26 2026 -0700
    Adding a QuickLift documentation link to the Notes sectiono on hgConvert, refs #36111
  • lines changed 1, context: html, text, full: html, text
    92b041beb28db2fb2fd2fe016c07b1b351a1c57b Sat Mar 28 13:40:36 2026 -0700
    Capitalize QuickLift in hgConvert error message, refs #35536
• src/hg/hgFetch/hgFetch.c
  • lines changed 141, context: html, text, full: html, text
    eb076410a62ea6a94b71358424080af261ba2c25 Thu Mar 26 03:20:14 2026 -0700
    Moved hgFetch into hgTrackUi; added etags, Cache-Control directives, and GET use instead of POST when udcTimeout isn't set, all to support browser caching of remote files; bumped the DataTables version for facetedComposite to facilitate making all the checkboxes have a consistent look; refs #36320
• src/hg/hgFetch/makefile
  • lines changed 18, context: html, text, full: html, text
    eb076410a62ea6a94b71358424080af261ba2c25 Thu Mar 26 03:20:14 2026 -0700
    Moved hgFetch into hgTrackUi; added etags, Cache-Control directives, and GET use instead of POST when udcTimeout isn't set, all to support browser caching of remote files; bumped the DataTables version for facetedComposite to facilitate making all the checkboxes have a consistent look; refs #36320
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 13, context: html, text, full: html, text
    1b1a0aa39ffd5c18dbb425fca096ea335ed154fe Wed Mar 25 06:42:39 2026 -0700
    superTrack hgTrackUi: auto-hide when all children hidden, grey dropdown on hide refs #37282 Route button clicks through superT.selChanged() by triggering the dropdown change event instead of just setting its value. This fixes three problems: (1) hiding all subtracks now auto-hides the superTrack container (matching composite track behavior), (2) the superTrack show/hide dropdown greys out when set to hide, and (3) clicking Hide on a subtrack no longer forces the superTrack to show. This makes the code actually simpler. I didn't know about selChanged() when I wrote the new superTrack code. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    f12abfa6cad0164a03d39d3968986874a8c9a6b8 Wed Mar 25 16:58:16 2026 -0700
    same change to track Ui to indicate how to get the data for the gcOnFly synthetic track refs #35958
  • lines changed 12, context: html, text, full: html, text
    e09c0d375e198e5c74164dbbbb4010a57bf13607 Wed Mar 25 17:44:45 2026 -0700
    correct UI operation on the synthetic bigWig gcOnFly track refs #35958
  • lines changed 146, context: html, text, full: html, text
    eb076410a62ea6a94b71358424080af261ba2c25 Thu Mar 26 03:20:14 2026 -0700
    Moved hgFetch into hgTrackUi; added etags, Cache-Control directives, and GET use instead of POST when udcTimeout isn't set, all to support browser caching of remote files; bumped the DataTables version for facetedComposite to facilitate making all the checkboxes have a consistent look; refs #36320
  • lines changed 4, context: html, text, full: html, text
    1a3400408892585e530f10d4b8c4b612f29e9473 Thu Mar 26 04:18:29 2026 -0700
    Adding parent link to UI for faceted composites in supertracks, refs #36320
  • lines changed 11, context: html, text, full: html, text
    bab95ebb424257082cb7fc62ae902e3e7218ddf6 Thu Mar 26 11:55:08 2026 -0700
    Adding description link to the light-blue 'title bar' in the faceted composite UI, refs #36320
  • lines changed 25, context: html, text, full: html, text
    956500207b58c263485009212f223836152176d3 Thu Mar 26 14:58:55 2026 -0700
    simplify the gcOnFly track - it does not need to by completely synthetic - it only comes in from trackDb stanzas refs #35958
  • lines changed 8, context: html, text, full: html, text
    3999034fa7f906054a5201e366d5e1c0b5193ff1 Sat Mar 28 11:06:45 2026 -0700
    Small code cleanup after moving hgFetch into hgTrackUi, refs #36320
  • lines changed 1, context: html, text, full: html, text
    4b47e4b865baf8944946c660f621fbbca0b74bee Sun Mar 29 08:51:43 2026 -0700
    Restoring line from over-ambitious cleanup. Turns out you still need variable definitions. refs #36320
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    2ca5303deabc42182eae8cb7f49c2c8e9784eabf Mon Mar 30 09:30:45 2026 -0700
    Added an error message for when the metadata file is missing for a faceted composite, refs #36320
• src/hg/hgTracks/bigWigTrack.c
  • lines changed 4, context: html, text, full: html, text
    a513cccc30dd0697dc78935f51a636e52a0793f0 Mon Mar 23 16:36:04 2026 -0700
    manage gcOnFly track regarding sessions refs #35958
  • lines changed 4, context: html, text, full: html, text
    6195179b836111bd4a82ae5f5c73b2f8d36e7abb Mon Mar 23 17:58:36 2026 -0700
    more simple vis restoration for gcOnFly no need for all the rigamerol refs #35958
  • lines changed 29, context: html, text, full: html, text
    1e04d78b65b35678e80d9f5929e6fec0f7b2fbbb Tue Mar 24 13:32:54 2026 -0700
    refactor the GC on fly calculation to move into a library function rfefs #35958
  • lines changed 4, context: html, text, full: html, text
    ab5f6fcc68340efac0c30cd90058d083594943ef Tue Mar 24 15:00:46 2026 -0700
    correctly manage gcOnFly visibility from click to click refs #35958
  • lines changed 10, context: html, text, full: html, text
    c3bb4207fb2a58064b937ba9fef1cc11852f7576 Wed Mar 25 10:48:49 2026 -0700
    allow trackDb entry to override the in-code defaults of the gcOnFly track refs #35958
  • lines changed 7, context: html, text, full: html, text
    4fd52b1b34d170c15d3aacfeaf4fbb26fff224b1 Wed Mar 25 12:52:00 2026 -0700
    fix bugs for chrom size at 2^31 and manage partial computation windows at beginning or end of drawing window for gcOnFly refs #35958
  • lines changed 58, context: html, text, full: html, text
    956500207b58c263485009212f223836152176d3 Thu Mar 26 14:58:55 2026 -0700
    simplify the gcOnFly track - it does not need to by completely synthetic - it only comes in from trackDb stanzas refs #35958
• src/hg/hgTracks/hgTracks.c
  • lines changed 12, context: html, text, full: html, text
    a513cccc30dd0697dc78935f51a636e52a0793f0 Mon Mar 23 16:36:04 2026 -0700
    manage gcOnFly track regarding sessions refs #35958
  • lines changed 12, context: html, text, full: html, text
    6195179b836111bd4a82ae5f5c73b2f8d36e7abb Mon Mar 23 17:58:36 2026 -0700
    more simple vis restoration for gcOnFly no need for all the rigamerol refs #35958
  • lines changed 3, context: html, text, full: html, text
    ab5f6fcc68340efac0c30cd90058d083594943ef Tue Mar 24 15:00:46 2026 -0700
    correctly manage gcOnFly visibility from click to click refs #35958
  • lines changed 11, context: html, text, full: html, text
    c3bb4207fb2a58064b937ba9fef1cc11852f7576 Wed Mar 25 10:48:49 2026 -0700
    allow trackDb entry to override the in-code defaults of the gcOnFly track refs #35958
  • lines changed 35, context: html, text, full: html, text
    956500207b58c263485009212f223836152176d3 Thu Mar 26 14:58:55 2026 -0700
    simplify the gcOnFly track - it does not need to by completely synthetic - it only comes in from trackDb stanzas refs #35958
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    a513cccc30dd0697dc78935f51a636e52a0793f0 Mon Mar 23 16:36:04 2026 -0700
    manage gcOnFly track regarding sessions refs #35958
  • lines changed 3, context: html, text, full: html, text
    6195179b836111bd4a82ae5f5c73b2f8d36e7abb Mon Mar 23 17:58:36 2026 -0700
    more simple vis restoration for gcOnFly no need for all the rigamerol refs #35958
  • lines changed 3, context: html, text, full: html, text
    ab5f6fcc68340efac0c30cd90058d083594943ef Tue Mar 24 15:00:46 2026 -0700
    correctly manage gcOnFly visibility from click to click refs #35958
  • lines changed 6, context: html, text, full: html, text
    c3bb4207fb2a58064b937ba9fef1cc11852f7576 Wed Mar 25 10:48:49 2026 -0700
    allow trackDb entry to override the in-code defaults of the gcOnFly track refs #35958
  • lines changed 6, context: html, text, full: html, text
    956500207b58c263485009212f223836152176d3 Thu Mar 26 14:58:55 2026 -0700
    simplify the gcOnFly track - it does not need to by completely synthetic - it only comes in from trackDb stanzas refs #35958
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    4ae8ea2a6a2bf765c62f1f12c35297e451419188 Tue Mar 24 11:53:43 2026 -0700
    exclude bigRmsk from canWiggle() to prevent crash when forceWiggle triggers, fixes #37229 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    12acd6f89f143e83dff59120d75d6111c9f8a4bc Thu Mar 26 10:25:57 2026 -0700
    quickLiftChain tracks don't wiggle. Fixes #36514
