Commits for angie

v443_preview2 to v443_base (2023-01-23 to 2023-01-30) v443

ed7e20316990e2e6e52e0baf73087222eb571b67 Fri Jan 20 12:58:02 2023 -0800

• Mask reversion G26530A in BA.1.1 because it made a mess of the branch leading to BA.1.1.1.
  • src/hg/utils/otto/sarscov2phylo/maskDelta.sh - lines changed 16, context: html, text, full: html, text

0a5af94686b36c7cc7389a447cd699c4ec421e48 Fri Jan 20 12:58:39 2023 -0800

• Correction to BA.2.18 path after re-checking designated sequences. New label BA.5.2_quad_22599T to prevent misassignment as CE.1 after reversion. New label BQ.1_17039 to prevent misassignment as BQ.1.1 after reversion. Added false A26530G to XD path due to new branch-specific masking in BA.1.1. New lineages.
  • src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 12, context: html, text, full: html, text

2a9d39b83afd2a71f4a0d57042b4a6fcee81a556 Thu Jan 26 14:54:41 2023 -0800

• Added two RSV clade systems (Goya et al. and Ramaekers et al.) and different sources (nextclade vs. tree vs. direct assignments) as coloring options in Nextstrain JSON output for RSV.
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 39, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/treeToAuspiceJson.c - lines changed 51, context: html, text, full: html, text