Commits for angie

ac5d7c6726a1d4ccbea22592fa64de309869e9bf Sun Feb 26 11:03:27 2023 -0800

Added many false reversions that were causing trouble in XBB, as well as a few for BQ.1, BQ.1.1, XBB.1(+27915) and XBB.1.5.
- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml - lines changed 40, context: html, text, full: html, text

01ea33002f66179857566a195021da375197557f Sun Feb 26 11:04:25 2023 -0800

Added sequences for pango-designation#1637.
- src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv - lines changed 34, context: html, text, full: html, text

618f548682d24816a2898b4e29c5787ac591f67f Sun Feb 26 11:05:27 2023 -0800

Adding comments after code review, thanks Jonathan.
- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.py - lines changed 5, context: html, text, full: html, text

0b01886bcc0f6e4f6019edc35f03052b7aa49156 Sun Feb 26 11:06:33 2023 -0800

Send verbose taxonium output to separate log file
- src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh - lines changed 2, context: html, text, full: html, text

6b76c158adf80081e080a8ebcb9157721663f1f5 Sun Feb 26 11:12:43 2023 -0800

Updated nextstrain clades & coloring, got rid of extra files for ancient oldClades, fixed bug that caused errors for reverted deletions, got rid of unused and now incredibly verbose mutation-labels in newick.
- src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 129, context: html, text, full: html, text