Commits for max

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

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/gnomadV4.1.html - 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>
  • src/hg/makeDb/doc/hg38/strVar.txt - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/scripts/trexplorer/trexplorer.as - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/scripts/trexplorer/trexplorerToBed.py - lines changed 140, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/strVar.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/strVar.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trexplorer.html - lines changed 124, context: html, text, full: html, text

f7c829bade73527f309fe014daffc593426520c7 Tue Mar 17 07:46:51 2026 -0700

• strVar docs update
  • src/hg/makeDb/trackDb/human/hg38/strVar.html - lines changed 3, context: html, text, full: html, text

5f7b866b6b7036475f9631251398b895d910149d Wed Mar 18 03:43:06 2026 -0700

• str var docs update
  • src/hg/makeDb/trackDb/human/hg38/strVar.html - lines changed 21, 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/scripts/webstr/webstrToBed.py - lines changed 12, context: html, text, full: html, text

9503ddb81a5f54677116bdf1b6d059350441c711 Wed Mar 18 09:00:18 2026 -0700

• str var docs update 2
  • src/hg/makeDb/doc/hg38/varFreqs.txt - lines changed 105, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trexplorer.html - lines changed 13, 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/doc/hg38/varFreqs.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/abraomToVcf.py - lines changed 242, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/alfa_to_vcf.py - lines changed 309, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/finngen_to_vcf.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/makeDb/scripts/varFreqs/hrcToVcf.py - lines changed 126, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/kovaToVcf.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/makeDb/scripts/varFreqs/saudiToVcf.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/makeDb/scripts/varFreqs/schema_addAcAnAf.py - lines changed 84, context: html, text, full: html, text
  • src/hg/makeDb/scripts/varFreqs/sparkMergeVcfAddCounts.sh - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/makeDb/trackDb/human/abraom.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/alfaVcf.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/allofus.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/finngen.html - lines changed 56, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/gasp.html - lines changed 50, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/gregor.html - lines changed 78, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hgdp1kFreq.html - lines changed 79, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hrc.html - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/indigenomes.html - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/kova.html - lines changed 59, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/mgrb.html - lines changed 45, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/mxbFreq.html - lines changed 78, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/npm.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/saudi.html - lines changed 51, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/schema.html - lines changed 73, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/sfariSparkExomes.html - lines changed 124, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/sgdpFreq.html - lines changed 69, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/swefreq.html - lines changed 68, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/tommo60kjpn.html - lines changed 50, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/topmed.html - lines changed 53, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.html - lines changed 739, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 226, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqsAll.html - lines changed 6, context: html, text, full: html, text

32210ea1b735a49d95ab5a8f7263e9dc13d47c8b Wed Mar 18 09:41:30 2026 -0700

• adding ncOrf docs page, refs #37036
  • src/hg/makeDb/trackDb/human/hg38/ncOrfs.html - lines changed 102, 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/abraom.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/alfaVcf.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/allofus.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/finngen.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/gasp.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/gregor.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trexplorer.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hgdp1kFreq.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hrc.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/indigenomes.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/kova.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/mgrb.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/mxbFreq.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/npm.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/saudi.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/schema.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/sfariSparkExomes.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/sgdpFreq.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/swefreq.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/tommo60kjpn.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/topmed.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 2, 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
  • src/hg/makeDb/trackDb/human/hg38/strVar.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - 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/hgc/bigBedClick.c - lines changed 89, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 21, context: html, text, full: html, text
  • src/hg/hgc/hgc.h - lines changed 4, context: html, text, full: html, text
  • src/hg/js/detailsHistogram.js - lines changed 132, context: html, text, full: html, text
  • src/hg/js/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/strVar.ra - lines changed 3, context: html, text, full: html, text

e82f973dc7a5a814f0fd23999aa27222fa1260da Fri Mar 20 09:56:15 2026 -0700

• primateAI track, refs #37274
  • src/hg/makeDb/doc/hg38/primateAi.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/scripts/primateAiToBigBed.py - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/predictionScoresSuper.html - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/predictionScoresSuper.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/primateAi.html - lines changed 86, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/primateAi.ra - lines changed 15, 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/gencNcOrfs.html - lines changed 117, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/metamorf.html - lines changed 222, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/ncOrfs.html - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/ncOrfs.ra - lines changed 49, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/nuorfdb.html - lines changed 120, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/openprot.html - lines changed 141, 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/primateAi.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/scripts/primateai/primateAi.as - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/scripts/primateai/primateAiToBigBed.py - lines changed 57, 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/bigBedClick.c - lines changed 17, context: html, text, full: html, text

a939f7e2ddc1a11f641e065b0d49a57f4ee8ae14 Mon Mar 23 06:21:52 2026 -0700

• moving genePredCompare tool to non-apps build, email from Hiram
  • src/utils/makefile - lines changed 11, 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/doc/hg38/varFreqs.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.html - lines changed 55, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqs.ra - lines changed 185, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/varFreqsAll.html - lines changed 151, context: html, text, full: html, text