File Changes for max

v496_preview to v496_preview2 (2026-03-16 to 2026-03-23) v496

• src/hg/hgc/bigBedClick.c
  • lines changed 89, context: html, text, full: html, text
    b33425c626414803bbddc702caecc256c5022277 Fri Mar 20 09:10:59 2026 -0700
    defining detailsHistogram tdb statements and an example histogram drawing code for it, used in the trexplorer track, refs #37273
  • lines changed 17, context: html, text, full: html, text
    cc9a51b3c9de74d78a0c7eeedb2b83d6336108c5 Mon Mar 23 04:36:13 2026 -0700
    automated code review found that we already have an escape function, so asked Claude to us it, refs #37273
• src/hg/hgc/hgc.c
  • lines changed 21, context: html, text, full: html, text
    b33425c626414803bbddc702caecc256c5022277 Fri Mar 20 09:10:59 2026 -0700
    defining detailsHistogram tdb statements and an example histogram drawing code for it, used in the trexplorer track, refs #37273
• src/hg/hgc/hgc.h
  • lines changed 4, context: html, text, full: html, text
    b33425c626414803bbddc702caecc256c5022277 Fri Mar 20 09:10:59 2026 -0700
    defining detailsHistogram tdb statements and an example histogram drawing code for it, used in the trexplorer track, refs #37273
• src/hg/js/detailsHistogram.js
  • lines changed 132, context: html, text, full: html, text
    b33425c626414803bbddc702caecc256c5022277 Fri Mar 20 09:10:59 2026 -0700
    defining detailsHistogram tdb statements and an example histogram drawing code for it, used in the trexplorer track, refs #37273
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    b33425c626414803bbddc702caecc256c5022277 Fri Mar 20 09:10:59 2026 -0700
    defining detailsHistogram tdb statements and an example histogram drawing code for it, used in the trexplorer track, refs #37273
• src/hg/makeDb/doc/hg38/primateAi.txt
  • lines changed 17, context: html, text, full: html, text
    e82f973dc7a5a814f0fd23999aa27222fa1260da Fri Mar 20 09:56:15 2026 -0700
    primateAI track, refs #37274
  • lines changed 2, context: html, text, full: html, text
    59e0ac66496c36893df2b1440a037557fed23ff4 Mon Mar 23 04:31:33 2026 -0700
    fixing up primateai makedoc, refs #37274
• src/hg/makeDb/doc/hg38/strVar.txt
  • lines changed 27, context: html, text, full: html, text
    f163cd6d8b443276863daa47c386072244dacc88 Tue Mar 17 07:27:58 2026 -0700
    Adding TRExplorer V2 tandem repeat catalog track to strVar supertrack, max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/hg38/varFreqs.txt
  • lines changed 105, context: html, text, full: html, text
    9503ddb81a5f54677116bdf1b6d059350441c711 Wed Mar 18 09:00:18 2026 -0700
    str var docs update 2
  • lines changed 9, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 5, context: html, text, full: html, text
    165a15d6a94d53f8162a01e69f3912a7a23a3b50 Mon Mar 23 06:47:55 2026 -0700
    mostly done with the variant frequencies track, refs#36642
• src/hg/makeDb/scripts/primateAiToBigBed.py
  • lines changed 57, context: html, text, full: html, text
    e82f973dc7a5a814f0fd23999aa27222fa1260da Fri Mar 20 09:56:15 2026 -0700
    primateAI track, refs #37274
• src/hg/makeDb/scripts/primateai/primateAi.as
  • lines changed 21, context: html, text, full: html, text
    59e0ac66496c36893df2b1440a037557fed23ff4 Mon Mar 23 04:31:33 2026 -0700
    fixing up primateai makedoc, refs #37274
• src/hg/makeDb/scripts/primateai/primateAiToBigBed.py
  • lines changed 57, context: html, text, full: html, text
    59e0ac66496c36893df2b1440a037557fed23ff4 Mon Mar 23 04:31:33 2026 -0700
    fixing up primateai makedoc, refs #37274
• src/hg/makeDb/scripts/trexplorer/trexplorer.as
  • lines changed 33, context: html, text, full: html, text
    f163cd6d8b443276863daa47c386072244dacc88 Tue Mar 17 07:27:58 2026 -0700
    Adding TRExplorer V2 tandem repeat catalog track to strVar supertrack, max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/trexplorer/trexplorerToBed.py
  • lines changed 140, context: html, text, full: html, text
    f163cd6d8b443276863daa47c386072244dacc88 Tue Mar 17 07:27:58 2026 -0700
    Adding TRExplorer V2 tandem repeat catalog track to strVar supertrack, max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/abraomToVcf.py
  • lines changed 242, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/alfa_to_vcf.py
  • lines changed 309, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/finngen_to_vcf.py
  • lines changed 0, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/hrcToVcf.py
  • lines changed 126, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/kovaToVcf.py
  • lines changed 0, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/saudiToVcf.py
  • lines changed 0, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/schema_addAcAnAf.py
