Commits for markd

v504_base to v505_preview (2026-09-21 to 2026-10-05) v505

5e83632c91c1c536880da1e364a41467856135bd Tue Sep 22 11:02:32 2026 -0700

• Rename the TSS container and trim the ProCapNet description. refs #35528 Both labels on the transcriptionStart container are now "Transcription Initiation (TSS)". Changed in proCapNetTrackDb and the two transcriptionStart.ra files regenerated from it, since they are generated and carry a do-not-edit header. Dropped the Processing at UCSC section from the ProCapNet page. How the files reached UCSC is not something a browser user needs; the makeDoc already records it, including the NaN bases dropped from the hg38 predictions. Replaced the Kundaje lab server link with the ENCODE portal. The six ENCODE records are BPNet-model annotations holding the trained model, contribution scores and predicted signal over a selected region set. The genome-wide predictions in this track are roughly fifty times larger than the ENCODE predicted-signal files and are not part of that release, so the page says so rather than naming ENCODE as their source. Claude-Session: https://claude.ai/code/session_01LAB6jWshLvB7eNXQKWVuW5
  • src/hg/makeDb/outside/proCapNet/proCapNetTrackDb - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/proCapNet.html - lines changed 27, context: html, text, full: html, text

6256dc2c93839878b3faef3ee64214d0abcd6d4e Tue Sep 22 11:32:49 2026 -0700

• used sameOk instead of sameString to protect agaisnt NULL dereference
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 1, context: html, text, full: html, text

0f951bfc96241a7362d1512ceecf59a02682a839 Thu Sep 24 20:40:52 2026 -0700

• Description page fixes from a QA pre-pass on the TSS tracks. refs #35528 Encode the non-ASCII character in the Avsec reference on proCapNet.html. getTrackReferences emits raw UTF-8, which the browser does not transcode. Use $db rather than a hardcoded hg38 in the proCapNet download-server link and the bigWigToBedGraph example. One page serves both assemblies, so an hs1 reader was being pointed at hg38 files. Add a Source subsection to proCapNet.html linking the makedoc, the build scripts, the trackDb file and the upstream kundajelab/ProCapNet repository. These links went missing when the Processing at UCSC section was dropped; the prose stays dropped. Drop the cross-links between the two track pages. Track names are prefixed hub_<id>_ on hs1, which is a curated hub, and the id is machine-specific, so a bare-name link cannot work there. Each page now states which assemblies the data is available on instead, naming both GRCh38/hg38 and T2T-CHM13/hs1. Bold the two UI control names on the proCapNet display conventions section.
  • src/hg/makeDb/trackDb/human/encode4ProCap.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/proCapNet.html - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/transcriptionStart.html - lines changed 10, context: html, text, full: html, text

79073841f4c544426db6c1f805af94844cabef23 Thu Sep 24 20:46:08 2026 -0700

• Say why the ProCapNet contribution scores are hg38 only. refs #35528 The page gave the reason as "that is the assembly they were computed against", which restates the fact rather than explaining it. The scores are computed at MANE Select transcription start sites and MANE is not defined for T2T-CHM13.
  • src/hg/makeDb/trackDb/human/proCapNet.html - lines changed 2, context: html, text, full: html, text

