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/scripts/tad/tadDomainEncode.as src/hg/makeDb/scripts/tad/tadDomainEncode.as
new file mode 100644
index 00000000000..75b3959b575
--- /dev/null
+++ src/hg/makeDb/scripts/tad/tadDomainEncode.as
@@ -0,0 +1,13 @@
+table tadDomainEncode
+"ENCODE contact-domain (TAD) interval with Arrowhead corner-detection scores"
+    (
+    string chrom;       "Chromosome"
+    uint   chromStart;  "Domain start"
+    uint   chromEnd;    "Domain end"
+    string name;        "Biosample"
+    float  cornerScore; "Arrowhead corner score: likelihood this is a contact-domain corner (higher = stronger)"
+    float  uVarScore;   "Variance of the upper triangle of the domain contact submatrix"
+    float  lVarScore;   "Variance of the lower triangle of the domain contact submatrix"
+    float  upSign;      "Upper-triangle sign score: -1 x sum of signs of upper-triangle entries"
+    float  loSign;      "Lower-triangle sign score: sum of signs of lower-triangle entries"
+    )