• src/hg/hgc/bigBedClick.c
  • lines changed 148, context: html, text, full: html, text
    ddb85ced5e8b6127a233b5cda5fcb1fbe2260578 Wed Mar 25 04:22:06 2026 -0700
    Add detailsScript trackDb mechanism for JS visualizations on bigBed details pages Changing based on feedback from Jonathan, Chris and Brian after group discussion. Refactored existing Claude-generated code, moving functions into libraries. This is the first use of ES6 modules in the kent js code. In 2026, this should be acceptable? New trackDb syntax: detailsScript.<plotType>.<fieldName> <jsonConfig> The C code (bigBedClick.c) collects these settings, exports field values as JSON (bedDetails object), and dynamically imports hgc.<plotType>.js as an ES6 module. Fields used by detailsScript are shown in the HTML table with empty values, filled by JavaScript. Includes hgc.histogram.js module for drawing SVG bar chart histograms from logfmt-encoded data (space-separated key=value pairs). Applied to both the trexplorer and webstr tracks in the strVar supertrack. Also adds jsonWriteJsonElement() helper to jsonWrite.c for writing parsed jsonElement trees into a jsonWrite stream. max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    2694cffb31b95f1729b2d8c5252e406e66a5e61d Thu Mar 26 02:18:25 2026 -0700
    changes after AI code review
• src/hg/hgc/hgc.c
  • lines changed 16, context: html, text, full: html, text
    2fc33abc4c89f2ca1881911666b7dbea8b6ae343 Tue Mar 24 15:05:26 2026 -0700
    refactor the GC on fly calculation to move into a library function rfefs #35958
  • lines changed 28, context: html, text, full: html, text
    ddb85ced5e8b6127a233b5cda5fcb1fbe2260578 Wed Mar 25 04:22:06 2026 -0700
    Add detailsScript trackDb mechanism for JS visualizations on bigBed details pages Changing based on feedback from Jonathan, Chris and Brian after group discussion. Refactored existing Claude-generated code, moving functions into libraries. This is the first use of ES6 modules in the kent js code. In 2026, this should be acceptable? New trackDb syntax: detailsScript.<plotType>.<fieldName> <jsonConfig> The C code (bigBedClick.c) collects these settings, exports field values as JSON (bedDetails object), and dynamically imports hgc.<plotType>.js as an ES6 module. Fields used by detailsScript are shown in the HTML table with empty values, filled by JavaScript. Includes hgc.histogram.js module for drawing SVG bar chart histograms from logfmt-encoded data (space-separated key=value pairs). Applied to both the trexplorer and webstr tracks in the strVar supertrack. Also adds jsonWriteJsonElement() helper to jsonWrite.c for writing parsed jsonElement trees into a jsonWrite stream. max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 21, context: html, text, full: html, text
    cc54e8ee46e408773d86ab0492d5aed3244baff6 Wed Mar 25 14:59:21 2026 -0700
    provide data access instruction for gcOnFly track data refs #35958
  • lines changed 1, context: html, text, full: html, text
    956500207b58c263485009212f223836152176d3 Thu Mar 26 14:58:55 2026 -0700
    simplify the gcOnFly track - it does not need to by completely synthetic - it only comes in from trackDb stanzas refs #35958
  • lines changed 20, context: html, text, full: html, text
    af085becd865f704b4fbe1c7cc643e939bea056c Fri Mar 27 10:57:11 2026 -0700
    when quickLifting decipherSnvs, use source coordinates to query into supporting table fixes #36061
• src/hg/hgc/hgc.h
  • lines changed 5, context: html, text, full: html, text
    ddb85ced5e8b6127a233b5cda5fcb1fbe2260578 Wed Mar 25 04:22:06 2026 -0700
    Add detailsScript trackDb mechanism for JS visualizations on bigBed details pages Changing based on feedback from Jonathan, Chris and Brian after group discussion. Refactored existing Claude-generated code, moving functions into libraries. This is the first use of ES6 modules in the kent js code. In 2026, this should be acceptable? New trackDb syntax: detailsScript.<plotType>.<fieldName> <jsonConfig> The C code (bigBedClick.c) collects these settings, exports field values as JSON (bedDetails object), and dynamically imports hgc.<plotType>.js as an ES6 module. Fields used by detailsScript are shown in the HTML table with empty values, filled by JavaScript. Includes hgc.histogram.js module for drawing SVG bar chart histograms from logfmt-encoded data (space-separated key=value pairs). Applied to both the trexplorer and webstr tracks in the strVar supertrack. Also adds jsonWriteJsonElement() helper to jsonWrite.c for writing parsed jsonElement trees into a jsonWrite stream. max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/ENCODE/analysis.html
  • lines changed 2, context: html, text, full: html, text
    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/ENCODE/fileFormats.html
  • lines changed 2, context: html, text, full: html, text
    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/ENCODE/usageResources.html
  • lines changed 2, context: html, text, full: html, text
    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/allTipsRaw.html
  • lines changed 1, context: html, text, full: html, text
    fab868fba7354bde3fe88a611e5f2224d61b6d45 Sat Mar 28 16:51:56 2026 -0700
    adding announcement for glossary page and tip for new page, refs #35259
  • lines changed 1, context: html, text, full: html, text
    677cd59d724e321a375348bb1ce738ee74156672 Sat Mar 28 16:57:36 2026 -0700
    Fixing typo in link, refs #35259
• src/hg/htdocs/contribTracks.html
  • lines changed 173, context: html, text, full: html, text
    944fa6bbf93daeaac9d5223930696cccccfa5197 Fri Mar 27 17:25:06 2026 -0700
    Updating the page to improve the flow, structure, be clear that the file names need to be identical, and include a new example hub, refs #36957
• src/hg/htdocs/goldenPath/help/assemblyHubGuidelines.html
  • lines changed 429, context: html, text, full: html, text
    cf4860b4081a799cdf522312689d334a3e28a129 Wed Mar 25 18:29:03 2026 -0700
    Code review edits, refs #37285
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    f4670e11533d6f2a8e2f4f575bb294a2fb0214cb Thu Mar 26 12:44:09 2026 -0700
    Removing the assemblyHubGuidelines.html since it is an early version draft of the assemblyHubHelp.html, refs #37285
• src/hg/htdocs/goldenPath/help/gcOnFly.html
  • lines changed 2, context: html, text, full: html, text
    f12abfa6cad0164a03d39d3968986874a8c9a6b8 Wed Mar 25 16:58:16 2026 -0700
    same change to track Ui to indicate how to get the data for the gcOnFly synthetic track refs #35958
• src/hg/htdocs/goldenPath/help/hgGeneGraph.html
  • lines changed 12, context: html, text, full: html, text
    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 2, context: html, text, full: html, text
    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/goldenPath/help/hubQuickStart.html
  • lines changed 2, context: html, text, full: html, text
    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/goldenPath/help/hubQuickStartFilter.html
  • lines changed 18, context: html, text, full: html, text
    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/goldenPath/help/hubQuickStartSearch.html
  • lines changed 4, context: html, text, full: html, text
    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/goldenPath/help/quickLift.html
  • lines changed 11, context: html, text, full: html, text
    3b7a323713edb0adefb48de6a5fc81e8265e4067 Sat Mar 28 11:22:26 2026 -0700
    Adding a QuickLift documentation link to the Notes sectiono on hgConvert, refs #36111
  • lines changed 69, context: html, text, full: html, text
    ac55018f46e1dbfe5def208680bd30c25c8f27cc Sat Mar 28 13:34:33 2026 -0700
    Edits to the quickLift.html help page, refs #35536
• src/hg/htdocs/goldenPath/help/sessions.html
  • lines changed 3, context: html, text, full: html, text
    6f00f33a31c1cec74f33b7e408165005f8b87e37 Wed Mar 25 13:45:08 2026 -0700
    Fix inaccurate alt text in sessions.html per QA feedback. refs #37254 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
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    89bbe52239ee55f5b3a1753b27d5592c8744ec5c Tue Mar 24 08:32:53 2026 -0700
    minor tweaks based on CR and feedback in ticket, refs #37250, #37080
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    762b6fd2e1d4be45270be9e643f4a4a74d68e8a1 Sat Mar 28 11:58:46 2026 -0700
    fixing missing double quote and adding a note about assembly search to genome setting description, no refs
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 5, context: html, text, full: html, text
