0c42aea56b751a2b4a58feb225a9659819a90994
markd
  Sat Oct 3 06:22:01 2026 -0700
Nest the TSS tracks on alpha only, leaving the release as it is. refs #35528

PRO-cap and ProCapNet sit inside a transcriptionStart superTrack on alpha. That
needs #38460, which is on master but not in a release, and these tracks are
already released, so each source is written twice with complementary release
tags: the nested copy alpha, the flat copy beta,public. hgTrackDb takes the copy
whose release matches and rejects two whose releases overlap.

Verified that beta and public are untouched: a public build from this file is
byte-identical to a public build from the released flat tree, same md5 over
tableName, shortLabel, type, visibility, priority and settings. tdbQuery -check
-strict passes on all three releases, and an alpha build has the container with
both members parented while beta and public have neither.

Drop the release tags and the flat copies once #38460 ships.

The makedocs also record that the alpha build needs hgTrackDb and trackDbToTxt
in /cluster/bin/x86_64 to carry the #38460 fix. make alpha does not install
there, BINDIR defaults to ~/bin/$MACHTYPE, so they were put in by hand and the
weekly utils build will overwrite them.

diff --git src/hg/makeDb/doc/hs1/transcriptionStart.txt src/hg/makeDb/doc/hs1/transcriptionStart.txt
index 9f5b959ee8b..b3620720205 100644
--- src/hg/makeDb/doc/hs1/transcriptionStart.txt
+++ src/hg/makeDb/doc/hs1/transcriptionStart.txt
@@ -1,93 +1,103 @@
 # Transcription start sites: ProCapNet predictions, #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.
 #
-# 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.
+# On alpha the two data-source superTracks sit inside a transcriptionStart
+# superTrack; on beta and public they stand on their own.  Nesting a superTrack
+# inside a superTrack needs the fix in #38460, which is on master but not in a
+# release, and these tracks are already released, so each source is written
+# twice with complementary release tags: the nested copy alpha, the flat copy
+# beta,public.  hgTrackDb takes the copy whose release matches and rejects two
+# whose releases overlap, so the tags have to stay complementary.  The public
+# build is byte-identical to what was released.  Drop the release tags and the
+# flat copies once #38460 ships.
+#
+# The alpha build here also needs hgTrackDb and trackDbToTxt in
+# /cluster/bin/x86_64 to carry the #38460 fix.  make alpha does not put anything
+# there: BINDIR defaults to ~/bin/$MACHTYPE, and that directory is updated by
+# the weekly utils build.  They were installed by hand on 2026-10-03 and the
+# next weekly build will overwrite them with whatever is in the branch then.
 
 # hs1 has the ProCapNet predictions only.  There is no PRO-cap experiment and no
 # sequence-contribution score set on this assembly.  See
 # makeDb/doc/hg38/transcriptionStart.txt for the hg38 build, which carries all
 # three.  Scripts are in ~/kent/src/hg/makeDb/outside/proCapNet.
 
 mkdir -p /hive/data/outside/proCapNet/hs1 /hive/data/genomes/hs1/bed/proCapNet
 cd /hive/data/genomes/hs1/bed/proCapNet
 ~/kent/src/hg/makeDb/outside/proCapNet/proCapNetDownload hs1 \
     ~/kent/src/hg/makeDb/outside/proCapNet/proCapNetExperiments.tsv \
     /hive/data/outside/proCapNet/hs1/pred
 # 300 GB, about 30 minutes at six parallel streams
 
 # Re-encode from one bedGraph interval per base into fixedStep sections.  Unlike
 # hg38 these files hold no NaN, so every base is kept.
 ~/kent/src/hg/makeDb/outside/proCapNet/proCapNetPredBuild \
     /hive/data/genomes/hs1/chrom.sizes /hive/data/outside/proCapNet/hs1/pred pred 6
 # all 12 files report:
 #   24 chroms, 3117275501 bases, 3117275501 with data, 0 dropped
 # about 25 GB in, 16.7 to 17.0 GB out per file
 
 # proCapNetPredBuild writes the minus strand negated, so it draws below the
 # baseline from its own values.  Doing it in the data rather than with the
 # trackDb negateValues setting is what makes the composite's own negate control
 # work: that control sets one shared value for the composite, which replaced the
 # per-track negateValues and sent both strands the same way, with no way back to
 # the default short of a cart reset.  encode4ProCap never had the problem,
 # because ENCODE already publishes its minus strand negative.
 
 # the mean matches the published file exactly, so nothing was altered
 bigWigInfo pred/K562.proCapNet.pos.bw | egrep 'basesCovered|mean'
 #   basesCovered: 3,117,275,501
 #   mean: 0.019773
 
 ##############################################################################
 # negating the minus strand, after the fact
 ##############################################################################
 
 # The prediction files were first built with the minus strand positive and
 # flipped at display time with the trackDb negateValues setting.  That broke the
 # composite's negate control, as described above, so the twelve minus-strand
 # files were rewritten with negated values rather than rebuilt from the
 # downloads, which had already been deleted:
 #
 #   for db in hg38 hs1 ; do
 #       base=/hive/data/genomes/$db/bed/proCapNet
 #       mkdir -p $base/previousPred
 #       ls $base/pred/*.neg.bw | while read f ; do
 #           ~/kent/src/hg/makeDb/outside/proCapNet/proCapNetPredToFixedStep \
 #               --negate /hive/data/genomes/$db/chrom.sizes $f $base/negated/$(basename $f)
 #       done
 #   done
 #
 # Each output was checked against its input: same nBasesCovered, value range
 # mirrored, sampled values exactly negated.  The originals were then moved to
 # previousPred/ and the negated files put in their place, so /gbdb needs no new
 # symlinks.  previousPred/ has since been deleted, 367 GB over the two
 # assemblies.  Nothing is lost by that: negation is its own inverse, so the
 # originals can be recovered from the files in pred/ by running the same command
 # again.  A rebuild from the downloads does not need any of this either:
 # proCapNetPredBuild negates the minus strand itself.
 
 cd ~/kent/src/hg/makeDb/outside/proCapNet
 ./proCapNetTrackDb hs1 proCapNetExperiments.tsv \
     ~/kent/src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra
 
 # transcriptionStart.ra is generated; the include line in human/hs1/trackDb.ra
 # is added by hand:
 #   include transcriptionStart.ra alpha
 
 # hs1 is a curated hub assembly, so the stanzas reach the browser through the
 # hub built under /gbdb/hs1/hubs/$USER by the trackDb make, and are visible only
 # when curatedHubPrefix in the sandbox hg.conf names that directory.
 
 # the downloads are only needed for the re-encoding
 rm -rf /hive/data/outside/proCapNet/hs1/pred