e314363411293556f33418abe8923ad1e8bc496a
markd
  Fri Oct 2 21:36:04 2026 -0700
Revert the TSS nesting on master; it lives on superTrackNesting. refs #35528

Putting PRO-cap and ProCapNet inside a transcriptionStart superTrack needs the
nesting fix in #38460, which is not released. These tracks were released in
3bee9e40921, so on beta and the RR hgTrackDb would drop the container and
trackDbToTxt would write an hs1 curated hub whose members name a parent stanza
that is not there.

The work is on the superTrackNesting branch and can come back once #38460 ships.

diff --git src/hg/makeDb/doc/hg38/transcriptionStart.txt src/hg/makeDb/doc/hg38/transcriptionStart.txt
index 8e8bfc5f548..f731063c44b 100644
--- src/hg/makeDb/doc/hg38/transcriptionStart.txt
+++ src/hg/makeDb/doc/hg38/transcriptionStart.txt
@@ -1,35 +1,32 @@
 # Transcription start sites: ENCODE 4 PRO-cap and ProCapNet, #35528, Claude
 Thu Sep 17 2026 (Claude/markd)
 
 # Layout: one superTrack per data source, each holding its multiWig overlays
 # directly, the way fantom5 does.  Not a composite: under a composite hgTrackUi
 # lists descendant leaves rather than containers, so an overlay gets no
 # configuration block of its own and hiding both strands of a cell line leaves an
 # empty row where the overlay was (#38441).  As a superTrack member each overlay
 # is a track in its own right, with a full configuration page, and hiding it
 # hides the whole overlay.  The cost is the subtrack matrix and the sample class
 # filter, neither of which a superTrack offers.
 #
-# The two data-source superTracks sit inside a transcriptionStart superTrack.
-# That needs the nesting fix in #38460: before it, a superTrack given a parent
-# passed tdbQuery -check -strict and was then silently dropped at load.  Until
-# that fix is released, a plain make here produces a half-built state, because
-# the trackDb make calls two installed binaries that predate it: hgTrackDb drops
-# the container from the table, and trackDbToTxt then writes an hs1 curated hub
-# whose member names a parent stanza that is not there.  Load with a build that
-# has the fix, and rebuild the hub, until it ships.
+# These two superTracks are top level rather than sitting inside a single
+# transcriptionStart folder, because superTracks do not nest: a superTrack given
+# a parent passes tdbQuery -check -strict and is then silently dropped at load
+# (#38460).  transcriptionStart.html is left in the tree unused against that
+# being fixed.
 
 # Scripts are in ~/kent/src/hg/makeDb/outside/proCapNet.  The cell lines, their
 # ENCODE accessions and their colors are in proCapNetExperiments.tsv there.
 
 ##############################################################################
 # ProCapNet predictions and sequence-contribution scores
 ##############################################################################
 
 # The predictions are 24 GB per file and are re-encoded, so they are fetched to
 # a working area outside the track directory.  The contribution scores are used
 # unaltered and go straight to their final home.
 
 mkdir -p /hive/data/outside/proCapNet/hg38 /hive/data/genomes/hg38/bed/proCapNet
 cd /hive/data/genomes/hg38/bed/proCapNet
 ~/kent/src/hg/makeDb/outside/proCapNet/proCapNetDownload hg38 \