    762b6fd2e1d4be45270be9e643f4a4a74d68e8a1 Sat Mar 28 11:58:46 2026 -0700
    fixing missing double quote and adding a note about assembly search to genome setting description, no refs
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 16, context: html, text, full: html, text
    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
  • lines changed 21, context: html, text, full: html, text
    fab868fba7354bde3fe88a611e5f2224d61b6d45 Sat Mar 28 16:51:56 2026 -0700
    adding announcement for glossary page and tip for new page, refs #35259
  • lines changed 1, context: html, text, full: html, text
    677cd59d724e321a375348bb1ce738ee74156672 Sat Mar 28 16:57:36 2026 -0700
    Fixing typo in link, refs #35259
  • lines changed 1, context: html, text, full: html, text
    39ee9b7086d503d62be50b0aa696f6563cfbf1b4 Sun Mar 29 09:17:06 2026 -0700
    fixing missing word found in automated CR, no refs
• src/hg/htdocs/images/QuickLift/hgConvertV496.png
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    ac55018f46e1dbfe5def208680bd30c25c8f27cc Sat Mar 28 13:34:33 2026 -0700
    Edits to the quickLift.html help page, refs #35536
• src/hg/htdocs/inc/hgCollectionHelpInclude.html
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    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/inc/hgMyData.html
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    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/indexNews.html
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    fab868fba7354bde3fe88a611e5f2224d61b6d45 Sat Mar 28 16:51:56 2026 -0700
    adding announcement for glossary page and tip for new page, refs #35259
• src/hg/htdocs/staff.html
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    41c485c8e4bda02a3de334444479d9ae92140c7c Fri Mar 27 16:13:20 2026 -0700
    Restore original alt text for images that already had alt attributes. The initial alt text commit incorrectly replaced 44 existing human-written descriptions with AI-generated generic text across 12 files. Feedback from CR. refs #37289
• src/hg/htdocs/style/facetedComposite.css
  • lines changed 10, context: html, text, full: html, text
    eb076410a62ea6a94b71358424080af261ba2c25 Thu Mar 26 03:20:14 2026 -0700
    Moved hgFetch into hgTrackUi; added etags, Cache-Control directives, and GET use instead of POST when udcTimeout isn't set, all to support browser caching of remote files; bumped the DataTables version for facetedComposite to facilitate making all the checkboxes have a consistent look; refs #36320
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    54feb9fd4ce482717780bc53c0bc2828a15cd9b7 Thu Mar 26 03:52:29 2026 -0700
    Putting a light border around the faceted composite table per request, refs #36320
• src/hg/inc/wiggle.h
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    1e04d78b65b35678e80d9f5929e6fec0f7b2fbbb Tue Mar 24 13:32:54 2026 -0700
    refactor the GC on fly calculation to move into a library function rfefs #35958
• src/hg/js/autocompleteCat.js
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    4ab22d829bff96467e64331dad271bcb0bc84de1 Tue Mar 24 15:22:00 2026 -0700
    Force genark autocomplete results to send their genome identifier like GC[AF]_XXX as the db field to hgGateway back end, refs #37276
• src/hg/js/detailsHistogram.js
  • lines changed 132, context: html, text, full: html, text
    ddb85ced5e8b6127a233b5cda5fcb1fbe2260578 Wed Mar 25 04:22:06 2026 -0700
    Add detailsScript trackDb mechanism for JS visualizations on bigBed details pages Changing based on feedback from Jonathan, Chris and Brian after group discussion. Refactored existing Claude-generated code, moving functions into libraries. This is the first use of ES6 modules in the kent js code. In 2026, this should be acceptable? New trackDb syntax: detailsScript.<plotType>.<fieldName> <jsonConfig> The C code (bigBedClick.c) collects these settings, exports field values as JSON (bedDetails object), and dynamically imports hgc.<plotType>.js as an ES6 module. Fields used by detailsScript are shown in the HTML table with empty values, filled by JavaScript. Includes hgc.histogram.js module for drawing SVG bar chart histograms from logfmt-encoded data (space-separated key=value pairs). Applied to both the trexplorer and webstr tracks in the strVar supertrack. Also adds jsonWriteJsonElement() helper to jsonWrite.c for writing parsed jsonElement trees into a jsonWrite stream. max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/js/facetedComposite.js
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    eb076410a62ea6a94b71358424080af261ba2c25 Thu Mar 26 03:20:14 2026 -0700
    Moved hgFetch into hgTrackUi; added etags, Cache-Control directives, and GET use instead of POST when udcTimeout isn't set, all to support browser caching of remote files; bumped the DataTables version for facetedComposite to facilitate making all the checkboxes have a consistent look; refs #36320
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    dcc1f38c219bbf48a1b99dc5d7e3f0df5a50eceb Thu Mar 26 04:19:23 2026 -0700
    Removing dependence on URL parameters that aren't always present for the faceted composite UI, refs #36320
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    2483e425a830f91215299318996847033b10131f Thu Mar 26 14:14:26 2026 -0700
    Changing facets to be expanded by default on page load, refs #36320
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    4f451cd79d08aa40353d077a2d014f9821581901 Thu Mar 26 16:16:28 2026 -0700
    Adding selected track count to the top of the table for faceted composites, refs #36320
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    d8ccab674ade18f74884056a5e020651f423d0f0 Mon Mar 30 08:25:10 2026 -0700
    Faceted composite UI has more consistent naming (track/sample vs row), facet counts update dynamically, and facet values are now case-insensitive (matching behavior elsewhere, so you don't see 27 but click it and get 34 tracks). refs #36320
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    2ca5303deabc42182eae8cb7f49c2c8e9784eabf Mon Mar 30 09:30:45 2026 -0700
    Added an error message for when the metadata file is missing for a faceted composite, refs #36320
• src/hg/js/hgGateway.js
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    4ab22d829bff96467e64331dad271bcb0bc84de1 Tue Mar 24 15:22:00 2026 -0700
    Force genark autocomplete results to send their genome identifier like GC[AF]_XXX as the db field to hgGateway back end, refs #37276
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    c9714d23710a9089473f5caafe6ec01934755a11 Fri Mar 27 09:37:09 2026 -0700
    Save position ranges search on hgGateway to the recent positions stack, refs #34588
• src/hg/js/hgc.histogram.js
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    ddb85ced5e8b6127a233b5cda5fcb1fbe2260578 Wed Mar 25 04:22:06 2026 -0700
    Add detailsScript trackDb mechanism for JS visualizations on bigBed details pages Changing based on feedback from Jonathan, Chris and Brian after group discussion. Refactored existing Claude-generated code, moving functions into libraries. This is the first use of ES6 modules in the kent js code. In 2026, this should be acceptable? New trackDb syntax: detailsScript.<plotType>.<fieldName> <jsonConfig> The C code (bigBedClick.c) collects these settings, exports field values as JSON (bedDetails object), and dynamically imports hgc.<plotType>.js as an ES6 module. Fields used by detailsScript are shown in the HTML table with empty values, filled by JavaScript. Includes hgc.histogram.js module for drawing SVG bar chart histograms from logfmt-encoded data (space-separated key=value pairs). Applied to both the trexplorer and webstr tracks in the strVar supertrack. Also adds jsonWriteJsonElement() helper to jsonWrite.c for writing parsed jsonElement trees into a jsonWrite stream. max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/js/hui.js
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    1b1a0aa39ffd5c18dbb425fca096ea335ed154fe Wed Mar 25 06:42:39 2026 -0700
    superTrack hgTrackUi: auto-hide when all children hidden, grey dropdown on hide refs #37282 Route button clicks through superT.selChanged() by triggering the dropdown change event instead of just setting its value. This fixes three problems: (1) hiding all subtracks now auto-hides the superTrack container (matching composite track behavior), (2) the superTrack show/hide dropdown greys out when set to hide, and (3) clicking Hide on a subtrack no longer forces the superTrack to show. This makes the code actually simpler. I didn't know about selChanged() when I wrote the new superTrack code. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/js/makefile
