Commits for gperez2

v504_base to v505_preview (2026-09-21 to 2026-10-05) v505

8adac4bab4fa18bf3cdea99b0da545272cf5652c Mon Sep 21 10:37:40 2026 -0700

• Stripping the \r character from the hubApi err37/err38 test output due to the header printing fix in commit cb99f0b11bd, No RM Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
  • src/hg/hubApi/tests/makefile - lines changed 2, context: html, text, full: html, text

1995fb5512978d502812e7693d5d487bea61f507 Wed Sep 23 15:26:14 2026 -0700

• Updating the ncOrfs description pages: Restructuring gencNcOrfs.html's Description and Display Conventions sections and cleaning up wording. Updating the Description section of fiveUltraUorfs.html. Updating ncOrfs.html's GENCODE and 5ULTRA sections to match their subtrack pages and trimming the GENCODE summary. Minor updates to ncOrfs.ra. Refs #37649
  • src/hg/makeDb/trackDb/human/hg38/fiveUltraUorfs.html - lines changed 50, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/gencNcOrfs.html - lines changed 100, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/ncOrfs.html - lines changed 56, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/ncOrfs.ra - lines changed 3, context: html, text, full: html, text

2ec957f2ac313ee21abfb3724042d681f5774eba Thu Sep 24 16:32:50 2026 -0700

• Updating the hgBlat all genomes checkbox locator to work on both the classic and new BLAT pages, No RM
  • src/utils/qa/qaTestScript.py - lines changed 1, context: html, text, full: html, text

b9bd7488e55a3124bb617290eccee4b544ce8600 Sun Sep 27 16:03:24 2026 -0700

• Updating hgLogin's change-recovery-email description wording: adding GitHub and CILogon and dropping ORCID from the sign-in options it names, and matching existing "sign-in options" phrasing instead of "buttons", refs #38197
  • src/hg/hgLogin/hgLogin.c - lines changed 4, context: html, text, full: html, text

a95e200266087402974f1b02831259d43009b085 Tue Sep 29 10:30:22 2026 -0700

• Updating hubApi schema06 expected output to include the colorFields setting added to crispr10K in commit cf9cfcd463d, No RM
  • src/hg/hubApi/tests/expected/schema06.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

b7b9978c92a2376d6d9ef4f0a4974cb8167295f8 Wed Sep 30 14:17:50 2026 -0700

• Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599
  • src/hg/makeDb/doc/hg38/tad.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/tad.ra - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/tads.html - lines changed 45, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/tadsMcArthur.html - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/tadsSchmitt.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/tad.ra - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/tads.html - lines changed 80, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/tads3dgb.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/tads3dgb.ra - lines changed 506, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/tadsDixon.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/tadsEncode.html - lines changed 52, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/tadsEncode.ra - lines changed 86, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/tadsDixon.html - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/tadsMcArthur.html - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/tadsSchmitt.html - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/tads3dgb.html - lines changed 66, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/tads3dgb.ra - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/tadsEncode.html - lines changed 68, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/tadsEncode.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/tads.html - lines changed 94, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/tads3dgb.ra - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/tadsDixon.html - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/tadsEncode.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/tads.html - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/tads3dgb.html - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/tadsDixon.html - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/tadsEncode.html - lines changed 33, context: html, text, full: html, text

49a1fd197eb0605976bbbe11b949ee425d6dad8a Thu Oct 1 09:48:50 2026 -0700

• Updating hubApi bigNarrowPeak expected output to match the onlyVisibility to visibility change on fiberSeqCompendium_PM00001_peaks in commit ab234fe6290, No RM
  • src/hg/hubApi/tests/expected/bigNarrowPeak.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

7a501bfcc6b8f658a1a3c2b3dfce70a5915243cb Fri Oct 2 15:09:30 2026 -0700

• Updating the /blat missing API key error message in hubApi from "My Track Hubs" to "Track Hubs" to match the My Data menu, refs #37858
  • src/hg/hubApi/blat.c - lines changed 1, context: html, text, full: html, text