  • lines changed 84, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/sparkMergeVcfAddCounts.sh
  • lines changed 0, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/webstr/webstrToBed.py
  • lines changed 12, context: html, text, full: html, text
    d2b7a0b56d985859c5deed015119edce22449b91 Wed Mar 18 03:45:53 2026 -0700
    Change webstr track name to motifxCopyCount format to match trexplorer, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/abraom.html
  • lines changed 63, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 3, context: html, text, full: html, text
    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/alfaVcf.html
  • lines changed 44, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 3, context: html, text, full: html, text
    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/allofus.html
  • lines changed 63, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 3, context: html, text, full: html, text
    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/finngen.html
  • lines changed 56, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 3, context: html, text, full: html, text
    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/gasp.html
  • lines changed 50, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 3, context: html, text, full: html, text
    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/gregor.html
  • lines changed 78, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 6, context: html, text, full: html, text
    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/gencNcOrfs.html
  • lines changed 117, context: html, text, full: html, text
    480184bd87fd28bc6979a6614994d8e5d32408d4 Fri Mar 20 16:10:47 2026 -0700
    finishing up the ncOrfs track, refs #35101
• src/hg/makeDb/trackDb/human/hg38/gnomadV4.1.html
  • lines changed 16, context: html, text, full: html, text
    7ee933ee520cbb5fb38a80c3e73104e3b183c4a9 Mon Mar 16 07:56:03 2026 -0700
    fixing typos found by Claude and adding some info from gnomad.html
• src/hg/makeDb/trackDb/human/hg38/metamorf.html
  • lines changed 222, context: html, text, full: html, text
    480184bd87fd28bc6979a6614994d8e5d32408d4 Fri Mar 20 16:10:47 2026 -0700
    finishing up the ncOrfs track, refs #35101
• src/hg/makeDb/trackDb/human/hg38/ncOrfs.html
  • lines changed 102, context: html, text, full: html, text
    32210ea1b735a49d95ab5a8f7263e9dc13d47c8b Wed Mar 18 09:41:30 2026 -0700
    adding ncOrf docs page, refs #37036
  • lines changed 150, context: html, text, full: html, text
    480184bd87fd28bc6979a6614994d8e5d32408d4 Fri Mar 20 16:10:47 2026 -0700
    finishing up the ncOrfs track, refs #35101
• src/hg/makeDb/trackDb/human/hg38/ncOrfs.ra
  • lines changed 49, context: html, text, full: html, text
    480184bd87fd28bc6979a6614994d8e5d32408d4 Fri Mar 20 16:10:47 2026 -0700
    finishing up the ncOrfs track, refs #35101
• src/hg/makeDb/trackDb/human/hg38/nuorfdb.html
  • lines changed 120, context: html, text, full: html, text
    480184bd87fd28bc6979a6614994d8e5d32408d4 Fri Mar 20 16:10:47 2026 -0700
    finishing up the ncOrfs track, refs #35101
• src/hg/makeDb/trackDb/human/hg38/openprot.html
  • lines changed 141, context: html, text, full: html, text
    480184bd87fd28bc6979a6614994d8e5d32408d4 Fri Mar 20 16:10:47 2026 -0700
    finishing up the ncOrfs track, refs #35101
• src/hg/makeDb/trackDb/human/hg38/strVar.html
  • lines changed 4, context: html, text, full: html, text
    f163cd6d8b443276863daa47c386072244dacc88 Tue Mar 17 07:27:58 2026 -0700
    Adding TRExplorer V2 tandem repeat catalog track to strVar supertrack, max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 3, context: html, text, full: html, text
    f7c829bade73527f309fe014daffc593426520c7 Tue Mar 17 07:46:51 2026 -0700
    strVar docs update
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    5f7b866b6b7036475f9631251398b895d910149d Wed Mar 18 03:43:06 2026 -0700
    str var docs update
• src/hg/makeDb/trackDb/human/hg38/strVar.ra
  • lines changed 16, context: html, text, full: html, text
    f163cd6d8b443276863daa47c386072244dacc88 Tue Mar 17 07:27:58 2026 -0700
    Adding TRExplorer V2 tandem repeat catalog track to strVar supertrack, max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 3, context: html, text, full: html, text
    8bc3d5c597d9a4a29dad3804e97752cbfb40629a Fri Mar 20 07:47:14 2026 -0700
    adding trexplorer track with special tdb tags, no redmine yet
  • lines changed 3, context: html, text, full: html, text
    b33425c626414803bbddc702caecc256c5022277 Fri Mar 20 09:10:59 2026 -0700