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    ddb85ced5e8b6127a233b5cda5fcb1fbe2260578 Wed Mar 25 04:22:06 2026 -0700
    Add detailsScript trackDb mechanism for JS visualizations on bigBed details pages Changing based on feedback from Jonathan, Chris and Brian after group discussion. Refactored existing Claude-generated code, moving functions into libraries. This is the first use of ES6 modules in the kent js code. In 2026, this should be acceptable? New trackDb syntax: detailsScript.<plotType>.<fieldName> <jsonConfig> The C code (bigBedClick.c) collects these settings, exports field values as JSON (bedDetails object), and dynamically imports hgc.<plotType>.js as an ES6 module. Fields used by detailsScript are shown in the HTML table with empty values, filled by JavaScript. Includes hgc.histogram.js module for drawing SVG bar chart histograms from logfmt-encoded data (space-separated key=value pairs). Applied to both the trexplorer and webstr tracks in the strVar supertrack. Also adds jsonWriteJsonElement() helper to jsonWrite.c for writing parsed jsonElement trees into a jsonWrite stream. max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/js/utils.js
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    4ab22d829bff96467e64331dad271bcb0bc84de1 Tue Mar 24 15:22:00 2026 -0700
    Force genark autocomplete results to send their genome identifier like GC[AF]_XXX as the db field to hgGateway back end, refs #37276
• src/hg/lib/hdb.c
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    c3bb4207fb2a58064b937ba9fef1cc11852f7576 Wed Mar 25 10:48:49 2026 -0700
    allow trackDb entry to override the in-code defaults of the gcOnFly track refs #35958
• src/hg/lib/hui.c
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    fba104f4456ba44aced822a59c849d04546a50b8 Fri Mar 13 16:46:01 2026 -0700
    Add refSeqComposite to quickLift vetted tracks and fix label cart var prefix trackHub.c: add refSeqComposite to vettedTracks list for quickLift. hui.c: use trackHubSkipHubName for label checkbox cart variable so it matches regardless of hub name prefix. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    e09c0d375e198e5c74164dbbbb4010a57bf13607 Wed Mar 25 17:44:45 2026 -0700
    correct UI operation on the synthetic bigWig gcOnFly track refs #35958
• src/hg/lib/trackHub.c
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    fba104f4456ba44aced822a59c849d04546a50b8 Fri Mar 13 16:46:01 2026 -0700
    Add refSeqComposite to quickLift vetted tracks and fix label cart var prefix trackHub.c: add refSeqComposite to vettedTracks list for quickLift. hui.c: use trackHubSkipHubName for label checkbox cart variable so it matches regardless of hub name prefix. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/lib/wigDataStream.c
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    1e04d78b65b35678e80d9f5929e6fec0f7b2fbbb Tue Mar 24 13:32:54 2026 -0700
    refactor the GC on fly calculation to move into a library function rfefs #35958
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    4fd52b1b34d170c15d3aacfeaf4fbb26fff224b1 Wed Mar 25 12:52:00 2026 -0700
    fix bugs for chrom size at 2^31 and manage partial computation windows at beginning or end of drawing window for gcOnFly refs #35958
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
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    19af47f0b0e49796e6f909b093b72eff2f480e4b Mon Mar 23 21:27:27 2026 -0700
    VGP update in progress
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
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    19af47f0b0e49796e6f909b093b72eff2f480e4b Mon Mar 23 21:27:27 2026 -0700
    VGP update in progress
• src/hg/makeDb/doc/hg38/encode4.regulation.txt
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    7e9cf9d7dace5cd9a0519bee134364b87b86d832 Fri Mar 27 12:01:25 2026 -0700
    Updating makedocs for hg38 and mm10 ENCODE4 Regulation tracks to reflect all changes from 2026-03-27: priorities, symlink renaming, color darkening, colorSettingsUrl, longLabel cleanup, Data Access sections, HTML audit fixes, code review fixes, and local ENCFF file cleanup (4.3 TB freed). refs #34923
• src/hg/makeDb/doc/hg38/nmd.txt
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    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
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    cf59add626c31740a9a65a4c576b71b822260ced Tue Mar 24 04:18:15 2026 -0700
    fixing up NMD track and adding decorator tdb, refs #33737
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    afbe6b6e1ac59c72526ce6515cca0abea576e9d9 Wed Mar 25 02:01:33 2026 -0700
    fix missing backslash and wrong year in nmd makedoc Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/hg38/promoterAi.txt
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    4e986673a37800eacf1d36309b0cd38564a4bb1f Wed Mar 25 07:55:59 2026 -0700
    PromoterAI track scripts, docs, and makeDoc; remove unused primateAiToBigBed.py, refs #37278 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
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    19af47f0b0e49796e6f909b093b72eff2f480e4b Mon Mar 23 21:27:27 2026 -0700
    VGP update in progress
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
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    3701c3297c0f24c57b3e4ec266ff2f3551eb5365 Mon Mar 23 21:26:00 2026 -0700
    fixing up GCA_040938575.1_UKY_AmexF1_1
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
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    19af47f0b0e49796e6f909b093b72eff2f480e4b Mon Mar 23 21:27:27 2026 -0700
    VGP update in progress
• src/hg/makeDb/doc/mm10.encode4.regulation.txt
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    7e9cf9d7dace5cd9a0519bee134364b87b86d832 Fri Mar 27 12:01:25 2026 -0700
    Updating makedocs for hg38 and mm10 ENCODE4 Regulation tracks to reflect all changes from 2026-03-27: priorities, symlink renaming, color darkening, colorSettingsUrl, longLabel cleanup, Data Access sections, HTML audit fixes, code review fixes, and local ENCFF file cleanup (4.3 TB freed). refs #34923
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
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    19af47f0b0e49796e6f909b093b72eff2f480e4b Mon Mar 23 21:27:27 2026 -0700
    VGP update in progress
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
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    19af47f0b0e49796e6f909b093b72eff2f480e4b Mon Mar 23 21:27:27 2026 -0700
    VGP update in progress
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
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    19af47f0b0e49796e6f909b093b72eff2f480e4b Mon Mar 23 21:27:27 2026 -0700
    VGP update in progress
• src/hg/makeDb/hgGcPercent/hgGcPercent.c
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    c6e82cfec526eeec7abb93e0610e303406d03820 Wed Mar 25 14:53:49 2026 -0700
    allow hgGcPercent to read a 2bit file from a URL and add unit tests as suggested by claude refs #35958
• src/hg/makeDb/hgGcPercent/makefile
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    c6e82cfec526eeec7abb93e0610e303406d03820 Wed Mar 25 14:53:49 2026 -0700
    allow hgGcPercent to read a 2bit file from a URL and add unit tests as suggested by claude refs #35958
• src/hg/makeDb/hgGcPercent/tests/expected/test0.out
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    c6e82cfec526eeec7abb93e0610e303406d03820 Wed Mar 25 14:53:49 2026 -0700
    allow hgGcPercent to read a 2bit file from a URL and add unit tests as suggested by claude refs #35958
• src/hg/makeDb/hgGcPercent/tests/expected/test1.out
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    c6e82cfec526eeec7abb93e0610e303406d03820 Wed Mar 25 14:53:49 2026 -0700
    allow hgGcPercent to read a 2bit file from a URL and add unit tests as suggested by claude refs #35958
• src/hg/makeDb/hgGcPercent/tests/expected/url.md5sum
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    c6e82cfec526eeec7abb93e0610e303406d03820 Wed Mar 25 14:53:49 2026 -0700
    allow hgGcPercent to read a 2bit file from a URL and add unit tests as suggested by claude refs #35958
• src/hg/makeDb/hgGcPercent/tests/inputs/test.2bit
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    c6e82cfec526eeec7abb93e0610e303406d03820 Wed Mar 25 14:53:49 2026 -0700