acf20930c5cdfa1e352826a702ad8f36344178c4 Thu Sep 24 21:16:13 2026 -0700

• Fixes from an independent review of the TSS tracks. refs #35528 The Data Access sections told users to pass the composite name to the API, which returns HTTP 400. The API serves one bigWig at a time, so both pages now name a single strand of one cell line, verified to return 200. encode4ProCap.html claimed the kent tree held the manifest of which ENCODE files went into each track, and it did not. Commit that manifest as proCapNetEncodeFiles.tsv and name it on the page. It matters because proCapNetEncodeMeta resolves each experiment's default analysis at run time, so re-running it after an ENCODE reprocessing can pick different files. Cite Shah et al. for the ENCODE 4 nascent transcriptome survey the six PRO-cap experiments come from. Sagar Shah was credited by name with no reference. The hg38 makedoc called the 164268582 dropped bases "the N regions", but gap on the primary chromosomes is 150610728. The extra 13.7 Mb is sequence flanking each gap, dropped because most of its 2114 bp window was unresolved.
  • src/hg/makeDb/doc/hg38/transcriptionStart.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/outside/proCapNet/proCapNetEncodeFiles.tsv - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/encode4ProCap.html - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/proCapNet.html - lines changed 3, context: html, text, full: html, text

49de9e93e4417083feb23522a71e3960595828a3 Fri Sep 25 22:46:28 2026 -0700

• ProCapNet label and facet color fixes from QA. refs #35528 The composite longLabel named the sequence-contribution scores, which only exist on hg38, so it was wrong on hs1. Use "ProCapNet predicted PRO-cap" on both assemblies; the scores are described on the track description page. The Sample class swatches reused two colors from the cell-line palette, so a track's color could be read as its class: A673 is a cancer line and drew in #0072B2, which was the Non-cancer swatch. Sample class is a binary facet and does not need a hue, so use black and gray, outside the Okabe-Ito palette. Say in the description that the contribution scores cover about 1% of the genome, so the limit is visible before the display conventions section.
  • src/hg/makeDb/outside/proCapNet/proCapNetTrackDb - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/proCapNet.html - lines changed 2, context: html, text, full: html, text

af96452e1c6ccf783697cead2630de1ca4e91635 Sat Sep 26 06:42:20 2026 -0700

• Put the primary citation first again on the TSS track pages. refs #35528 Alphabetical order buried the paper each track is actually built on: Cochran et al. for ProCapNet, behind Avsec, and Shah et al. for the ENCODE 4 PRO-cap experiments, behind Kwak and Luo. Lead with the primary paper and leave the rest in the order they stood. Reordering only. The years and DOIs added in 38ccb38771e are unchanged.
  • src/hg/makeDb/trackDb/human/encode4ProCap.html - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/proCapNet.html - lines changed 22, context: html, text, full: html, text

40264d0668926b51da94d2ca038dc7349dfc3405 Sat Sep 26 07:59:34 2026 -0700

• Shorten the Methods sections on the two TSS data pages. refs #35528 Both read like a paper's methods section rather than a track description: 43 lines over four subsections on proCapNet, 35 on encode4ProCap. Cut each to three paragraphs, what the model or assay is, how the files we serve were produced, and where the build is recorded. The subsection headings go with it. Kept every fact a user of the track needs: the window and stride, the MANE Select limit on the contribution scores, the unresolved-sequence handling on hg38, the replicate summing, the six ENCODE accessions and the file manifest. Dropped the detail that belongs to the papers, such as the DeepSHAP scalarization and the loss weighting. The container page keeps no Methods section, which is correct for a page that only points at the two data pages.
  • src/hg/makeDb/trackDb/human/encode4ProCap.html - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/proCapNet.html - lines changed 42, context: html, text, full: html, text

31e95f0d1dd4ca08feba9b081a356527bd4b45e6 Sat Sep 26 20:36:20 2026 -0700

• Drop the hand-built Files column from the TSS faceted tables. refs #35528 UCSC will generate the download links in the faceted table, so the Files column each composite built for itself is redundant. Remove downloadCell, the Files header and cell, the Files entry in subtrackUrls, and the DOWNLOAD constant that only fed them. The table is now Tissue, Sample class, Experiment, Cell line on all three composites. writeMetadata no longer needs db or track; the metadata files it writes are byte-identical. Lead each Data Access section with the link to the hgdownload directory, since that is now the way to a single file, and keep the naming convention beside it. Drop the paragraph describing the Files column.
  • src/hg/makeDb/outside/proCapNet/proCapNetTrackDb - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/encode4ProCap.html - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/proCapNet.html - lines changed 27, context: html, text, full: html, text

