Commits for angie

462e893f28fe026bc87f7ffdc9c88dbabfe13193 Mon Aug 14 13:06:40 2023 -0700

Updated Omicron labels for Nexstrain clades and added new clades.
- src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv - lines changed 14, context: html, text, full: html, text

0d6e7229499aa6fdfc9a77433f5bd2fc4fe60047 Mon Aug 14 13:08:30 2023 -0700

Added B.1.1.7_dropout label and made B.1.1.7 more complete in terms of expected mutations - refs https://github.com/andersen-lab/Freyja/issues/151 . Added new lineages.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 84, context: html, text, full: html, text

0380553f88742abdadd8d99301b9209fd5140249 Thu Aug 17 20:14:56 2023 -0700

More new lineages for pango-designation v1.22. Replaced some Ns with expected alleles. Added XBB.1.5_17124 because base XBB.1.5 moved to a different flip-flop branch.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 36, context: html, text, full: html, text

0b6529d0ca040778605cb0e1537813bbce276493 Thu Aug 17 20:18:32 2023 -0700

Fix format string, check __name__ before calling main so this can be used as a module.
- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.py - lines changed 2, context: html, text, full: html, text

6765acb3e5e0fe4dec0403f7803ca170c080f19c Thu Aug 17 20:19:09 2023 -0700

Update representative for XBB.1.5 to accommodate shuffling of branches.
- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml - lines changed 1, context: html, text, full: html, text

74115dfde3f8c981f8f9119875d8bb014cce7b50 Thu Aug 17 20:23:19 2023 -0700

Script to identify most specific branch and total number of sites masked for each sample, for https://github.com/iqbal-lab/improve-sc2-phylo-paper/issues/1
- src/hg/utils/otto/sarscov2phylo/branchSpecificMaskStats.py - lines changed 118, context: html, text, full: html, text