    defining detailsHistogram tdb statements and an example histogram drawing code for it, used in the trexplorer track, refs #37273
• src/hg/makeDb/trackDb/human/hg38/trexplorer.html
  • lines changed 124, context: html, text, full: html, text
    f163cd6d8b443276863daa47c386072244dacc88 Tue Mar 17 07:27:58 2026 -0700
    Adding TRExplorer V2 tandem repeat catalog track to strVar supertrack, max, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • lines changed 13, context: html, text, full: html, text
    9503ddb81a5f54677116bdf1b6d059350441c711 Wed Mar 18 09:00:18 2026 -0700
    str var docs update 2
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hgdp1kFreq.html
  • lines changed 79, context: html, text, full: html, text
    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hrc.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/indigenomes.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/kova.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/mgrb.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/mxbFreq.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/npm.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/predictionScoresSuper.html
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    e82f973dc7a5a814f0fd23999aa27222fa1260da Fri Mar 20 09:56:15 2026 -0700
    primateAI track, refs #37274
• src/hg/makeDb/trackDb/human/predictionScoresSuper.ra
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    e82f973dc7a5a814f0fd23999aa27222fa1260da Fri Mar 20 09:56:15 2026 -0700
    primateAI track, refs #37274
• src/hg/makeDb/trackDb/human/primateAi.html
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    e82f973dc7a5a814f0fd23999aa27222fa1260da Fri Mar 20 09:56:15 2026 -0700
    primateAI track, refs #37274
• src/hg/makeDb/trackDb/human/primateAi.ra
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    e82f973dc7a5a814f0fd23999aa27222fa1260da Fri Mar 20 09:56:15 2026 -0700
    primateAI track, refs #37274
• src/hg/makeDb/trackDb/human/saudi.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/schema.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/sfariSparkExomes.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/sgdpFreq.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/swefreq.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/tommo60kjpn.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/topmed.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/varFreqs.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    165a15d6a94d53f8162a01e69f3912a7a23a3b50 Mon Mar 23 06:47:55 2026 -0700
    mostly done with the variant frequencies track, refs#36642
• src/hg/makeDb/trackDb/human/varFreqs.ra
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    383da828477aad2b3c6053880a64fdbfc2a00cd9 Thu Mar 19 02:30:41 2026 -0700
    Fix varFreqs HTML issues and trexplorer citation, from AI code review 2026-03-19, refs #36642 Fix broken $db download URLs to hg38 in 14 HTML files, correct "Japanese" to "Korean" in kova.html, fix "area" typo in schema.html, fix "Finnland" to "Finland" in varFreqs.ra, normalize GREGoR capitalization, fix grammar, quote all target=_blank attributes, capitalize GitHub consistently, and fix bioRxiv citation formatting in trexplorer.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    165a15d6a94d53f8162a01e69f3912a7a23a3b50 Mon Mar 23 06:47:55 2026 -0700
    mostly done with the variant frequencies track, refs#36642
• src/hg/makeDb/trackDb/human/varFreqsAll.html
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    aa61ebc800429515f9ced7e28f669c6042219f43 Wed Mar 18 09:09:13 2026 -0700
    varFreqs supertrack: add GREGoR track, update all HTML docs, move scripts to varFreqs/, refs #36642 Add GREGoR R04 WGS track to varFreqs superTrack. Update Data Access and Methods sections for all 20+ subtrack HTML files with consistent formatting, sequencing methods from source papers, and links to makeDoc and Github scripts. Move all varFreqs conversion scripts into scripts/varFreqs/ subdirectory and update makeDoc paths accordingly. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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    165a15d6a94d53f8162a01e69f3912a7a23a3b50 Mon Mar 23 06:47:55 2026 -0700
    mostly done with the variant frequencies track, refs#36642
• src/hg/makeDb/trackDb/tagTypes.tab
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    8bc3d5c597d9a4a29dad3804e97752cbfb40629a Fri Mar 20 07:47:14 2026 -0700
    adding trexplorer track with special tdb tags, no redmine yet
• src/utils/makefile
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    a939f7e2ddc1a11f641e065b0d49a57f4ee8ae14 Mon Mar 23 06:21:52 2026 -0700
    moving genePredCompare tool to non-apps build, email from Hiram