File Changes for max

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

• 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>
• 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>
  • lines changed 2, context: html, text, full: html, text
    2694cffb31b95f1729b2d8c5252e406e66a5e61d Thu Mar 26 02:18:25 2026 -0700
    changes after AI code review
• src/hg/hgc/hgc.c
  • 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>
• 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/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/hgc.histogram.js
  • lines changed 163, 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/hui.js
  • lines changed 10, 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>
• src/hg/js/makefile
  • 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/doc/hg38/nmd.txt
  • lines changed 59, context: html, text, full: html, text
    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
  • lines changed 5, context: html, text, full: html, text
    cf59add626c31740a9a65a4c576b71b822260ced Tue Mar 24 04:18:15 2026 -0700
    fixing up NMD track and adding decorator tdb, refs #33737
  • lines changed 2, context: html, text, full: html, text
    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
  • lines changed 32, context: html, text, full: html, text
    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/nmd/genePredNmdEsc
  • lines changed 265, context: html, text, full: html, text
    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
• src/hg/makeDb/scripts/nmd/lindeboomToBigWig.sh
  • lines changed 25, context: html, text, full: html, text
    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
  • lines changed 1, context: html, text, full: html, text
    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
  • lines changed 15, context: html, text, full: html, text
    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
• src/hg/makeDb/scripts/nmd/nmdEscDecoration.as
  • lines changed 21, context: html, text, full: html, text
    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
• src/hg/makeDb/scripts/primateAiToBigBed.py
  • lines changed 57, context: html, text, full: html, text
    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
  • lines changed 18, context: html, text, full: html, text
    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
  • lines changed 94, context: html, text, full: html, text
    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
  • lines changed 17, 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/varFreqs/databases.tsv
  • lines changed 24, context: html, text, full: html, text
    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
  • lines changed 28, context: html, text, full: html, text
    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
  • lines changed 94, context: html, text, full: html, text
    093f3160b963cc1b05b409732f6a233d11bdfecf Wed Mar 25 04:41:12 2026 -0700
    changed after code review, refs #37291
• src/hg/makeDb/scripts/webstr/webstr.as
  • lines changed 11, 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/webstr/webstrToBed.py
  • lines changed 4, 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/trackDb/human/hg38/knownGene.nmd_deco.ra
  • lines changed 1, context: html, text, full: html, text
    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
  • lines changed 7, context: html, text, full: html, text
    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
  • lines changed 84, context: html, text, full: html, text
    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
  • lines changed 10, context: html, text, full: html, text
    e9d2a1912a2614531cd517c8cb6adab86d94f3a5 Tue Mar 24 04:26:33 2026 -0700
    nmd docs, refs#33737
  • lines changed 9, context: html, text, full: html, text
    536f961aba550065f88bd667b17bcddf10ae56d1 Tue Mar 24 04:35:33 2026 -0700
    nmd docs update again, refs #33737
  • lines changed 1, context: html, text, full: html, text
    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
  • lines changed 102, context: html, text, full: html, text
    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
• src/hg/makeDb/trackDb/human/hg38/nmdDetective.html
  • lines changed 105, context: html, text, full: html, text
    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
  • lines changed 1, context: html, text, full: html, text
    2694cffb31b95f1729b2d8c5252e406e66a5e61d Thu Mar 26 02:18:25 2026 -0700
    changes after AI code review
• src/hg/makeDb/trackDb/human/hg38/nmdEscTranscripts.html
  • lines changed 113, context: html, text, full: html, text
    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
  • lines changed 1, context: html, text, full: html, text
    45fe522cdfda1196c83624e8cce9d13a73cb18f4 Tue Mar 24 04:29:47 2026 -0700
    nmd docs update, refs #33737
• src/hg/makeDb/trackDb/human/hg38/strVar.ra
  • lines changed 8, 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/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    bfa91627a224f0ca4a9e10718297df25f163847a Tue Mar 24 04:09:48 2026 -0700
    adding NMD escape supertrack, refs #33737
• src/hg/makeDb/trackDb/human/hg38/utrAnnotUorfs.html
  • lines changed 124, context: html, text, full: html, text
    3365286ae98d7d34824fd15a2d9e084c5a68f5a5 Wed Mar 25 06:28:33 2026 -0700
    adding utrAnnotator ORF, for the ncORFs track, refs #35101
• src/hg/makeDb/trackDb/human/predictionScoresSuper.html
  • lines changed 19, context: html, text, full: html, text
    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
  • lines changed 1, context: html, text, full: html, text
    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
  • lines changed 72, context: html, text, full: html, text
    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
  • lines changed 77, context: html, text, full: html, text
    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
  • lines changed 28, context: html, text, full: html, text
    305b083ab4b1ccda250da6f79b092f8aeb4137fb Tue Mar 24 07:57:20 2026 -0700
    small doc updates to varFreqs track
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 3, 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/inc/jsonWrite.h
  • lines changed 3, 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 2, context: html, text, full: html, text
    48791463f4a686c550d4515888b0e466c21e0fc9 Wed Mar 25 13:32:51 2026 -0700
    broke build with previous commit, fixing it now
• src/lib/jsonWrite.c
  • lines changed 43, 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/utils/bigGuessDb/bigGuessDb
  • lines changed 31, context: html, text, full: html, text
    80f3f48aa2295da051eebc3b19c56a46ee39788b Thu Mar 26 06:43:36 2026 -0700
    adding VCF support to bigGuessDb, no redmine
• src/utils/redmineCli
  • lines changed 51, context: html, text, full: html, text
    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>