66fafe88184bb3a8a45a50026f4d6c7fbbc24109 markd Tue Sep 29 10:12:53 2026 -0700 Rebuild the TSS tracks as traditional composites, for wiggle control. refs #35528 A faceted composite is routed to facetedCompositeUi(), which returns before cfgByCfgType(), so it never draws the wiggle controls: no data view scaling, no viewing range, no windowing function, no track height. Signal tracks need those, so proCapNet and encode4ProCap are now traditional composites. They stay separate composites under the TSS container. The multiWig strand overlays survive the change. The old comment here claimed a multiWig under a plain composite "is flattened away and never drawn"; that is wrong for drawing, which #36320 fixed. Only the hgTrackUi subtrack list flattens, because compositeUiSubtracks() walks to leaves, so the overlays get no inline config block and are configured from their own pages. Raised as #38441. The matrix has to be declared over the leaves, since that is the level hgTrackDb checks: declaring it on the containers fails -strict with "has groups not defined in parent". So a strand is a matrix cell, and the containers carry no subGroups. Sample class survives as a filterComposite dimension, replacing the facet. configurable on gives each subtrack its own config namespace. Drop the faceted machinery: the metadata table, the color file, the constants feeding them and the gbdbDir argument, 39 lines. The metadata.tsv and colors.json already written under /gbdb are now unreferenced and can be deleted. Put the ENCODE accession in each subtrack longLabel, and add a linked table of them to both description pages. A longLabel cannot carry a link, since printSubtrackTableBody() htmlEncodes it, hence the table. The label wording is shortened to keep the longest at 74 characters. diff --git src/hg/makeDb/doc/hs1/transcriptionStart.txt src/hg/makeDb/doc/hs1/transcriptionStart.txt index 4c4be06e33e..476bfdbe0be 100644 --- src/hg/makeDb/doc/hs1/transcriptionStart.txt +++ src/hg/makeDb/doc/hs1/transcriptionStart.txt @@ -1,42 +1,42 @@ # Transcription start sites: ProCapNet predictions, #35528, Claude Thu Sep 17 2026 (Claude/markd) # 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 # 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 cd ~/kent/src/hg/makeDb/outside/proCapNet ./proCapNetTrackDb hs1 proCapNetExperiments.tsv \ - ~/kent/src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra /gbdb/hs1 + ~/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