Commits for angie

644aca2e8d7af3d037a6fc29a400c5d79484756e Wed Feb 8 20:49:24 2023 -0800

Data-driven branch-specific masking: replaced the contents of maskDelta.sh with a YAML specification of branches and sites/ranges/reversions to mask and a python script that reads the spec and then makes a matUtils mask file and runs matUtils mask as before. Did this so I could point people to the YAML spec instead of a non-portable bash script when they asked what sites are masked in what branches. See https://github.com/yatisht/usher/issues/324
- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.py - lines changed 141, context: html, text, full: html, text
- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml - lines changed 107, context: html, text, full: html, text
- src/hg/utils/otto/sarscov2phylo/maskDelta.sh - lines changed 219, context: html, text, full: html, text

c4776f376543fd420aa6024619f950c49f651c30 Wed Feb 8 20:51:36 2023 -0800

Added a few more sequences from cov-lineages/pango-designation#1505
- src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv - lines changed 4, context: html, text, full: html, text

18a7959f18910bf26ec02f4ae21b839024d94230 Wed Feb 8 20:52:35 2023 -0800

Fixed some bash syntax so the usage message appears when needed.
- src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh - lines changed 1, context: html, text, full: html, text

b3beba6edcc5ba334a756b83a11b66ec9350255a Wed Feb 8 21:10:19 2023 -0800

Ever more lineages. Changed XBB.1.5 to not require T17124C.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 58, context: html, text, full: html, text