66fafe88184bb3a8a45a50026f4d6c7fbbc24109 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.
  • src/hg/makeDb/doc/hg38/transcriptionStart.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/hs1/transcriptionStart.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/proCapNet/proCapNetTrackDb - lines changed 111, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/encode4ProCap.html - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra - lines changed 96, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra - lines changed 42, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/proCapNet.html - lines changed 19, context: html, text, full: html, text

32048e16a50722894cf28d9b7b4b050302e38c75 Wed Sep 30 17:54:58 2026 -0700

• Spell the acronym PCLAI, not pcLAI. refs #35415 The authors write it PCLAI throughout: the upstream README at AI-sandbox/hprc-pclai uses PCLAI 18 times and pcLAI never, under the title "Point Cloud Local Ancestry Inference (PCLAI)". We had pcLAI in 517 places, across the track labels, both description pages, the makedocs, the build scripts and the autoSql. hprcPclai.ra holds 467 of those, in shortLabel, longLabel, dataVersion and comments. It is generated, so the fix went into hprcPclaiMakeTrackDb.py and the file was rebuilt; every line of the resulting diff differs only by the rename. Track names, file names and the lowercase pclai in URLs and data file names are untouched. None of them contained the string pcLAI, and renaming the tracks would break saved sessions for no user-visible gain.
  • src/hg/makeDb/doc/contrib/hprc2annot/hprc2annot.txt - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/hprcPclai.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/scripts/hprc2annot/hprc2annotBuild.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/hprc2annot/hprc2annotMakePclaiRefPanel.py - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/scripts/hprc2annot/pclai.as - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/scripts/hprcPclai/hprcPclai.as - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/scripts/hprcPclai/hprcPclaiDownload.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/hprcPclai/hprcPclaiMakeBb.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/hprcPclai/hprcPclaiMakeTrackDb.py - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hprcPclai.html - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hprcPclai.ra - lines changed 467, context: html, text, full: html, text

bdf448295c10bee74b6baa773f6733ce33171996 Thu Oct 1 20:56:37 2026 -0700

• Store the ProCapNet minus strand negated, and fix group autoscale. refs #35528 Two of the three problems Jairo found on the composite. The negate control did not work on ProCapNet. Its minus-strand files held positive values and were flipped at display time with trackDb negateValues. The composite's control sets one shared value, which replaced the per-track setting and sent both strands the same way, with no route back to the default short of a cart reset. encode4ProCap was fine because ENCODE publishes its minus strand negative already. So put the sign in the data: proCapNetPredToFixedStep gains --negate, proCapNetPredBuild passes it for the minus strand, and negateValues is gone from the stanzas. The twelve existing files were rewritten rather than rebuilt, since the downloads had been deleted; each was checked against its original for identical nBasesCovered, a mirrored value range and exactly negated values. The originals are kept in previousPred, about 197 GB, until QA is done. Group autoscale on the composite did nothing, which was my error: the multiWig containers and the contribution leaves each carried autoScale on, and the child setting wins. The wiggle settings now live only on the composite. The third, an empty row when both strands of a cell line are deselected, is #38441 and is not fixed here. Note in both makedocs and in the generator that this arrangement only partly works and is expected to become a superTrack of multiWig overlays: under a composite, hgTrackUi lists leaves rather than containers, so an overlay gets no inline config block and leaves an empty row when deselected.
  • src/hg/makeDb/doc/hg38/transcriptionStart.txt - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/hs1/transcriptionStart.txt - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/outside/proCapNet/proCapNetPredBuild - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/outside/proCapNet/proCapNetPredToFixedStep - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/outside/proCapNet/proCapNetTrackDb - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra - lines changed 72, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra - lines changed 30, context: html, text, full: html, text

