Commits for gperez2

v499_preview2 to v499_base (2026-05-25 to 2026-06-01) v499

9ad79ae3a13f2d326f7c38298eaef31949bb49c7 Sun May 24 15:04:49 2026 -0700

• Adding the BoG 2026 and ISV 2026 posters to the poster gallery, refs #36182
  • src/hg/htdocs/goldenPath/help/posters.html - lines changed 33, context: html, text, full: html, text

5724ad5d9290148a32893884949a9455d5a32012 Sun May 24 15:44:48 2026 -0700

• Fixing typo in Publications link in hardcoded footer (pubs.htm to pubs.html). Related to the "Fixing 404 links for the 2026-03-15 Static Page Cronjob" commit but was not committed at the time. No RM.
  • src/hg/htdocs/inc/gbFooterHardcoded.html - lines changed 1, context: html, text, full: html, text

ca24bbc74b74174bec0fa1713fbb1250d1e5ef4e Mon May 25 21:44:07 2026 -0700

• Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923 - DNase/ATAC/Histone/CTCF (Indiv.): added experiment counts (3,201 hg38, 589 mm10) per code review feedback (refs #37577 note-7), updated Signal/Peak bullet header wording. - TF rPeaks: added grayscale legend table, reworded peak shading description, colored the word "green" to match the motif decorator color. - TF ChIP-seq (Indiv.): updates to opening paragraph, added Signal/Peak bullet block with grayscale legend to Description. - ENCODE4 Regulation supertrack: added (Layered)/(Indiv.) explanation paragraph, bolded track names, fixed Indiv. capitalization and DNase/ATAC order to match shortLabels. hg38: alphabetized References, mirrored TF rPeaks grayscale wording, changed inline PMID citation to author/year. - DNase, ATAC, H3K4me3, H3K27ac, CTCF (Layered): added "By default," to transparent overlay sentence in shared HTML. - RNA-seq (Indiv.): updated experiment counts (523 hg38, 216 mm10), updated filter list to match hgTrackUi facet names, added Available Organs and Tissues table. - Transcription (Layered): restructured Available Organs and Tissues table, added "By default," to transparent overlay sentence.
  • src/hg/makeDb/trackDb/encode4RegLayeredDisplay.shared.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.html - lines changed 43, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.html - lines changed 56, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.html - lines changed 87, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfPeaks.html - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Txn.html - lines changed 55, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.html - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.html - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.html - lines changed 66, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegTxn.html - lines changed 14, context: html, text, full: html, text

94087f3f31945d133c187137ebbf0eddaf808dc3 Tue May 26 10:50:26 2026 -0700

• Per author request, reordered the bars shown on the Genome Browser image to follow the biological tissue order. Following Max's suggestion in #37619, added the barChartReorder.py script and documented the reorder step in the mm10 and mm39 makedocs. refs #37001
  • src/hg/makeDb/doc/mm10.txt - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm39/mouseDevTimecourse.txt - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/scripts/barChartReorder/barChartReorder.py - lines changed 200, context: html, text, full: html, text

6db91c5823e6f55265fc2e2a06343110786ccd66 Tue May 26 13:41:50 2026 -0700

• Removed the 2026-05-26 mouseDevTimecourse bigBed and categories reorder per team feedback in #36998 notes 54-56. Restored the original bigBed files from the Wold Lab hub, kept the new colors, and removed the reorder steps from the mm10 and mm39 makedocs. refs #37001
  • src/hg/makeDb/doc/mm10.txt - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm39/mouseDevTimecourse.txt - lines changed 32, context: html, text, full: html, text

0201b9f4a7d4f665dc54b51073adc87705d616ec Thu May 28 19:19:34 2026 -0700

• Updating filterPriority documentation and adding highlightPriority section. refs #29223
  • src/hg/htdocs/goldenPath/help/trackDb/changes.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html - lines changed 6, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html - lines changed 5, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 46, context: html, text, full: html, text

b6079eda943a2a12159306cf7194ffdd90f53d96 Fri May 29 12:09:35 2026 -0700

• Updating the Cancel button XPath in the shift+drag (Drag-and-select) test, No RM
  • src/utils/qa/qaTestScript.py - lines changed 1, context: html, text, full: html, text

2d68c3e32f7f241d7d34034d3e13671287b51d28 Fri May 29 16:06:18 2026 -0700

• Following Max's email suggestion, moved the mouseDevTimecourse bigBarChart subtracks on mm10 under the ENCODE3 Regulation superTrack. On alpha, made that superTrack visible by default and hid the Chromatin State and Open Chromatin tracks so they don't show up when the superTrack is now on. refs #37001
  • src/hg/makeDb/trackDb/mouse/mm10/encode3.atac.ra - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode3.chromHmm.ra - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/mouseDevTimecourse.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.alpha.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 2, context: html, text, full: html, text