Commits for gperez2

v502_preview to v502_preview2 (2026-07-27 to 2026-08-04) v502

e71e94fff952fcc0a569e3c89a687a3250396f97 Wed Jul 29 09:44:31 2026 -0700

• Excluding the clade field from hubApi list27/list27b test comparison due to the cron complaining, No RM
  • src/hg/hubApi/tests/makefile - lines changed 1, context: html, text, full: html, text

7a561e21d2bc570f2602bae5150f91c0d4d36ec9 Wed Jul 29 10:27:56 2026 -0700

• Updating hubApi list27 expected output to include the clade field, and removing clade from excludeLines (added in commit e71e94fff95), No RM
  • src/hg/hubApi/tests/expected/list27.gz - 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/hubApi/tests/makefile - lines changed 1, context: html, text, full: html, text

fe36c1b0cd47c32282b161d2f5abd89f19b168da Wed Jul 29 15:27:29 2026 -0700

• Made updates to the hg38 MPC track Description section, Display Conventions and Configuration section (added a legend table and other edits), and Methods section. Also updated gnomadMpc.ra to unhide transcript fields on the details page, reformat the mouseOver display, and clarify the Score field's scale, refs #37478
  • src/hg/makeDb/trackDb/human/hg38/gnomadMpc.html - lines changed 114, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/gnomadMpc.ra - lines changed 3, context: html, text, full: html, text

10db3769dd9edfa38ac8d900ca400fdfb514d9a7 Wed Jul 29 22:41:46 2026 -0700

• An in-place update for gnomad v4.1 to v4.1.1 that swaps bigDataUrl, labels, dataVersion, detailsTabUrls, search descriptions, and removes the alpha-only gnomadVariantsV4.1.1 composite. Updates to gnomad.html, gnomadV4.1.html, and gnomadPLI.html regarding the addition of the gnomad v4.1.1 data, refs #37351
  • src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.alpha.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/gnomad.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/gnomad.ra - lines changed 123, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/gnomadPLI.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/gnomadV4.1.html - lines changed 15, context: html, text, full: html, text

19b8bfeadc8dc28380404a15e39ba662040dd279 Thu Jul 30 09:27:03 2026 -0700

• Adding v4.1.1 to gnomad.html's Constraint Metrics bullet, and updating gnomadPLI.html's general LOEUF threshold recommendation from <0.35 to <0.45. refs #37351
  • src/hg/makeDb/trackDb/human/hg38/gnomad.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/gnomadPLI.html - lines changed 1, context: html, text, full: html, text

195d8eff01e3453a9027c0b679c68410e197f3c7 Fri Jul 31 13:58:07 2026 -0700

• Adding release tags to the gnomadVariantsV4.1 composite and its gnomadExomesVariantsV4_1/gnomadGenomesVariantsV4_1 subtracks. refs #37351
  • src/hg/makeDb/trackDb/human/hg38/gnomad.ra - lines changed 82, context: html, text, full: html, text

062e08e4116be810b29621d9863e22bffdedcf50 Sun Aug 2 23:45:08 2026 -0700

• Updating gnomad.html's Constraint Metrics bullet to say per-gene is only available for v2.1.1, and gnomadPLI.html's flags-section field count, Transcripts Included version list, shading description (pLI to LOEUF), and missense track color description. refs #37351
  • src/hg/makeDb/trackDb/human/hg38/gnomad.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/gnomadPLI.html - lines changed 16, context: html, text, full: html, text