Commits for angie

5d2d3c7da2b3486fce37bbf4f268ea4ff85f4f91 Sun Nov 7 10:03:09 2021 -0800

Fixing mutations for Nextstrain clades 21A (Delta) and 21H (Mu): A28461G is not required by clades.tsv and can occur later in the big tree path; 24410 is now masked & needs to be N in both Delta and Mu.
- src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv - lines changed 2, context: html, text, full: html, text

9fb997565b120c0e299e5c421e9ed6a409d18da9 Sun Nov 7 10:08:07 2021 -0800

Added new lineages from pango-designation releases v1.2.92 and v1.2.93. Adjusted sets of mutations (mostly adding masked bases, most of those for sites deleted in Delta but reported as mutations by some genome assembly pipelines) for existing lineages.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 163, context: html, text, full: html, text

883a8a9699c47c71ab36838cc0ec878b1831cd0f Sun Nov 7 10:10:26 2021 -0800

Nextstrain clades are now completely specified by nextstrain.clade-mutations.tsv; -c (--clade-names) input file is ignored, so no need to pass it in.
- src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh - lines changed 2, context: html, text, full: html, text

bcb2ebe2ea3d2023b54ffd993b646db0bc81183c Wed Nov 10 16:53:29 2021 -0800

Updating dataVersion for problematicSites (release alpha).
- src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 1, context: html, text, full: html, text

62b4b182a499b110f3bc2045b7859bc20e82e5e8 Wed Nov 10 17:03:41 2021 -0800

Adding missing mutation C1427T to P.1.10 (also mask 11296).
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 1, context: html, text, full: html, text