Commits for angie

v460_base to v461_preview (2024-01-29 to 2024-02-06) v461

d6e1c182b3f78991221452f89d940a6bea7d4b5f Sun Feb 4 09:13:25 2024 -0800

• New lineages and correction to C.37 (Lambda)
  • src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 28, context: html, text, full: html, text

71a5bf4d42948792ba96729c01bec373eed86918 Sun Feb 4 09:16:38 2024 -0800

• Use nextclade v3 output column indices.
  • src/hg/utils/otto/sarscov2phylo/getCncb.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/getCogUk.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/getNcbi.sh - lines changed 2, context: html, text, full: html, text

28e901dcf7f05026044feb8f4cc0fe9a267df7be Sun Feb 4 09:21:18 2024 -0800

• Mask the range 21610-21624 due to Ns/run-of-muts. sars-cov-2-variants/lineage-proposals#1347
  • src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml - lines changed 3, context: html, text, full: html, text

a087918aa0bbba12853825bd8a588ab26b0b70bd Sun Feb 4 09:24:02 2024 -0800

• Update to nextclade v3 output column indices.
  • src/hg/utils/otto/sarscov2phylo/combineMetadata.sh - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/findDropoutContam.pl - lines changed 22, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh - lines changed 4, context: html, text, full: html, text

7f46acdf8f879de28c3ba40534e58a881941e168 Sun Feb 4 09:24:53 2024 -0800

• CNCB is updated daily so make version.txt more concise.
  • src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh - lines changed 4, context: html, text, full: html, text