File Changes for angie

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

• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 39, 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/treeToAuspiceJson.c
  • lines changed 51, 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/utils/otto/sarscov2phylo/maskDelta.sh
  • lines changed 16, context: html, text, full: html, text
    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/pango.clade-mutations.tsv
  • lines changed 12, 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.