Commits for hiram

v467_base to v468_preview (2024-06-24 to 2024-07-01) v468

4da4e0f781b1bd70efc468ff3217951408ad087f Mon Jun 24 16:35:44 2024 -0700

• adding some algae sequences per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 4, context: html, text, full: html, text

858f679f166bccf06aca0a82267afa3193feeb1c Tue Jun 25 17:56:02 2024 -0700

• adding five bacteria per user requests refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 5, context: html, text, full: html, text

733bfccc6366eca9cdb40718caff16406b38efee Wed Jun 26 14:41:14 2024 -0700

• creating file to load into genomePriority.hgcentral for search purpose refs #32897
  • src/hg/hubApi/dbDb.name.clade.tsv - lines changed 239, context: html, text, full: html, text
  • src/hg/hubApi/genomePriority.py - lines changed 495, context: html, text, full: html, text

c1f3643c3e308c7819a375ee5ea4170a45c679e5 Wed Jun 26 14:51:38 2024 -0700

• clean up cruft refs #32897
  • src/hg/hubApi/genomePriority.py - lines changed 34, context: html, text, full: html, text

6afca455c54a8978418619a55933beb76897e09c Wed Jun 26 14:59:55 2024 -0700

• code to work with genomePriority.hgcentral table refs #32897
  • src/hg/lib/genomePriority.as - lines changed 10, context: html, text, full: html, text
  • src/hg/lib/genomePriority.c - lines changed 238, context: html, text, full: html, text
  • src/hg/lib/genomePriority.h - lines changed 86, context: html, text, full: html, text
  • src/hg/lib/genomePriority.sql - lines changed 16, context: html, text, full: html, text

54748ed558ead689973cb71209e4367d16f8450b Thu Jun 27 23:20:53 2024 -0700

• more specific sorting of primates and mammals database vs GenArk listings refs #32897
  • src/hg/hubApi/genomePriority.py - lines changed 59, context: html, text, full: html, text

c3786681696b93476299dfbfb832b355035861b1 Sat Jun 29 15:13:45 2024 -0700

• ready for an upgrade to the genark table to add columns currently maintain compatible behavior with previous genark table refs #32596;
  • src/hg/hubApi/list.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hubApi/tests/expected/list26.gz - 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/hubApi/tests/expected/list27.gz - 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/inc/genark.h - lines changed 11, context: html, text, full: html, text
  • src/hg/lib/genark.as - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/genark.c - lines changed 66, context: html, text, full: html, text
  • src/hg/lib/genark.sql - lines changed 2, context: html, text, full: html, text

08ebbbe8912ac1a5a38c3630162855827975f4c4 Sat Jun 29 20:52:13 2024 -0700

• better common names from user for the algae refs #29545
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 6, context: html, text, full: html, text

c269976e78f8b2fe44cd6e64d639a84da13ff4f3 Sun Jun 30 23:36:34 2024 -0700

• adding 2 to catch up with the fish group alignment set 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 2, context: html, text, full: html, text

437a749af8e09f831e84acbbde0d43928e01fd45 Mon Jul 1 09:30:49 2024 -0700

• adding two mouse T2T assemblies per Thomas Keane request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 4, context: html, text, full: html, text