Commits for braney

v485_preview2 to v485_base (2025-07-14 to 2025-07-21) v485

0f62f220d9099e6db7b4f3423caf5e0595831f4c Wed Jul 16 16:43:36 2025 -0700

• add table browser support for bedMethyl
  • src/hg/hgTables/custom.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTables/filterFields.c - lines changed 5, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h - lines changed 9, context: html, text, full: html, text
  • src/hg/hgTables/joining.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTables/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTables/schema.c - lines changed 2, context: html, text, full: html, text

909e7e221b0f321d5d43c6507c1edcda89699875 Wed Jul 16 17:54:51 2025 -0700

• oops, forgot the new bedMethyl.c file
  • src/hg/hgTables/bedMethyl.c - lines changed 52, context: html, text, full: html, text

586f7cc282b1e3a2992ee81c4060277613c636a3 Thu Jul 17 11:30:34 2025 -0700

• fix problem with hgLiftOver not setting default new assembly correctly
  • src/hg/hgLiftOver/hgLiftOver.c - lines changed 12, context: html, text, full: html, text

f2f1a28c921a6f9c2bf1838d0940293492de4141 Thu Jul 17 11:42:05 2025 -0700

• Revert "fix problem with hgLiftOver not setting default new assembly correctly" This reverts commit 586f7cc282b1e3a2992ee81c4060277613c636a3.
  • src/hg/hgLiftOver/hgLiftOver.c - lines changed 12, context: html, text, full: html, text

93166927fccf9b848073b06e239a17e70aaa8886 Thu Jul 17 11:48:55 2025 -0700

• oops, I wasn't dealing with the no cart variable case. Return the funky scoring method for choosing default when no cart variables exist
  • src/hg/hgLiftOver/hgLiftOver.c - lines changed 5, context: html, text, full: html, text

124c43d2511935aab2d1f56d0aea92c1bdb97d7c Fri Jul 18 10:40:59 2025 -0700

• more fixin's to hgLiftOver
  • src/hg/hgLiftOver/hgLiftOver.c - lines changed 4, context: html, text, full: html, text

f59e5f01716dc12ed4546fd5a0d23657b86fa704 Fri Jul 18 14:49:10 2025 -0700

• more futzing around with hgLiftOver
  • src/hg/lib/hdb.c - lines changed 7, context: html, text, full: html, text

601d8ad878b9cd491de411fde57453f2da7608bb Fri Jul 18 18:00:28 2025 -0700

• it turns out that hOrganism and hGenome are basically the same thing but both have to be working with Genark
  • src/hg/lib/hdb.c - lines changed 10, context: html, text, full: html, text