1c32191759769c28cf763342f5e405420add0170
markd
  Thu Oct 1 21:20:54 2026 -0700
Make the TSS tracks superTracks of multiWig overlays. refs #35528

The composite held the multiWig overlays as children, which drew correctly but
left two faults, both from hgTrackUi listing descendant leaves rather than
containers: an overlay got no configuration block of its own, and hiding both
strands of a cell line left an empty row where the overlay had been. That is
#38441.

As superTrack members the overlays are tracks in their own right. Each gets a
full configuration page, including overlay method and negate values, and hiding
one hides the whole overlay. Verified: hiding proCapNet_K562_pred removes the
row and leaves the other five.

Two top-level superTracks, PRO-cap and ProCapNet, rather than one
transcriptionStart folder holding both. superTracks do not nest. A superTrack
given a parent passes tdbQuery -check -strict and is then dropped at load, since
trackDbSuperMarkup refuses to set a parent on a superTrack and hgTrackDb only
writes a superTrack that some track names as its parent. Filed as #38460, with
the test case; transcriptionStart.html stays in the tree unused in case it is
fixed.

What this costs: the subtrack matrix and the sample class filter, which a
superTrack does not offer. Each overlay now carries its own wiggle settings and
its own html, neither being inherited from a container any more.

diff --git src/hg/makeDb/doc/hs1/transcriptionStart.txt src/hg/makeDb/doc/hs1/transcriptionStart.txt
index 9e123f340bf..628bcd0c8c0 100644
--- src/hg/makeDb/doc/hs1/transcriptionStart.txt
+++ src/hg/makeDb/doc/hs1/transcriptionStart.txt
@@ -1,86 +1,91 @@
 # Transcription start sites: ProCapNet predictions, #35528, Claude
 Thu Sep 17 2026 (Claude/markd)
 
-# STATUS: the composite only partly works, and the plan is to replace it with a
-# superTrack holding the multiWig overlays directly, the way fantom5 does.  A
-# multiWig under a composite draws correctly and the composite's wiggle controls
-# apply, but hgTrackUi lists descendant leaves rather than containers, so the
-# overlays get no inline config block and turning off both strands of a cell line
-# leaves an empty row where the overlay was (#38441).  Under a superTrack each
-# overlay is a track in its own right, with its own full configuration page and
-# no flattening.  The cost is losing the subtrack matrix and the sample class
-# filter.
+# 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.
 
 # 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/ is about 197 GB and can be removed once the track has
 # been through QA.  A rebuild from the downloads does not need any of this:
 # 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