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/hg38/transcriptionStart.txt src/hg/makeDb/doc/hg38/transcriptionStart.txt index 4d27b960c4f..f731063c44b 100644 --- src/hg/makeDb/doc/hg38/transcriptionStart.txt +++ src/hg/makeDb/doc/hg38/transcriptionStart.txt @@ -1,27 +1,32 @@ # Transcription start sites: ENCODE 4 PRO-cap and ProCapNet, #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. # 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 \