1c32191759769c28cf763342f5e405420add0170 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.
  • src/hg/makeDb/doc/hg38/transcriptionStart.txt - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/hs1/transcriptionStart.txt - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/outside/proCapNet/proCapNetTrackDb - lines changed 106, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra - lines changed 217, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra - lines changed 81, context: html, text, full: html, text

0ca316803a93c570fc7614479afd322194f17217 Fri Oct 2 06:53:26 2026 -0700

• Drop priority from the two TSS superTrack stanzas. refs #35528 The folders take whatever position the group gives them. The member tracks keep their own priorities, which order each overlay within its folder.
  • src/hg/makeDb/outside/proCapNet/proCapNetTrackDb - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra - lines changed 1, context: html, text, full: html, text

1a9c722ad341c178dc418034e51a1d015507db9b Fri Oct 2 20:23:47 2026 -0700

• Let superTracks nest inside superTracks. refs #38460 A superTrack given a parent used to pass tdbQuery -check -strict and then be dropped at load, with no warning: the browser reported the outer folder as not found. Seven places each looked exactly one level up the parent chain, which is what trackDb.h means by "Folders are superTracks. Currently only one level deep". trackDbSuperMarkup skipped any track that was itself a superTrack when resolving parent, so the link was never made rFindTrack looked "to the sky" one level, so the outer super could not be found by name addChildRefsToParents only walked tdbList, which excludes superTracks, so an inner super never reached its parent's children list findSuperTrack matched tdb->parent->track only, so hgTrackUi could not find the outer folder of a hub assembly flatten rescued the immediate super parent only, so the outer one was never written to the table polishSupers polished the immediate parent only, so the outer super reached the write with a NULL shortLabel and segfaulted groupTrackListAddSuper made a track for one super above a member setSuperTrackHasVisibleMembers marked one level visible Each now walks the chain. The group list still shows only the outermost folder, since superTrack members are not listed there; the inner folders appear on its page with their own controls, as members always have. Walking the chain makes a parent loop fatal where it used to be harmless, so trackDbSuperMarkup now checks that the supertracks form a tree once every link is set, and breaks a loop at the supertrack that closes it, naming that track. Verified by planting a loop: before, hgTrackDb spun in trackDbSetting and had to be killed; now it warns and loads. The same hazard in composite parents is untouched and filed as #38471. Regression: trackDb built with this and with the released hgTrackDb is byte-identical on mm39 (20377 rows) and, on a tree with no nesting, on hg38 (55629) and hs1 (782). With a nested trackDb the only difference on hg38 is the one rescued container row. hgTracks on hg38 renders the same 32 rows and the same 10 supertrack controls as dev, and the wgEncodeReg member list is unchanged. Note for whoever deploys this: trackDbToTxt also has to be rebuilt. It writes the curated hub trackDb.txt from the table, and a released one emits a member whose parent stanza is missing, which breaks the hub.
  • src/hg/hgTracks/hgTracks.c - lines changed 35, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 13, context: html, text, full: html, text
  • src/hg/lib/hubConnect.c - lines changed 12, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/hgTrackDb/hgTrackDb.c - lines changed 15, context: html, text, full: html, text

d0ddd717713f275dc2f567c9b6d733fd3f55bd90 Fri Oct 2 21:27:25 2026 -0700

• Put PRO-cap and ProCapNet inside a Transcription Initiation folder. refs #35528 The two data sources were top-level superTracks because a superTrack could not be a member of another one. #38460 fixes that, so they now sit inside a transcriptionStart superTrack, which is what the collection was meant to be. The container is written before either of its children, and both children before any of their members: tdbQuery -strict rejects a file in which another track comes between a superTrack and one of its children. This depends on the #38460 build. A plain make here with the installed binaries produces a half-built state, since hgTrackDb drops the container from the table and trackDbToTxt then writes an hs1 curated hub whose member names a parent stanza that is not there. Both makedocs say so.
  • src/hg/makeDb/doc/hg38/transcriptionStart.txt - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/hs1/transcriptionStart.txt - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/outside/proCapNet/proCapNetTrackDb - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra - lines changed 7, context: html, text, full: html, text

