Commits for angie

v466_base to v467_preview (2024-06-03 to 2024-06-10) v467

c7b3d23e420c71e53411d283b13ab3ac1c7ce84c Tue Jun 4 14:55:02 2024 -0700

• New lineages and a tweak to JN.1.39.1.
  • src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 49, context: html, text, full: html, text

39232e1eb0b5b78c0e3f6ea360a5f70195f70840 Thu Jun 6 10:53:05 2024 -0700

• BA.2.86 representative has a name now. I removed 21627 (S:22) from BA.2.86's masking at @FedeGueli's request (sequences with mutation there were removed and added back).
  • src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml - lines changed 4, context: html, text, full: html, text

0b3aed10ba50cdda1d27a4b3cb170fbde09b6060 Thu Jun 6 10:55:24 2024 -0700

• Minor: move compression of new*.fa files into updateCombinedTree.sh to make manual copy-paste run completion a little easier.
  • src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/updatePublic.sh - lines changed 3, context: html, text, full: html, text

e1ea58d34faf4e8fcbaa7a20d0a665575dfca76d Thu Jun 6 13:53:30 2024 -0700

• Fix: don't prepend server directory twice when telling server to reload protobufs.
  • src/hg/hgPhyloPlace/runUsher.c - lines changed 1, context: html, text, full: html, text