    allow hgGcPercent to read a 2bit file from a URL and add unit tests as suggested by claude refs #35958
• src/hg/makeDb/hgGcPercent/tests/inputs/test.fa
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    c6e82cfec526eeec7abb93e0610e303406d03820 Wed Mar 25 14:53:49 2026 -0700
    allow hgGcPercent to read a 2bit file from a URL and add unit tests as suggested by claude refs #35958
• src/hg/makeDb/hgGcPercent/tests/makefile
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    c6e82cfec526eeec7abb93e0610e303406d03820 Wed Mar 25 14:53:49 2026 -0700
    allow hgGcPercent to read a 2bit file from a URL and add unit tests as suggested by claude refs #35958
• src/hg/makeDb/scripts/encode4regulation/convert_to_bigcomposite.py
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/encode4regulation/generate_composites.py
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/encode4regulation/generate_multiwig_ra.py
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/encode4regulation/validate_encode_urls.py
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/nmd/genePredNmdEsc
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    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
• src/hg/makeDb/scripts/nmd/lindeboomToBigWig.sh
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    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
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    cf59add626c31740a9a65a4c576b71b822260ced Tue Mar 24 04:18:15 2026 -0700
    fixing up NMD track and adding decorator tdb, refs #33737
• src/hg/makeDb/scripts/nmd/nmdEscCollapsed.as
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    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
• src/hg/makeDb/scripts/nmd/nmdEscDecoration.as
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    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
• src/hg/makeDb/scripts/primateAiToBigBed.py
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    4e986673a37800eacf1d36309b0cd38564a4bb1f Wed Mar 25 07:55:59 2026 -0700
    PromoterAI track scripts, docs, and makeDoc; remove unused primateAiToBigBed.py, refs #37278 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/promoterAiOverlaps.as
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    4e986673a37800eacf1d36309b0cd38564a4bb1f Wed Mar 25 07:55:59 2026 -0700
    PromoterAI track scripts, docs, and makeDoc; remove unused primateAiToBigBed.py, refs #37278 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/promoterAiToBigWig.py
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    4e986673a37800eacf1d36309b0cd38564a4bb1f Wed Mar 25 07:55:59 2026 -0700
    PromoterAI track scripts, docs, and makeDoc; remove unused primateAiToBigBed.py, refs #37278 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/trexplorer/trexplorer.as
  • lines changed 5, context: html, text, full: html, text
    ddb85ced5e8b6127a233b5cda5fcb1fbe2260578 Wed Mar 25 04:22:06 2026 -0700
    Add detailsScript trackDb mechanism for JS visualizations on bigBed details pages Changing based on feedback from Jonathan, Chris and Brian after group discussion. Refactored existing Claude-generated code, moving functions into libraries. This is the first use of ES6 modules in the kent js code. In 2026, this should be acceptable? New trackDb syntax: detailsScript.<plotType>.<fieldName> <jsonConfig> The C code (bigBedClick.c) collects these settings, exports field values as JSON (bedDetails object), and dynamically imports hgc.<plotType>.js as an ES6 module. Fields used by detailsScript are shown in the HTML table with empty values, filled by JavaScript. Includes hgc.histogram.js module for drawing SVG bar chart histograms from logfmt-encoded data (space-separated key=value pairs). Applied to both the trexplorer and webstr tracks in the strVar supertrack. Also adds jsonWriteJsonElement() helper to jsonWrite.c for writing parsed jsonElement trees into a jsonWrite stream. max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/trexplorer/trexplorerToBed.py
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    ddb85ced5e8b6127a233b5cda5fcb1fbe2260578 Wed Mar 25 04:22:06 2026 -0700
    Add detailsScript trackDb mechanism for JS visualizations on bigBed details pages Changing based on feedback from Jonathan, Chris and Brian after group discussion. Refactored existing Claude-generated code, moving functions into libraries. This is the first use of ES6 modules in the kent js code. In 2026, this should be acceptable? New trackDb syntax: detailsScript.<plotType>.<fieldName> <jsonConfig> The C code (bigBedClick.c) collects these settings, exports field values as JSON (bedDetails object), and dynamically imports hgc.<plotType>.js as an ES6 module. Fields used by detailsScript are shown in the HTML table with empty values, filled by JavaScript. Includes hgc.histogram.js module for drawing SVG bar chart histograms from logfmt-encoded data (space-separated key=value pairs). Applied to both the trexplorer and webstr tracks in the strVar supertrack. Also adds jsonWriteJsonElement() helper to jsonWrite.c for writing parsed jsonElement trees into a jsonWrite stream. max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/databases.tsv
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    1d55b24b30b2f1d69cf1f99f6da7cf5aac40ae40 Wed Mar 25 07:57:36 2026 -0700
    Add database and population config TSV files for varFreqsAll combined track These config files drive the vcfToBigBed.py script that builds the combined variant frequency bigBed. Externalizing the config makes it easy to add new databases or population breakdowns without editing Python code, refs #36642 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/populations.tsv
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    1d55b24b30b2f1d69cf1f99f6da7cf5aac40ae40 Wed Mar 25 07:57:36 2026 -0700
    Add database and population config TSV files for varFreqsAll combined track These config files drive the vcfToBigBed.py script that builds the combined variant frequency bigBed. Externalizing the config makes it easy to add new databases or population breakdowns without editing Python code, refs #36642 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/vcfFilterParallel.sh
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    093f3160b963cc1b05b409732f6a233d11bdfecf Wed Mar 25 04:41:12 2026 -0700
    changed after code review, refs #37291
• src/hg/makeDb/scripts/webstr/webstr.as
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    ddb85ced5e8b6127a233b5cda5fcb1fbe2260578 Wed Mar 25 04:22:06 2026 -0700
    Add detailsScript trackDb mechanism for JS visualizations on bigBed details pages Changing based on feedback from Jonathan, Chris and Brian after group discussion. Refactored existing Claude-generated code, moving functions into libraries. This is the first use of ES6 modules in the kent js code. In 2026, this should be acceptable? New trackDb syntax: detailsScript.<plotType>.<fieldName> <jsonConfig> The C code (bigBedClick.c) collects these settings, exports field values as JSON (bedDetails object), and dynamically imports hgc.<plotType>.js as an ES6 module. Fields used by detailsScript are shown in the HTML table with empty values, filled by JavaScript. Includes hgc.histogram.js module for drawing SVG bar chart histograms from logfmt-encoded data (space-separated key=value pairs). Applied to both the trexplorer and webstr tracks in the strVar supertrack. Also adds jsonWriteJsonElement() helper to jsonWrite.c for writing parsed jsonElement trees into a jsonWrite stream. max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/webstr/webstrToBed.py
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    ddb85ced5e8b6127a233b5cda5fcb1fbe2260578 Wed Mar 25 04:22:06 2026 -0700
    Add detailsScript trackDb mechanism for JS visualizations on bigBed details pages Changing based on feedback from Jonathan, Chris and Brian after group discussion. Refactored existing Claude-generated code, moving functions into libraries. This is the first use of ES6 modules in the kent js code. In 2026, this should be acceptable? New trackDb syntax: detailsScript.<plotType>.<fieldName> <jsonConfig> The C code (bigBedClick.c) collects these settings, exports field values as JSON (bedDetails object), and dynamically imports hgc.<plotType>.js as an ES6 module. Fields used by detailsScript are shown in the HTML table with empty values, filled by JavaScript. Includes hgc.histogram.js module for drawing SVG bar chart histograms from logfmt-encoded data (space-separated key=value pairs). Applied to both the trexplorer and webstr tracks in the strVar supertrack. Also adds jsonWriteJsonElement() helper to jsonWrite.c for writing parsed jsonElement trees into a jsonWrite stream. max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/encode.cCREs.override.ra
