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/trackDb/human/hg38/transcriptionStart.ra src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra
index 1a362b0ba74..ee5361eadf8 100644
--- src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra
+++ src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra
@@ -1,29 +1,54 @@
 # Generated by hg/makeDb/outside/proCapNet/proCapNetTrackDb for hg38.
 # Do not edit by hand, edit the script and regenerate.
 
+track transcriptionStart
+superTrack on show
+group rna
+shortLabel Transcription Initiation (TSS)
+longLabel Transcription initiation (TSS)
+release alpha
+
     track encode4ProCap
     superTrack on show
+    parent transcriptionStart
     group rna
     shortLabel PRO-cap
     longLabel PRO-cap nascent RNA transcription start sites from ENCODE 4
+    release alpha
+
+track encode4ProCap
+superTrack on show
+group rna
+shortLabel PRO-cap
+longLabel PRO-cap nascent RNA transcription start sites from ENCODE 4
+release beta,public
+
+    track proCapNet
+    superTrack on show
+    parent transcriptionStart
+    group rna
+    shortLabel ProCapNet
+    longLabel ProCapNet predicted PRO-cap
+    release alpha
 
 track proCapNet
 superTrack on show
 group rna
 shortLabel ProCapNet
 longLabel ProCapNet predicted PRO-cap
+release beta,public
 
 track encode4ProCap_A673_procap
 superTrack encode4ProCap full
 container multiWig
 aggregate solidOverlay
 showSubtrackColorOnUi on
 type bigWig
 autoScale on
 alwaysZero on
 maxHeightPixels 100:40:8
 windowingFunction maximum
 configurable on
 html encode4ProCap
 color 0,114,178
 shortLabel A673 PRO-cap