Commits for angie

v438_preview to v438_preview2 (2022-09-26 to 2022-10-03) v438

612e090ae2bd69331bf2b612961eaeb834e5c19c Mon Sep 26 13:07:49 2022 -0700

• Added a ridiculous number of new lineages: BLs, BMs, BN-CA, BA.4s, BA.5s, XAW-XBC. Also old lineages B.1.631 and XB, and proposed1006. Removed BA.5.1.13 (withdrawn). Tweaked some paths and removed BF.3.1_revs after adding branch-specific masking on BA.2.75 and BA.5.
  • src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 100, context: html, text, full: html, text

9cd6960c3ab7292990b5c8a9c29085e30266c890 Tue Sep 27 10:48:21 2022 -0700

• Resolve some unnecessary Ns to expected values in sublineages of BA.2 and BA.5.
  • src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 237, context: html, text, full: html, text

ed83da4edfadf6a6952d43aee9853a69a7d3ca06 Tue Sep 27 10:57:09 2022 -0700

• Accumulated changes over the past month: Change BA.2 representative sequence after pruning a bunch of basal incomplete sequences. Expand masking of 28362-28370 deletion in BA.2 branch to 28361-28371. Mask 21765-21770 and 686-694 deletions in BA.4. Mask homoplasic 28877+28878 in BA.2 branch. Mask a bunch of 5' UTR sites that were causing a lot of messes in BA.2 branch. Mask a bunch of reversion sites in BA.2.75 and BA.5.
  • src/hg/utils/otto/sarscov2phylo/maskDelta.sh - lines changed 56, context: html, text, full: html, text