Commits for lrnassar

v503_preview2 to v503_base (2026-08-24 to 2026-08-31) v503

6a8e756b47341a5584f5c3fca4031401fe507020 Mon Aug 24 11:21:22 2026 -0700

• Updating GeneCards links to their new URL format per their request, also fixes dead cardsearch.pl links on RefSeq and denovoDb click pages. refs #38171
  • src/hg/hgGene/gencodeSection.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Human/links.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Mouse/links.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/hgGeneGraph/hgGeneGraph - lines changed 1, context: html, text, full: html, text
  • src/hg/hgc/gencodeClick.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/genCC.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/denovoDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/mane.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.geneHancer.ra - lines changed 4, context: html, text, full: html, text

87f5ac2d9279932b8d45b75e9c7d30fdd062a5b7 Mon Aug 24 18:21:40 2026 -0700

• Fixes from nightly CR: guard FLOSSIES carrier count, drop dead variable. refs #37399 refs #38139 Hardening on the FLOSSIES carrier-count fix, per nightly code review: - Add a consistency guard: carriers are summed from the per-population het and hom counts, and the build now raises if sum(pop_hets)+sum(pop_homs) does not equal allele_count. In this export the two are identical (allele_count is het+hom, not the usual het+2*hom), so this catches a future re-fetch that renames pop_hets/pop_homs or switches to standard allele-count semantics, instead of silently zeroing carriers and mis-tiering every coding variant. Verified the identity holds for all 118 current records. - Remove the now-dead hom (hom_count) local, left over from the old allele_count - hom_count formula. No output change (FLOSSIES bigBed is byte-identical; tiers unchanged).
  • src/hg/makeDb/scripts/tp53/tp53Flossies.py - lines changed 10, context: html, text, full: html, text

df4fcc5d86a76fbc325da43d3f1b9b5ab5f6f4eb Mon Aug 24 18:39:38 2026 -0700

• Adding release tags since this track is a new default, refs #37001
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra - lines changed 1, context: html, text, full: html, text

f4996889d4fcf17c5290b81d1863c06fa3738e40 Tue Aug 25 12:09:32 2026 -0700

• redmineCli: add --target-version filter to the list subcommand. No RM.
  • src/utils/redmineCli - lines changed 6, context: html, text, full: html, text

1cf4925201a690fa236b77d604269d6aa739b4af Fri Aug 28 14:06:50 2026 -0700

• Add the alpha,beta release tag to the mm10 signal composite include line. refs #37001 The previous commit tagged mouseDevTimecourse.ra but not developmentTimecourseSignalMm10.ra. On mm10 the superTrack parent and the bigWig composite child live in separate files with separate include lines, so the parent became alpha,beta while the untagged child stayed at all three levels. At public the child outlived its parent, and tdbQuery -strict reported "parent mouseDevTimecourse of developmentTimecourseSignalMm10 release n/a doesn't exist". Note this only shows up at -release=public; a default -strict run is alpha, where the parent still exists, so it looks clean. mm39 was never affected because both its subtracks are inside the one included file.
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 1, context: html, text, full: html, text