File Changes for angie

src/hg/hgPhyloPlace/runUsher.c
- lines changed 1, 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/utils/otto/sarscov2phylo/branchSpecificMask.yml
- lines changed 4, 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/pango.clade-mutations.tsv
- lines changed 49, context: html, text, full: html, text
  c7b3d23e420c71e53411d283b13ab3ac1c7ce84c Tue Jun 4 14:55:02 2024 -0700
  New lineages and a tweak to JN.1.39.1.
src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
- lines changed 3, 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/updatePublic.sh
- lines changed 3, 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.