17b7d3c37be41135afaf8e91e365e3847af96ca5
lrnassar
  Mon Jun 22 10:56:56 2026 -0700
Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599

New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra
alpha in each assembly's trackDb.ra.

hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra
2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples),
and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets).
hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur).
mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE
(faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted
from mm10, lift noted in the long labels.

Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into
/gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under
makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch
for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt,
doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt).

diff --git src/hg/makeDb/trackDb/human/hg19/trackDb.ra src/hg/makeDb/trackDb/human/hg19/trackDb.ra
index 8d7858648a3..46a1c45f51e 100644
--- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
+++ src/hg/makeDb/trackDb/human/hg19/trackDb.ra
@@ -2431,15 +2431,17 @@
 url https://enhancer.lbl.gov/vista/element?vistaId=$$
 type bigBed 9 +
 mouseOverField patternExpression
 urlLabel View on the VISTA Enhancer Browser
 bigDataUrl /gbdb/hg19/vistaEnhancers/vistaEnhancers.bb
 itemRgb on
 
 track ncbiRefSeq override
 parent refSeqComposite off
 
 include ../../trackDb.mgc-orfeome.ra
 include denovoDb.ra
 
 track jaspar2024 override
 parent jaspar on
+
+include tad.ra alpha