Commits for lrnassar

v492_base to v493_preview (2025-12-15 to 2026-01-12) v493

d02300cbe391cf7cbea38da034b4826c305076d5 Fri Jan 2 09:25:34 2026 -0800

• Extending the check to 45 days as sometimes the asia logs are about 35 days before updating. No RM.
  • src/utils/qa/checkErrorLogsAreUpToDate.py - lines changed 2, context: html, text, full: html, text

d3e77d28330c5c21d88a9deaef31d80dadd966ea Mon Jan 5 11:09:33 2026 -0800

• Squashing stale pennantIcons, no RM.
  • src/hg/makeDb/trackDb/human/g2p.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/knownGene.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV49lift37.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/knownGene.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/long_read_transcripts.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/mavedb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/problematic.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra - lines changed 1, 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/unusualcons.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV49.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/longReadVariants.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/panelApp.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/predictionScoresSuper.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/spliceAIWt.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/spliceImpactSuper.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/long_read_transcripts.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM38.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac10/trackDb.ra - lines changed 1, context: html, text, full: html, text

d8000af8628f18a03b5fa88b0734a7d8d57e2138 Tue Jan 6 13:25:17 2026 -0800

• Feedback from Zhiping, refs #34109
  • src/hg/makeDb/trackDb/human/hg38/encode4.ccres.ra - lines changed 340, context: html, text, full: html, text

cffb8890582724fc07e5319b3b46e1cbb3a479f9 Wed Jan 7 10:34:48 2026 -0800

• More CfFeedback from Zhiping, adding numbers to all the data types refs #34109
  • src/hg/makeDb/trackDb/human/hg38/encode4.ccres.ra - lines changed 850, context: html, text, full: html, text

828e8fde956c566c299dd09ccde15f217de365a3 Wed Jan 7 16:54:30 2026 -0800

• Final touches to the track, feedback from Zhiping. Reordering the registry tracks to be alphbetical by longLabel, but still keep data types together and updating the refences to the nature article that has now published. Refs #34109
  • src/hg/makeDb/trackDb/human/hg38/cCREregistry.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/cCREsSuper.html - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/coreCollection.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/encode4.ccres.ra - lines changed 850, context: html, text, full: html, text

9aca47b7143b576d084806a387fae54a16cf76f6 Fri Jan 9 14:11:54 2026 -0800

• Updating our latest publication, refs #36899
  • src/hg/htdocs/cite.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/pubs.html - lines changed 9, context: html, text, full: html, text

1c01e2809ff01dfe507a9977be2b5f3682133a4a Fri Jan 9 15:26:16 2026 -0800

• Forgot one spot to add the new publication, apparently it goes in 3 different places.
  • src/hg/htdocs/cite.html - lines changed 6, context: html, text, full: html, text