e314363411293556f33418abe8923ad1e8bc496a Fri Oct 2 21:36:04 2026 -0700

• Revert the TSS nesting on master; it lives on superTrackNesting. refs #35528 Putting PRO-cap and ProCapNet inside a transcriptionStart superTrack needs the nesting fix in #38460, which is not released. These tracks were released in 3bee9e40921, so on beta and the RR hgTrackDb would drop the container and trackDbToTxt would write an hs1 curated hub whose members name a parent stanza that is not there. The work is on the superTrackNesting branch and can come back once #38460 ships.
  • src/hg/makeDb/doc/hg38/transcriptionStart.txt - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/hs1/transcriptionStart.txt - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/outside/proCapNet/proCapNetTrackDb - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra - lines changed 7, context: html, text, full: html, text

314d1a9a41231220ae79fc971758da141c21f233 Fri Oct 2 21:36:10 2026 -0700

• Revert the superTrack nesting fix on master; it lives on superTrackNesting. refs #38460 Taken off master with its only consumer, the TSS trackDb change reverted in the previous commit. It is a library change every CGI links, in trackDbCustom.c, hdb.c, hubConnect.c and hgTracks.c, and nothing on master needs it until the TSS tracks nest again. Kept on the superTrackNesting branch with its regression evidence. Note for whoever lands it: trackDbToTxt has to be rebuilt too, or the curated hub it writes names a parent stanza it did not emit.
  • src/hg/hgTracks/hgTracks.c - lines changed 35, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 13, context: html, text, full: html, text
  • src/hg/lib/hubConnect.c - lines changed 12, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/hgTrackDb/hgTrackDb.c - lines changed 15, context: html, text, full: html, text

93a3129444064c4d19b4cb49e24b6de4bd0e06a6 Fri Oct 2 21:41:15 2026 -0700

• Restore the superTrack nesting fix. refs #38460 Taking this off master was over-cautious. It is wanted on its own: #38460 is a real bug, a superTrack given a parent passes tdbQuery -check -strict and is then silently dropped at load, and the fix should get into a release rather than wait on a trackDb change that uses it. Nothing on master nests yet, and the fix is behaviour-identical where nothing does: trackDb built with it and with the released hgTrackDb is byte-identical on hg38, hs1 and mm39, and hgTracks renders the same rows and supertrack controls as dev. The TSS trackDb change that uses this stays reverted, on superTrackNesting, until this ships. Whoever releases it: trackDbToTxt has to be rebuilt too, or the curated hub it writes names a parent stanza it did not emit.
  • src/hg/hgTracks/hgTracks.c - lines changed 35, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 13, context: html, text, full: html, text
  • src/hg/lib/hubConnect.c - lines changed 12, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/hgTrackDb/hgTrackDb.c - lines changed 15, context: html, text, full: html, text

1e8f4a189b1ad69e1cc4d60177b74ab1fd249da9 Fri Oct 2 22:22:36 2026 -0700

• Record that previousPred has been deleted. refs #35528 367 GB of un-negated minus-strand predictions, kept while the negated files went through QA. Deleting them loses nothing recoverable: negation is its own inverse, so an original comes back by running proCapNetPredToFixedStep --negate over the file now in pred/.
  • src/hg/makeDb/doc/hg38/transcriptionStart.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/hs1/transcriptionStart.txt - lines changed 4, context: html, text, full: html, text

0c42aea56b751a2b4a58feb225a9659819a90994 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.
  • src/hg/makeDb/doc/hg38/transcriptionStart.txt - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/doc/hs1/transcriptionStart.txt - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/outside/proCapNet/proCapNetTrackDb - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra - lines changed 16, context: html, text, full: html, text