Commits for lrnassar

v494_base to v495_preview (2026-02-16 to 2026-02-23) v495

5f9d00bf2c7cc68a49c72aac71e91451680b6019 Tue Feb 17 08:00:59 2026 -0800

• Feedback from CR, refs #37093
  • src/hg/makeDb/trackDb/human/dnaMethylation.html - lines changed 1, context: html, text, full: html, text

0db15879749b6753035c8f365e9d69b5987f4c79 Tue Feb 17 16:33:46 2026 -0800

• Adding assembly specific filters, and updating the track desc page based on author feedback, refs #36264
  • src/hg/makeDb/trackDb/drosophila/trackDb.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/jaspar.html - lines changed 99, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/sacCer/trackDb.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirt/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/trackDb.ra - lines changed 3, context: html, text, full: html, text

f8fcc3e5fcb5fa70d28bf67d104519fc75f68b20 Wed Feb 18 09:03:02 2026 -0800

• Updating the emails and 2026 release description based on author feedback, refs #36261
  • src/hg/makeDb/trackDb/jaspar.html - lines changed 34, context: html, text, full: html, text

e9c3757c29ec6d08b6232e0a671fe5970bb58e2e Wed Feb 18 19:21:54 2026 -0800

• Feedback from CR, refs #37124
  • src/hg/hgTracks/hgTracks.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/hubCheck/hubCheck.c - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/hubCheck/tests/expected/autoScaleHub.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/hubCheck/tests/expected/manyErrors.output.txt - lines changed 1, context: html, text, full: html, text

e309de9305cf4536b2813e100473272c7316fd82 Thu Feb 19 17:46:33 2026 -0800

• First draft of new encode cCREs track for mm10, refs #37131
  • src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html - lines changed 121, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/cCREsSuper.html - lines changed 52, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/coreCollection.html - lines changed 143, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode.cCREs.override.ra - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encode4.ccres.ra - lines changed 1222, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/encodeCcreCombined.old.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 1, context: html, text, full: html, text

e124da635e46cce4ce2dc3eae2154339ee10d311 Fri Feb 20 17:13:37 2026 -0800

• Updating the type and urls linkout with the new GenCC file format, refs #37135
  • src/hg/makeDb/trackDb/human/genCC.ra - lines changed 2, context: html, text, full: html, text

1331fff6434827b6c138f9e18f3b5491917c63b0 Fri Feb 20 17:31:34 2026 -0800

• Many updates to the GenCC pipeline. 1 It was using GencodeV40 hardcoded; now it uses the latest GENCODE table. 2. Better handling of the comment field of the tsv, which used to include even HTML, so I wasn't parsing it correctly, leading to some items being excluded from the track. 3. Fixed a bug where I was treating numbers as strings, leading to a few corner cases (only came up in this latest GenCC update) where the coordinates were wrong. 4. GenCC emailed us that they are updating their format, much to our chagrin, since we usually just extend fields at the end to not break pipelines. I just adopted their new format, which changed the UUID to a versioned ID and added a version number field. So, overall, the field count went up by 1. 5. Handle multi-chrom genes (only a few) by picking the chrom with the most transcripts. 6. Add a fallback to look up genes missing from GENCODE by checking kgXref. Refs #37135
  • src/hg/utils/otto/genCC/doGenCC.py - lines changed 235, context: html, text, full: html, text