Commits for markd

v504_preview2 to v504_base (2026-09-14 to 2026-09-21) v504

7713a08da69691ba499d5b9d44379c43e8cdb608 Fri Sep 18 09:27:52 2026 -0700

• Adding Transcription Start container with ENCODE 4 PRO-cap and ProCapNet tracks. refs #35528 New superTrack transcriptionStart in the rna group, holding two faceted composites: encode4ProCap with PRO-cap measurements and proCapNet with the model predictions and sequence-contribution scores. hg38 has all three data types, hs1 the predictions only. ENCODE 4 PRO-cap comes from the portal rather than the submitter's hub copy. For each of the six experiments only the plus and minus strand signal of unique reads files of that experiment's default analysis are taken, which drops files superseded by a later reprocessing. ENCODE publishes no pooled file, so the per-replicate files are summed per cell line and strand, the same merge the ProCapNet models were trained on. Total signal is conserved exactly. The published ProCapNet prediction bigWigs store one bedGraph interval per base and hold a literal NaN at every unresolved (N) base on hg38, which makes autoScale and every summary statistic NaN. They are re-encoded into fixedStep sections, a third smaller with no value changed, dropping 164,268,582 NaN bases of 3,088,269,832 on hg38 and none on hs1. Losslessness verified against the originals on random windows across five chromosomes. The composites are faceted rather than plain because a container multiWig under a plain composite is flattened away by hgTrackUi and never drawn. Each cell line is one row with a checkbox per data type, a Sample class facet, ENCODE accession links and a Files column linking each bigWig on hgdownload. Scripts and the cell line configuration are in makeDb/outside/proCapNet; the trackDb stanzas and the faceted metadata tables are generated, not hand edited. Claude-Session: https://claude.ai/code/session_01LAB6jWshLvB7eNXQKWVuW5
  • src/hg/makeDb/doc/hg38/transcriptionStart.txt - lines changed 124, context: html, text, full: html, text
  • src/hg/makeDb/doc/hs1/transcriptionStart.txt - lines changed 42, context: html, text, full: html, text
  • src/hg/makeDb/outside/proCapNet/proCapNetDownload - lines changed 42, context: html, text, full: html, text
  • src/hg/makeDb/outside/proCapNet/proCapNetEncodeBuild - lines changed 38, context: html, text, full: html, text
  • src/hg/makeDb/outside/proCapNet/proCapNetEncodeMeta - lines changed 81, context: html, text, full: html, text
  • src/hg/makeDb/outside/proCapNet/proCapNetExperiments.tsv - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/outside/proCapNet/proCapNetMergeSignal - lines changed 109, context: html, text, full: html, text
  • src/hg/makeDb/outside/proCapNet/proCapNetPredBuild - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/outside/proCapNet/proCapNetPredToFixedStep - lines changed 87, context: html, text, full: html, text
  • src/hg/makeDb/outside/proCapNet/proCapNetTrackDb - lines changed 245, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/encode4ProCap.html - lines changed 160, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/transcriptionStart.ra - lines changed 517, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra - lines changed 224, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/proCapNet.html - lines changed 227, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/transcriptionStart.html - lines changed 100, context: html, text, full: html, text

6d4c020673160d1f301931782f56085fff8967ae Fri Sep 18 12:35:14 2026 -0700

• Fix hgTrackUi 400 when fetching faceted composite metadata on a curated hub assembly. refs #38384 handleFileFetch authorizes a fileUrl either by it sitting under a connected hub's hub.txt directory, or by it matching a whitelisted trackDb setting (metaDataUrl, colorSettingsUrl). The second check was gated on the track not being a hub track, because user hub settings could point anywhere. On a curated hub assembly such as hs1 both checks failed: the track name is hub-prefixed, so the whitelist was skipped, and the metadata sits at /gbdb/hs1/proCapNet/, outside the hub.txt directory /gbdb/hs1/hubs/alpha/. The ProCapNet config page showed "Error loading metadata: HTTP Status: 400" in place of the faceted table. The same track on hg38, a native database, worked. A curated hub's trackDb is admin-written and as trustworthy as a native track's, so let the whitelist check run for it. New trackIsFromCuratedHub matches the track's own hub id against the hub url dbDb names for the assembly, so a user hub attached to the same assembly still does not qualify. Claude-Session: https://claude.ai/code/session_01LAB6jWshLvB7eNXQKWVuW5
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 30, context: html, text, full: html, text

67d52a65f28f7f85656b89616c6012501bbdbabc Sun Sep 20 09:38:48 2026 -0700

• Add DOI links to the ProCapNet and PRO-cap track references. refs #35528 Regenerated both reference sections with getTrackReferences --doi, keeping the citation order each page already had rather than the tool's alphabetical order, so the Cochran and Tome primary papers stay first. Claude-Session: https://claude.ai/code/session_01LAB6jWshLvB7eNXQKWVuW5
  • src/hg/makeDb/trackDb/human/encode4ProCap.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/proCapNet.html - lines changed 7, context: html, text, full: html, text