5d23e68307f894bdcd024c138adc588591eceaaa
lrnassar
  Mon Jun 29 12:11:44 2026 -0700
Polish TAD description pages and bold the track mouseOvers. refs #21599

Description pages (tads.html on hg19, hg38, mm10, mm39): add a Methods resolution
summary table (track / feature / calling method / resolution), placed at the end of
the Description section; add GitHub source links (makedoc, build scripts, trackDb.ra)
to the Methods section; sentence-case the "How to use these tracks" heading.

mouseOvers: wrap the field labels in <b> across all subtracks - Dixon ("Cell type:"),
Schmitt ("Sample:"), ENCODE ("Biosample:" / "Arrowhead corner score:", now on separate
lines), 3D Genome Browser ("3DGB TAD domain:"), and McArthur boundary stability
("Boundary recurrent:" / "Percentile:"). Updated the ENCODE and 3D Genome Browser build
scripts so regenerated stanzas carry the same formatting.

diff --git src/hg/makeDb/scripts/tad/buildTadsEncode.py src/hg/makeDb/scripts/tad/buildTadsEncode.py
index a75ad07a72b..446f308331a 100644
--- src/hg/makeDb/scripts/tad/buildTadsEncode.py
+++ src/hg/makeDb/scripts/tad/buildTadsEncode.py
@@ -284,32 +284,32 @@
 longLabel ENCODE contact domains (TADs) across %d %s biosamples (Arrowhead/Hi-C)
 type bigBed 4 + 5
 group regulation
 visibility pack
 metaDataUrl %s/tadsEncode_metadata.tsv
 primaryKey Accession
 colorSettingsUrl %s/organ_colors.json
 subtrackUrls Accession=https://www.encodeproject.org/experiments/$$/
 maxCheckboxes 50
 html tadsEncode
 
 """ % (len(subtracks), SPECIES, GBDB, GBDB))
         for s in sorted(subtracks,key=lambda s:(s["on"]!="on", s["term"].lower())):
             short=scap(shortlab(s["term"],22,ENC_ABBR))
             long="ENCODE TADs in %s (%s)"%(s["dterm"],s["encsr"])
-            mouse=("Biosample: %s | TAD lifted from hg19 (no Arrowhead score)"%s["dterm"] if s["lifted"]
-                   else "Biosample: %s | Arrowhead corner score: $cornerScore"%s["dterm"])
+            mouse=("<b>Biosample:</b> %s<br>TAD lifted from hg19 (no Arrowhead score)"%s["dterm"] if s["lifted"]
+                   else "<b>Biosample:</b> %s<br><b>Arrowhead corner score:</b> $cornerScore"%s["dterm"])
             fh.write(
 """    track tadsEncode_%s
     parent tadsEncode %s
     shortLabel %s
     longLabel %s
     type bigBed 4 + 5
     bigDataUrl %s/tadsEncode/%s.bb
     color %s
     visibility dense
     mouseOver %s
 
 """%(s["encsr"],s["on"],short,long,GBDB,s["symbol"],s["rgb"],mouse))
     print("wrote %d subtracks -> %s"%(len(subtracks),RA))
 
 if __name__=="__main__":