Commits for lrnassar

v497_preview2 to v497_base (2026-04-13 to 2026-04-20) v497

925304757ea50469b4f20b5880ba58e2667e29db Mon Apr 13 10:18:21 2026 -0700

• Add defaultSortField to ENCODE4 bigComposite tracks to group peak/signal pairs. refs #34923 Added _Experiment column (hidden from facets via underscore prefix) to metadata TSVs for hg38 and mm10 Epigenetics and TF ChIP composites. Set defaultSortField to _Experiment so peak and signal subtracks from the same experiment sort adjacent. Also fixed pre-existing CRLF line endings in three metadata TSVs.
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra - lines changed 1, context: html, text, full: html, text

af291f82582af89f7c623eb4d13b8141d28e9862 Mon Apr 13 10:19:16 2026 -0700

• Update ENCODE4 makedocs with defaultSortField step. refs #34923
  • src/hg/makeDb/doc/hg38/encode4.regulation.txt - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.encode4.regulation.txt - lines changed 22, context: html, text, full: html, text

ed3cb243b9151cae7d1859712148fa1d1e1a2196 Mon Apr 13 17:34:17 2026 -0700

• Adding makedoc and build scripts for InSiGHT VCEP track hub. refs #36582
  • src/hg/makeDb/doc/InSiGHT.txt - lines changed 156, context: html, text, full: html, text
  • src/hg/makeDb/scripts/insight/buildInsightClinVar.py - lines changed 593, context: html, text, full: html, text
  • src/hg/makeDb/scripts/insight/insightAFfrequencies.py - lines changed 464, context: html, text, full: html, text
  • src/hg/makeDb/scripts/insight/insightClinDomains.py - lines changed 333, context: html, text, full: html, text
  • src/hg/makeDb/scripts/insight/insightFunctionalAssays.py - lines changed 963, context: html, text, full: html, text
  • src/hg/makeDb/scripts/insight/insightHCIPriors.py - lines changed 383, context: html, text, full: html, text
  • src/hg/makeDb/scripts/insight/insightPVS1.py - lines changed 348, context: html, text, full: html, text

eff4c5c82d82b41a6dc377aa4c48b65c1a4ce135 Mon Apr 13 18:30:27 2026 -0700

• Add track ticket custom field support to redmineCli update subcommand. refs #37339 New named options: --release-log-text, --release-log-url, --released-to-rr, --file-list, --table-list, --assemblies. Also adds generic --custom-field ID=VALUE for arbitrary custom fields.
  • src/utils/redmineCli - lines changed 47, context: html, text, full: html, text

55225be4fa1c5b6c1d886c524606b67701e86448 Tue Apr 14 10:32:57 2026 -0700

• Fix typo, comment error, and bare except in InSiGHT build scripts per code review. refs #36582
  • src/hg/makeDb/scripts/insight/buildInsightClinVar.py - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/insight/insightAFfrequencies.py - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/scripts/insight/insightClinDomains.py - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/scripts/insight/insightFunctionalAssays.py - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/scripts/insight/insightHCIPriors.py - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/scripts/insight/insightPVS1.py - lines changed 2, context: html, text, full: html, text

dc7ac233e8848cee5087dca606f4d638ca8a3be1 Tue Apr 14 11:58:42 2026 -0700

• Update InSiGHT scripts per v2.0.0 CSpec: fix PMS2 BS1 threshold, add PMS2 PVS1 Moderate region. refs #36582
  • src/hg/makeDb/doc/InSiGHT.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/scripts/insight/insightAFfrequencies.py - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/scripts/insight/insightPVS1.py - lines changed 2, context: html, text, full: html, text

159988dc8595c08c87164253d8d09997c925661c Tue Apr 14 13:03:07 2026 -0700

• Creating a new RTS for the InSiGHT VCEP, refs #36582
  • src/hg/htdocs/inc/recTrackSets.hg19.tab - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/inc/recTrackSets.hg38.tab - lines changed 1, context: html, text, full: html, text

444a2b070e48370587223105f4428d94cb796e51 Tue Apr 14 15:09:09 2026 -0700

• Adding weekly otto cron for InSiGHT ClinVar curated variants track, Tuesdays 3:08am. refs #36582
  • src/hg/utils/otto/otto.crontab - lines changed 3, context: html, text, full: html, text

04b359f6abe6b9c526f19fe7a59cda77d8daed51 Tue Apr 14 16:35:37 2026 -0700

• QA fixes for NMD Escape supertrack: labels, HTML descriptions, PMIDs. refs #33737 Fix shortLabels exceeding 20 chars and longLabels exceeding 80 chars across all subtracks. Fix wrong PMIDs for Nagy and Kurosaki references in nmd.html. Reorder references alphabetically and add DOI/PMC links. Add Data Access and Credits sections to all three description pages.
  • src/hg/makeDb/trackDb/human/hg38/nmd.html - lines changed 38, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/nmd.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/nmdDetective.html - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/nmdEscTranscripts.html - lines changed 20, context: html, text, full: html, text

2f0deaf88df6e28e28ac768f9c600d46ae1966c1 Wed Apr 15 14:25:23 2026 -0700

• Deleting an old mane.alpha track from 2022, I accidentally bumped into it updating the MANE labels. No RM.
  • src/hg/makeDb/trackDb/human/hg38/mane.alpha.ra - lines changed 21, context: html, text, full: html, text

01428b5a058a1d0ebdd0582235ad05ddd13e6528 Wed Apr 15 15:33:19 2026 -0700

• Adding new improved label matches on search results to MANE, refs #37299
  • src/hg/makeDb/trackDb/human/hg38/mane.ra - lines changed 1, context: html, text, full: html, text

65189b08b3a2b7efe27670b30379feb200187541 Fri Apr 17 09:14:07 2026 -0700

• Link accession column to ENCODE portal for ENCODE4 Regulation bigComposites. refs #34923 Add subtrackUrl https://www.encodeproject.org/files/$$/ to all 6 hg38 and mm10 bigComposite tracks (Epigenetics, RnaSeq, TfChip). The new trackDb setting (refs #36320 note 157) replaces $$ with the value from the primaryKey column, making each accession in the configuration table a clickable link to the corresponding file details page on the ENCODE portal. Also added a note in the Data Access section of each composite's HTML, and updated both makedocs.
  • src/hg/makeDb/doc/hg38/encode4.regulation.txt - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.encode4.regulation.txt - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra - lines changed 1, context: html, text, full: html, text

be7a61203ddd2ae5a51aed21ee093b2e712a0312 Fri Apr 17 10:04:18 2026 -0700

• Fix Core Collection cCRE class list in mm10 description to match actual data: rename 'Chromatin accessibility (CA)' to 'CA-only' and remove 'Transcription factor (TF)' (TF class is Registry-only, not present in any of the 18 Core Collection bigBeds). refs #37131
  • src/hg/makeDb/trackDb/mouse/mm10/coreCollection.html - lines changed 3, context: html, text, full: html, text

ac1e5ad678524308ef32df6154f7f1632a54a266 Fri Apr 17 10:27:56 2026 -0700

• Adding snowflake pennantIcon to AVADA pointing to the VARAICO news archive release, and adding reciprocal relatedTracks entries between AVADA and Varaico for hg19 and hg38. No RM.
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/relatedTracks.ra - lines changed 6, context: html, text, full: html, text