Commits for gperez2

v499_base to v500_preview (2026-06-01 to 2026-06-08) v500

ce17d11af0cc02a8aef4f0588a92ac6ff9c0e14d Mon Jun 1 16:53:29 2026 -0700

• Code review edits: closing <A name> anchor tags in the filter and highlight section of trackDbDoc.html. refs #37674
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html - lines changed 9, context: html, text, full: html, text

4509fab8ce258ede7421c8112edb67f956b96e35 Mon Jun 1 19:23:28 2026 -0700

• Updating ENCODE4 Regulation Indiv. subtrack labels. Removes leading "with " from 818 hg38 longLabels, capitalizes the first letter of 8,559 longLabels, and updates 8,497 shortLabels to end with "Peak" or "Signal". refs #34923
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra - lines changed 7851, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.ra - lines changed 860, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.ra - lines changed 5839, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra - lines changed 1162, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.ra - lines changed 1054, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra - lines changed 652, context: html, text, full: html, text

0aff2d78b3be1b2bcd0839173cddbe359e4bd379 Tue Jun 2 09:53:24 2026 -0700

• Removing the barChartReorder.py script since Diane rebuilt the Wold Lab public hub with the new tissue order. refs #37001 #37619
  • src/hg/makeDb/scripts/barChartReorder/barChartReorder.py - lines changed 200, context: html, text, full: html, text

df99c448f8e0386bb718da0044b22752fc145713 Thu Jun 4 00:15:12 2026 -0700

• Updating ENCODE4 Regulation labels and description pages for hg38 and mm10. refs #34923 - Capitalized 363 hg38 Layered organ shortLabels and shortened the over-length TF rPeaks and Indiv. composite longLabels; updated the mm10 TF ChIP container longLabel. - TF rPeaks: added the missing SHOX2 to filterValues.factor (now 912), and updated "911 factors"/"2,502 experiments" to "912"/"2,509". - Supertrack pages: changed Layered bullets from "highlights" to "displays", reworded the histone and CTCF bullets, updated the default-organ note, and updated stale hg38 organ counts to 38/41/26/38/36. - Updated the TF ChIP facet name "Tf" -> "TF" on both description pages. - Makedoc: updated hg38 "911-factor" -> "912-factor" and mm10 RNA-seq Unstranded "26" -> "8".
  • src/hg/makeDb/doc/hg38/encode4.regulation.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.encode4.regulation.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.html - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.ra - lines changed 365, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfPeaks.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.html - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra - lines changed 1, context: html, text, full: html, text

aba7745711570d17c8bcc1cc2236eeaaae1857f9 Thu Jun 4 00:27:41 2026 -0700

• Staging the ENCODE4 Regulation track for hg38 and mm10 on hgwbeta, refs #34923
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 1, context: html, text, full: html, text

8069aa69b6f4d04621a7bcae3b43cea2bb6623c5 Thu Jun 4 11:17:27 2026 -0700

• Updating the accession metadata column header to uppercase (Accession) in the six ENCODE4 Regulation faceted composites' primaryKey and subtrackUrls. refs #34923
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra - lines changed 2, context: html, text, full: html, text

e5116de1d75b89b28693d3df2a3531f7b6c4a6eb Fri Jun 5 11:49:58 2026 -0700

• Restored the standalone ENCODE Expression superTrack on mm10 per team discussion on #37001. Added ENCODE3 Regulation and ENCODE4 Regulation as related tracks on mm10. Added a Released TBD pennantIcon on the mm10 and mm39 superTracks. 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 13, 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
  • src/hg/makeDb/trackDb/mouse/mm39/mouseDevTimecourse.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/relatedTracks.ra - lines changed 4, context: html, text, full: html, text