File Changes for gperez2

v501_base to v502_preview (2026-07-20 to 2026-07-27) v502

• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 129, context: html, text, full: html, text
    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
• src/hg/htdocs/images/encode4Regulation.png
  • lines changed 0, context: html, text, full: html, text
    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
• src/hg/htdocs/images/encode4Release.png
  • lines changed 0, context: html, text, full: html, text
    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
• src/hg/makeDb/trackDb/human/hg38/nmd.html
  • lines changed 8, context: html, text, full: html, text
    b86eab362ce697c350764ffe438ccdba8829e0f3 Mon Jul 20 17:37:35 2026 -0700
    Fixing the NMDetective-A/B score-range text (0 to 1, not -1 to +1), updating the citation to Lindeboom et al. 2019, and changing viewLimits to -0.3:1.5 on all four NMDetective subtracks. refs #37843
• src/hg/makeDb/trackDb/human/hg38/nmd.ra
  • lines changed 4, context: html, text, full: html, text
    b86eab362ce697c350764ffe438ccdba8829e0f3 Mon Jul 20 17:37:35 2026 -0700
    Fixing the NMDetective-A/B score-range text (0 to 1, not -1 to +1), updating the citation to Lindeboom et al. 2019, and changing viewLimits to -0.3:1.5 on all four NMDetective subtracks. refs #37843
• src/hg/makeDb/trackDb/human/hg38/nmdDetective.html
  • lines changed 16, context: html, text, full: html, text
    b86eab362ce697c350764ffe438ccdba8829e0f3 Mon Jul 20 17:37:35 2026 -0700
    Fixing the NMDetective-A/B score-range text (0 to 1, not -1 to +1), updating the citation to Lindeboom et al. 2019, and changing viewLimits to -0.3:1.5 on all four NMDetective subtracks. refs #37843
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.alpha.ra
  • lines changed 407, context: html, text, full: html, text
    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra
  • lines changed 4, context: html, text, full: html, text
    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
  • lines changed 1, context: html, text, full: html, text
    42e67e7ac80677bec2f1d71e01dba92625f0078c Thu Jul 23 11:10:20 2026 -0700
    Hiding the default hg38 ENCODE3 Regulation supertrack now that ENCODE4 Regulation is on by default. refs #37845 refs #34923
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.ra
  • lines changed 2, context: html, text, full: html, text
    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/encode.cCREs.override.ra
  • lines changed 2, context: html, text, full: html, text
    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/encode4.ccres.ra
  • lines changed 1, context: html, text, full: html, text
    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131
• src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.ra
  • lines changed 2, context: html, text, full: html, text
    c7a78bd7342f93f63acaf6759ca7077b9caaa64c Wed Jul 22 22:05:43 2026 -0700
    Announcing the ENCODE4 cCREs and ENCODE4 Regulation tracks. Adding pennantIcons on mm10 cCREs/cCREregistry/coreCcres and hg38/mm10 ENCODE4 Regulation supertracks, making ENCODE4 Regulation show by default and adding a deprecation pennantIcon on ENCODE3 Regulation. Renaming ENCODE Regulation to ENCODE3 Regulation on hg38 and removing the separate wgEncodeReg.alpha.ra file. refs #37845 refs #34923 refs #37131