Commits for hiram

v478_base to v479_preview (2025-02-24 to 2025-03-03) v479

64095df6b21cc5f7a424a7fef692d6c5d7e2199f Mon Feb 24 16:44:28 2025 -0800

• fixup some incorrect classifications refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 71, context: html, text, full: html, text
  • src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 5, context: html, text, full: html, text

240a9e73c64e3d2072e6c8e7141d7f0c670fcee2 Tue Feb 25 09:31:27 2025 -0800

• continuing VGP update refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 3, context: html, text, full: html, text

d5fe70b3e6a9a2ce1fa0557ec745fa83ac9075f2 Wed Feb 26 11:19:30 2025 -0800

• VGP update no redmine
  • src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv - lines changed 51, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt - lines changed 92, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.trio.orderList.tsv - lines changed 13, context: html, text, full: html, text

0b79f38c15c80abf6f73f62916530c06e7efe99b Thu Feb 27 12:22:35 2025 -0800

• VGP update and a couple user requests refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 2, context: html, text, full: html, text

2ec1c55ec6f3139ed9952b1b1d085b9ffa83b150 Fri Feb 28 11:16:01 2025 -0800

• VGP update refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text

3649a56fe72fd579be33eae0c33e93c2be0b727b Sat Mar 1 13:35:05 2025 -0800

• a couple per user request and VGP update refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 1, context: html, text, full: html, text

db2c189b474c037cb383b96c06b71acdcf364dd7 Sun Mar 2 17:56:46 2025 -0800

• lastz chainNet procedures for xenTro10 refs #31490
  • src/hg/makeDb/doc/xenTro10/lastzChainNet.txt - lines changed 504, context: html, text, full: html, text