Commits for max

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

e6c80060e99101f891cea314cd796a82ed1055fd Wed Apr 8 02:24:44 2026 -0700

• Add detailsScript trackDb setting documentation, refs #37273 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • src/hg/htdocs/goldenPath/help/trackDb/changes.html - lines changed 8, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html - lines changed 4, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html - lines changed 4, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 45, context: html, text, full: html, text

b65520b87b2f80ac7fd537e8c361223d0a9dc72d Thu Apr 9 01:42:08 2026 -0700

• fixing various gbic issues found by Theo/Jorge and Claude code review, no redmine
  • src/product/installer/browserSetup.sh - lines changed 19, context: html, text, full: html, text

ed005215c7fdd3e97c61edb41931c89805d9566b Thu Apr 9 03:06:48 2026 -0700

• Add repeatId field to webstr bigBed for outlinks, update webstr and strVar docs, refs #36652 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • src/hg/makeDb/scripts/webstr/webstr.as - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/webstr/webstrToBed.py - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/strVar.html - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/strVar.ra - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/webstr.html - lines changed 22, context: html, text, full: html, text

814472876eac4d004d61f0ed89bd2aaa07459d33 Thu Apr 9 06:42:24 2026 -0700

• Fix composite vis: prefer pack over full, fix [-] button hide, refs #37182 Two issues from QA (note-17): 1) exposeAll() and onUserCbChange() always set composite to "full" when re-enabling subtracks on tracks without a "pack" option. Now tries pack first, then dense, then full as last resort. 2) The matrix [-] button (btn_minus_all_left_top) did not hide the composite. _matSetMatrixCheckBoxes() called hideAll() which triggered propagateVis, and propagateVis re-checked all subCBs when checkedCount===0, undoing the hide. Fix: set composite to hide directly via prop('selectedIndex', 0) without triggering propagateVis. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • src/hg/js/hui.js - lines changed 28, context: html, text, full: html, text
  • src/hg/js/subCfg.js - lines changed 8, context: html, text, full: html, text

fdded708bc8405da6d0ff43d42f0092a872a0a97 Fri Apr 10 01:51:06 2026 -0700

• fixing dumb bug in install script, no redmine
  • src/product/installer/browserSetup.sh - lines changed 1, context: html, text, full: html, text

f1f04f7cc152203f17d587f10b1bc176e45e9eae Fri Apr 10 01:52:03 2026 -0700

• fixing up after claude
  • src/hg/js/hui.js - lines changed 12, context: html, text, full: html, text

a37d4ffb473b6ebf6c66545f2b7d5f7eef35ef4b Fri Apr 10 03:00:33 2026 -0700

• Color strVar subtracks by expected heterozygosity instead of motif period, fix hgTrackUi filter label truncation, refs #36652 Change all four strVar subtracks (webstr, tommoStr, trexplorer, viennaVntr) from motif-period-based coloring to expected heterozygosity (het = 1 - sum(p_i^2)), using a blue-to-red heat map: dark blue (het<0.1) through medium blue, light purple, salmon, to dark red (het>=0.7). Add het as a filterable bigBed field with scoreFilter and filterByRange on each track. Update mouseOver, track docs, and makedoc. Also fix hgTrackUi to strip the "|..." suffix from autoSql comments when displaying numeric filter labels. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • src/hg/lib/hui.c - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/strVar.txt - lines changed 59, context: html, text, full: html, text
  • src/hg/makeDb/scripts/tommoStr/tommoStr.as - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/scripts/tommoStr/tommoStrToBed.py - lines changed 172, context: html, text, full: html, text
  • src/hg/makeDb/scripts/trexplorer/trexplorer.as - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/trexplorer/trexplorerToBed.py - lines changed 53, context: html, text, full: html, text
  • src/hg/makeDb/scripts/viennaVntr/viennaVntr.as - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/scripts/viennaVntr/viennaVntrHet.py - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/scripts/viennaVntr/viennaVntrToBed.py - lines changed 126, context: html, text, full: html, text
  • src/hg/makeDb/scripts/webstr/webstr.as - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/webstr/webstrToBed.py - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/strVar.ra - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/tommoStr.html - lines changed 118, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trexplorer.html - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/viennaVntr.html - lines changed 108, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/webstr.html - lines changed 12, context: html, text, full: html, text

089edf62bb8a818c89d8e696c8d1a09d53ecdb84 Fri Apr 10 05:49:40 2026 -0700

• document new sampleMetadataFile trackDb statement for VCF tracks, refs #37306 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • src/hg/htdocs/goldenPath/help/trackDb/changes.html - lines changed 8, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 28, context: html, text, full: html, text

412b01f1c0c78dd890c3d0d00fc121727e6085dd Fri Apr 10 05:59:34 2026 -0700

• warn on column count mismatch in sampleMetadataFile parsing, refs #37334 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
  • src/hg/hgc/vcfClick.c - lines changed 14, context: html, text, full: html, text

ff128a6ed0d1f03aa6ca3808669f4109e1d05542 Fri Apr 10 20:29:24 2026 -0700

• moving mpra back into regulation, typo, refs #34284
  • src/hg/makeDb/trackDb/human/hg38/mpra.ra - lines changed 1, context: html, text, full: html, text