Commits for markd

v486_preview to v486_preview2 (2025-07-28 to 2025-08-04) v486

1a856b5d1ebbb6ff8761c331716af73b3c8aaa1e Tue Jul 29 12:15:26 2025 -0700

• import of GENCODE Versions V49, V49lift37, and VM38
  • src/hg/makeDb/doc/hg19.gencode.txt - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/gencode.txt - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm39/gencode.txt - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/schema/all.joiner - lines changed 277, 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/wgEncodeGencodeV49lift37.html - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV49lift37.ra - lines changed 210, 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/wgEncodeGencodeV48.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV49.html - lines changed 47, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV49.ra - lines changed 247, 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.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM38.ra - lines changed 247, context: html, text, full: html, text

d194838295ec57173a17c36c1552b9aca464cf29 Wed Jul 30 13:18:15 2025 -0700

• fixed HGNC filter; comma+space between allowed values caused very weird breakage
  • src/hg/makeDb/outside/hgnc/hgncToBigBed - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/makeDb/outside/hgnc/tests/expected/hg38Test.locus_type.filter.txt - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

5df12e00d92dfc710671d73ed7bb3a173e2cd789 Mon Aug 4 13:17:44 2025 -0700

• adjustments to clsLongReadRna trackDb to added
  • src/hg/makeDb/outside/clsLongReadRna/clsTrackTool - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/clsLongReadRna.ra - lines changed 120, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/clsLongReadRna.ra - lines changed 97, context: html, text, full: html, text

46849f2053370ff9c0ff9594936d95a51124b162 Mon Aug 4 13:17:44 2025 -0700

• adjustments to clsLongReadRna trackDb to address composite behavior problems
  • src/hg/makeDb/outside/clsLongReadRna/clsTrackTool - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/clsLongReadRna.ra - lines changed 120, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/clsLongReadRna.ra - lines changed 97, context: html, text, full: html, text