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/mouse/mm39/trackDb.ra src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
index 150e0ce30dd..7a6386aaa84 100644
--- src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
+++ src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
@@ -1,63 +1,65 @@
 include mouseDevTimecourse.ra
 
 # Local declaration so that local gold.html is picked up.
 track gold override
 html gold
 
 # Local declaration so that local gap.html is picked up.
 track gap override
 html gap
 
 #track chainNetCalJac4 override
 #chainMinScore 3000
 
 #track ensGene override
 #priority 2.02
 
 track xenoRefGene override
 visibility hide
 #priority 2.03
 
 track mrna override
 priority 2.1
 
 searchTable gold
 shortCircuit 1
 termRegex [ABCFLM][ACEFGHLNOPQRTUXY][AEKJQR0-9]+(\.[0-9_]+)?
 query select chrom,chromStart,chromEnd,frag from %s where frag like '%s%%'
 searchPriority 8
 
 #include evaSnp.ra
 include xenoRefGene.ra
 include trackDb.35way.ra
 include trackDb.chainNet.ra
 include trackDb.syntenicNet.ra alpha
 include trackDb.rbestNet.ra alpha
 include trackDb.gencode.ra
 include knownGene.ra
 include knownGeneArchive.ra
 include reMap.ra
 
 include liftOverMm10.ra
 
 track vistaEnhancersBb
 shortLabel VISTA Enhancers
 longLabel VISTA Enhancers
 group regulation
 url https://enhancer.lbl.gov/vista/element?vistaId=$$
 type bigBed 9 +
 mouseOverField patternExpression
 urlLabel View on the VISTA Enhancer Browser
 bigDataUrl /gbdb/mm39/vistaEnhancers/vistaEnhancers.bb
 itemRgb on
 
 include ../refSeqComposite.mm10.mm39.ra
 
 include cytoBand.ra
 
 track ucscGenePfam override
 shortLabel Pfam in GENCODE
 longLabel Pfam Domains in GENCODE Genes
 html gencodePfam
 
 include vgp577way.trackDb.ra alpha
+
+include tad.ra alpha