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    95860982a496454aec2aab3df0e6cb2c4b7760b4 Thu Mar 26 17:47:15 2026 -0700
    Adjusting track priorities in regulation group for hg38 and mm10. hg38: cCREs 0.8, wgEncodeReg4 0.9, wgEncodeReg 1. mm10: cCREs 0.4, encode4Reg 0.5, tabulaMuris 1. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/gnomad.html
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    58c584d70ab7585e72d3511dccc7dbb934068f55 Thu Mar 26 16:37:46 2026 -0700
    Cleaned up gnomAD hg38 track description html files and moved the detailed track descriptions into dedicated pages, refs #37236
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    25093768bbdd968b55aac0a4ea9b77840b72dbb9 Thu Mar 26 16:58:26 2026 -0700
    Removing inaccurate text display conventions that Claude included and updating the html trackDb setting lines, refs #37236
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
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    25093768bbdd968b55aac0a4ea9b77840b72dbb9 Thu Mar 26 16:58:26 2026 -0700
    Removing inaccurate text display conventions that Claude included and updating the html trackDb setting lines, refs #37236
• src/hg/makeDb/trackDb/human/hg38/gnomadConstraint.html
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    58c584d70ab7585e72d3511dccc7dbb934068f55 Thu Mar 26 16:37:46 2026 -0700
    Cleaned up gnomAD hg38 track description html files and moved the detailed track descriptions into dedicated pages, refs #37236
• src/hg/makeDb/trackDb/human/hg38/gnomadV2.html
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    58c584d70ab7585e72d3511dccc7dbb934068f55 Thu Mar 26 16:37:46 2026 -0700
    Cleaned up gnomAD hg38 track description html files and moved the detailed track descriptions into dedicated pages, refs #37236
• src/hg/makeDb/trackDb/human/hg38/gnomadV3.html
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    58c584d70ab7585e72d3511dccc7dbb934068f55 Thu Mar 26 16:37:46 2026 -0700
    Cleaned up gnomAD hg38 track description html files and moved the detailed track descriptions into dedicated pages, refs #37236
• src/hg/makeDb/trackDb/human/hg38/gnomadV4.1.html
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    58c584d70ab7585e72d3511dccc7dbb934068f55 Thu Mar 26 16:37:46 2026 -0700
    Cleaned up gnomAD hg38 track description html files and moved the detailed track descriptions into dedicated pages, refs #37236
• src/hg/makeDb/trackDb/human/hg38/knownGene.nmd_deco.ra
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    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
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    cf59add626c31740a9a65a4c576b71b822260ced Tue Mar 24 04:18:15 2026 -0700
    fixing up NMD track and adding decorator tdb, refs #33737
• src/hg/makeDb/trackDb/human/hg38/nmd.html
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    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
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    e9d2a1912a2614531cd517c8cb6adab86d94f3a5 Tue Mar 24 04:26:33 2026 -0700
    nmd docs, refs#33737
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    536f961aba550065f88bd667b17bcddf10ae56d1 Tue Mar 24 04:35:33 2026 -0700
    nmd docs update again, refs #33737
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    9ed76b65538d48795930ced5462ed6f45340c160 Wed Mar 25 01:59:35 2026 -0700
    fix typo in nmd.html: 'there were used' -> 'that were used' Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/nmd.ra
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    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
• src/hg/makeDb/trackDb/human/hg38/nmdDetective.html
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    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
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    2694cffb31b95f1729b2d8c5252e406e66a5e61d Thu Mar 26 02:18:25 2026 -0700
    changes after AI code review
• src/hg/makeDb/trackDb/human/hg38/nmdEscTranscripts.html
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    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
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    45fe522cdfda1196c83624e8cce9d13a73cb18f4 Tue Mar 24 04:29:47 2026 -0700
    nmd docs update, refs #33737
• src/hg/makeDb/trackDb/human/hg38/recombRate2.html
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    1595e1d28609457b981272075e82e332736a3e23 Sat Mar 28 13:44:58 2026 -0700
    Fixing broken link reported by user in refs #37301
• src/hg/makeDb/trackDb/human/hg38/strVar.ra
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    ddb85ced5e8b6127a233b5cda5fcb1fbe2260578 Wed Mar 25 04:22:06 2026 -0700
    Add detailsScript trackDb mechanism for JS visualizations on bigBed details pages Changing based on feedback from Jonathan, Chris and Brian after group discussion. Refactored existing Claude-generated code, moving functions into libraries. This is the first use of ES6 modules in the kent js code. In 2026, this should be acceptable? New trackDb syntax: detailsScript.<plotType>.<fieldName> <jsonConfig> The C code (bigBedClick.c) collects these settings, exports field values as JSON (bedDetails object), and dynamically imports hgc.<plotType>.js as an ES6 module. Fields used by detailsScript are shown in the HTML table with empty values, filled by JavaScript. Includes hgc.histogram.js module for drawing SVG bar chart histograms from logfmt-encoded data (space-separated key=value pairs). Applied to both the trexplorer and webstr tracks in the strVar supertrack. Also adds jsonWriteJsonElement() helper to jsonWrite.c for writing parsed jsonElement trees into a jsonWrite stream. max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/utrAnnotUorfs.html
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    3365286ae98d7d34824fd15a2d9e084c5a68f5a5 Wed Mar 25 06:28:33 2026 -0700
    adding utrAnnotator ORF, for the ncORFs track, refs #35101
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.alpha.ra
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
    Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel 912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark") in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics, and TF ChIP individual track HTML for both assemblies. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.ra
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    95860982a496454aec2aab3df0e6cb2c4b7760b4 Thu Mar 26 17:47:15 2026 -0700
    Adjusting track priorities in regulation group for hg38 and mm10. hg38: cCREs 0.8, wgEncodeReg4 0.9, wgEncodeReg 1. mm10: cCREs 0.4, encode4Reg 0.5, tabulaMuris 1. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
    Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel 912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark") in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics, and TF ChIP individual track HTML for both assemblies. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Atac.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Dnase.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
    Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel 912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark") in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics, and TF ChIP individual track HTML for both assemblies. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    c082365b4bc8445dfa4decc7e8569fd82d995115 Thu Mar 26 17:53:13 2026 -0700
    Moving individual experiment composites (Indiv.) to end of supertrack container by setting priority 2.0/2.1/2.2 for Epigenetics/RnaSeq/TfChip on both hg38 and mm10. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    7c4f2e656763f789dafcabae4c2c82f5b581d43f Fri Mar 27 10:15:45 2026 -0700
    Replacing underscores with spaces in all 6,747 hg38 bigComposite subtrack longLabels for readability. Converts e.g. "Homo_sapiens_K562_stably_expressing" to "Homo sapiens K562 stably expressing". mm10 labels were already correct. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkCtcf.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k27ac.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k4me3.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
    Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel 912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark") in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics, and TF ChIP individual track HTML for both assemblies. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.ra
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    c082365b4bc8445dfa4decc7e8569fd82d995115 Thu Mar 26 17:53:13 2026 -0700
    Moving individual experiment composites (Indiv.) to end of supertrack container by setting priority 2.0/2.1/2.2 for Epigenetics/RnaSeq/TfChip on both hg38 and mm10. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    7c4f2e656763f789dafcabae4c2c82f5b581d43f Fri Mar 27 10:15:45 2026 -0700
    Replacing underscores with spaces in all 6,747 hg38 bigComposite subtrack longLabels for readability. Converts e.g. "Homo_sapiens_K562_stably_expressing" to "Homo sapiens K562 stably expressing". mm10 labels were already correct. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
    Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel 912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark") in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics, and TF ChIP individual track HTML for both assemblies. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.ra
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    c082365b4bc8445dfa4decc7e8569fd82d995115 Thu Mar 26 17:53:13 2026 -0700
    Moving individual experiment composites (Indiv.) to end of supertrack container by setting priority 2.0/2.1/2.2 for Epigenetics/RnaSeq/TfChip on both hg38 and mm10. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    7c4f2e656763f789dafcabae4c2c82f5b581d43f Fri Mar 27 10:15:45 2026 -0700
    Replacing underscores with spaces in all 6,747 hg38 bigComposite subtrack longLabels for readability. Converts e.g. "Homo_sapiens_K562_stably_expressing" to "Homo sapiens K562 stably expressing". mm10 labels were already correct. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfPeaks.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Txn.html
  • lines changed 81, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 63, context: html, text, full: html, text
    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 19, context: html, text, full: html, text
    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/predictionScoresSuper.html
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    3e31f74afa0c70f1d0484c9f4ad6406ac89e53b3 Wed Mar 25 04:42:08 2026 -0700
    forgot to add the promoterAi trackDb include, refs #37278
• src/hg/makeDb/trackDb/human/predictionScoresSuper.ra
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    3e31f74afa0c70f1d0484c9f4ad6406ac89e53b3 Wed Mar 25 04:42:08 2026 -0700
    forgot to add the promoterAi trackDb include, refs #37278
• src/hg/makeDb/trackDb/human/promoterAi.html
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    4e986673a37800eacf1d36309b0cd38564a4bb1f Wed Mar 25 07:55:59 2026 -0700
    PromoterAI track scripts, docs, and makeDoc; remove unused primateAiToBigBed.py, refs #37278 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/promoterAi.ra
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    afd8803bc4a0b4992d7676b35c58d4d9cc076e2b Wed Mar 25 06:27:17 2026 -0700
    adding promoterAi trackDb file that I missed earlier today
• src/hg/makeDb/trackDb/human/varFreqs.html
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    305b083ab4b1ccda250da6f79b092f8aeb4137fb Tue Mar 24 07:57:20 2026 -0700
    small doc updates to varFreqs track
• src/hg/makeDb/trackDb/mouse/mm10/encode.cCREs.override.ra
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    95860982a496454aec2aab3df0e6cb2c4b7760b4 Thu Mar 26 17:47:15 2026 -0700
    Adjusting track priorities in regulation group for hg38 and mm10. hg38: cCREs 0.8, wgEncodeReg4 0.9, wgEncodeReg 1. mm10: cCREs 0.4, encode4Reg 0.5, tabulaMuris 1. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
    Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel 912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark") in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics, and TF ChIP individual track HTML for both assemblies. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.ra
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    95860982a496454aec2aab3df0e6cb2c4b7760b4 Thu Mar 26 17:47:15 2026 -0700
    Adjusting track priorities in regulation group for hg38 and mm10. hg38: cCREs 0.8, wgEncodeReg4 0.9, wgEncodeReg 1. mm10: cCREs 0.4, encode4Reg 0.5, tabulaMuris 1. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 18, context: html, text, full: html, text
    197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
    Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel 912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark") in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics, and TF ChIP individual track HTML for both assemblies. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 76, context: html, text, full: html, text
    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegAtac.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegDnase.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 39, context: html, text, full: html, text
    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 19, context: html, text, full: html, text
    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
    Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel 912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark") in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics, and TF ChIP individual track HTML for both assemblies. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    c082365b4bc8445dfa4decc7e8569fd82d995115 Thu Mar 26 17:53:13 2026 -0700
    Moving individual experiment composites (Indiv.) to end of supertrack container by setting priority 2.0/2.1/2.2 for Epigenetics/RnaSeq/TfChip on both hg38 and mm10. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 187, context: html, text, full: html, text
    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkCtcf.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k27ac.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k4me3.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.html
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
    Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel 912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark") in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics, and TF ChIP individual track HTML for both assemblies. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.ra
  • lines changed 12130, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    c082365b4bc8445dfa4decc7e8569fd82d995115 Thu Mar 26 17:53:13 2026 -0700
    Moving individual experiment composites (Indiv.) to end of supertrack container by setting priority 2.0/2.1/2.2 for Epigenetics/RnaSeq/TfChip on both hg38 and mm10. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.html
  • lines changed 58, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 7, context: html, text, full: html, text
    197a2368b8099d4291396c029adb4308fd7483ab Fri Mar 27 08:43:01 2026 -0700
    Code review fixes for ENCODE4 Regulation tracks. Fixes TF rPeaks longLabel 912->911 in wgEncodeReg4.ra, resolves duplicate multiWig subtrack priorities in mm10 encode4Reg.ra by sequential renumbering, fixes grammar ("marks" -> "mark") in Epigenetics HTML, corrects "Tn5 transposase integration" to "insertion" in supertrack HTML, and adds missing Data Access sections to RNA-seq, Epigenetics, and TF ChIP individual track HTML for both assemblies. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 22, context: html, text, full: html, text
    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    c082365b4bc8445dfa4decc7e8569fd82d995115 Thu Mar 26 17:53:13 2026 -0700
    Moving individual experiment composites (Indiv.) to end of supertrack container by setting priority 2.0/2.1/2.2 for Epigenetics/RnaSeq/TfChip on both hg38 and mm10. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegTxn.html
  • lines changed 81, context: html, text, full: html, text
    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    8ad7628334f44196832ae4618d2a67a3ebe6d5c7 Thu Mar 26 18:18:07 2026 -0700
    Updating HTML description pages for ENCODE4 Regulation tracks on hg38 and mm10. Fixes mm10 organ counts to match actual data, corrects TF rPeaks factor count from 912 to 911 (removes phantom SHOX2 from filterValues), adds organ/tissue availability tables to all layered track descriptions, updates production lab credits to match original hub per assembly, removes UCSC staff mentions from credits, adds cCRE cross-reference to mm10 supertrack, and notes mixed signal+peak Data Type facet in mm10 Epi and TF composite descriptions. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    46b52b437f5db9948abb553d4bfb1538ab5903a3 Fri Mar 27 10:50:02 2026 -0700
    Darkening too-light track colors for better contrast against white background, adding colorSettingsUrl for faceted organ/assay color indicators (Epi by assay, RnaSeq by organ, TfChip none since score-colored), and updating all Data Access sections to mitomap-style format with bigWigToWig/bigBedToBed examples and representative file URLs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.alpha.ra
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.ra
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/relatedTracks.ra
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    2cb2236b2ebb81e95c173a35ec590f5a086b86d0 Thu Mar 26 17:32:56 2026 -0700
    Adding ENCODE4 Integrated Regulation tracks for hg38 (wgEncodeReg4) and mm10 (encode4Reg). Each supertrack contains 6 organ-averaged multiWig signal tracks (H3K27ac, DNase, ATAC, H3K4me3, CTCF, Transcription) and 3 bigComposite faceted individual experiment composites (Epigenetics, RNA-seq, TF ChIP-seq) using S3 URLs and the new faceted composite UI. hg38 also includes a TF rPeaks track. ENCODE3 regulation tracks are release-tagged to show a snowflake deprecation notice on alpha while remaining unchanged on beta/public. Includes generation scripts, makedocs, HTML descriptions, relatedTracks, and metadata TSVs. refs #34923 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/tagTypes.tab
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    ddb85ced5e8b6127a233b5cda5fcb1fbe2260578 Wed Mar 25 04:22:06 2026 -0700
    Add detailsScript trackDb mechanism for JS visualizations on bigBed details pages Changing based on feedback from Jonathan, Chris and Brian after group discussion. Refactored existing Claude-generated code, moving functions into libraries. This is the first use of ES6 modules in the kent js code. In 2026, this should be acceptable? New trackDb syntax: detailsScript.<plotType>.<fieldName> <jsonConfig> The C code (bigBedClick.c) collects these settings, exports field values as JSON (bedDetails object), and dynamically imports hgc.<plotType>.js as an ES6 module. Fields used by detailsScript are shown in the HTML table with empty values, filled by JavaScript. Includes hgc.histogram.js module for drawing SVG bar chart histograms from logfmt-encoded data (space-separated key=value pairs). Applied to both the trexplorer and webstr tracks in the strVar supertrack. Also adds jsonWriteJsonElement() helper to jsonWrite.c for writing parsed jsonElement trees into a jsonWrite stream. max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    c7302b60850a3f7f99088a8a99b0a7d389f64605 Wed Mar 25 10:49:52 2026 -0700
    allow trackDb entry to override the in-code defaults of the gcOnFly track refs #35958
• src/hg/makeDb/trackDb/trackDb.ra
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    69b00a9ddead8bdc0c3717a33a620f103f70bf94 Wed Mar 25 17:47:26 2026 -0700
    a default entry for gcOnFly synthetic track so it will correctly work with saves sessions refs #35958
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    778a5fc121bbf71e8ed92064eee8d8869a94ad41 Thu Mar 26 15:42:38 2026 -0700
    set the gcOnFly track to release alpha refs #35958
• src/hg/utils/hubCheck/hubCheck.c
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    86f72a48aa5e300161f9b14bcb15fa8499122838 Wed Mar 25 16:11:04 2026 -0700
    Fix array length calcuation for a chopByChar call that caused a segfault. Stop at 5 failing sequence names per genome to speed up checking, refs #37174
• src/inc/jsonWrite.h
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    ddb85ced5e8b6127a233b5cda5fcb1fbe2260578 Wed Mar 25 04:22:06 2026 -0700
    Add detailsScript trackDb mechanism for JS visualizations on bigBed details pages Changing based on feedback from Jonathan, Chris and Brian after group discussion. Refactored existing Claude-generated code, moving functions into libraries. This is the first use of ES6 modules in the kent js code. In 2026, this should be acceptable? New trackDb syntax: detailsScript.<plotType>.<fieldName> <jsonConfig> The C code (bigBedClick.c) collects these settings, exports field values as JSON (bedDetails object), and dynamically imports hgc.<plotType>.js as an ES6 module. Fields used by detailsScript are shown in the HTML table with empty values, filled by JavaScript. Includes hgc.histogram.js module for drawing SVG bar chart histograms from logfmt-encoded data (space-separated key=value pairs). Applied to both the trexplorer and webstr tracks in the strVar supertrack. Also adds jsonWriteJsonElement() helper to jsonWrite.c for writing parsed jsonElement trees into a jsonWrite stream. max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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    48791463f4a686c550d4515888b0e466c21e0fc9 Wed Mar 25 13:32:51 2026 -0700
    broke build with previous commit, fixing it now
• src/lib/jsonWrite.c
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    ddb85ced5e8b6127a233b5cda5fcb1fbe2260578 Wed Mar 25 04:22:06 2026 -0700
    Add detailsScript trackDb mechanism for JS visualizations on bigBed details pages Changing based on feedback from Jonathan, Chris and Brian after group discussion. Refactored existing Claude-generated code, moving functions into libraries. This is the first use of ES6 modules in the kent js code. In 2026, this should be acceptable? New trackDb syntax: detailsScript.<plotType>.<fieldName> <jsonConfig> The C code (bigBedClick.c) collects these settings, exports field values as JSON (bedDetails object), and dynamically imports hgc.<plotType>.js as an ES6 module. Fields used by detailsScript are shown in the HTML table with empty values, filled by JavaScript. Includes hgc.histogram.js module for drawing SVG bar chart histograms from logfmt-encoded data (space-separated key=value pairs). Applied to both the trexplorer and webstr tracks in the strVar supertrack. Also adds jsonWriteJsonElement() helper to jsonWrite.c for writing parsed jsonElement trees into a jsonWrite stream. max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/utils/bigGuessDb/bigGuessDb
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    80f3f48aa2295da051eebc3b19c56a46ee39788b Thu Mar 26 06:43:36 2026 -0700
    adding VCF support to bigGuessDb, no redmine
• src/utils/qa/buildPublicSessionThumbnailsIndexPage.py
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    c2d63f068433c6f321c57b380733ace4bbec12b7 Thu Mar 26 13:21:13 2026 -0700
    Fix UnboundLocalError in buildPublicSessionThumbnailsIndexPage.py when sessions have unusual names that cause the trash line parsing to fail. Skip sessions where sessionUrl was not set instead of crashing. No RM. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/utils/qa/mlqAutomate.py
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    bc70099d05e549ea2cd85689d7eaeac3d62bef3e Fri Mar 27 15:05:41 2026 -0700
    Fix mlqAutomate quote stripping for Apple Mail/Outlook Mac format. refs #37297 The From:/Date:/To: multi-line quote header used by Apple Mail and Outlook for Mac was not being detected, only From:/Sent:/To: (Windows Outlook). This caused quoted thread history to remain in the email body, triggering false-positive duplicate detection and skipping legitimate new replies.
• src/utils/qa/qaTestScript.py
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    b8e1ef1c46936830b5066f7917d1af149679a65a Thu Mar 26 13:36:47 2026 -0700
    Fixing Selenium timing crashes by replacing time.sleep() with WebDriverWait and fixing ActionChains reuse in cartReset, No RM
• src/utils/redmineCli
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    8634e6bb43da3e4118c9d66a425fb8ed2e112537 Wed Mar 25 07:55:41 2026 -0700
    redmineCli: accept status names in --status, not just numeric IDs Add STATUS_IDS mapping and resolve_status() so update --status accepts names like "QA Ready" or "In Progress" in addition to numeric IDs, matching the existing name-based --assigned-to behavior. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

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• files changed: 292