Commits for angie

v442_base to v443_preview (2023-01-09 to 2023-01-17) v443

00ae0ed0644312e30a2227d71a92e6b1ca9efc8c Mon Jan 9 10:49:20 2023 -0800

• Add support for RSV-A and RSV-B viruses.
  • src/hg/hgPhyloPlace/hgPhyloPlace.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 3, context: html, text, full: html, text

c71577525f5e69232510269be6dd6e20ef9dfd79 Mon Jan 9 17:56:49 2023 -0800

• Many new lineages -- pango-designation release v1.18
  • src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 82, context: html, text, full: html, text

23036e8b97ae73f56eeee54d68a7668d4881e77b Mon Jan 9 18:00:29 2023 -0800

• Don't make old taxodium/v1 protobuf anymore, everyone has moved on to taxonium/v2. Make names file for big tree so hgPhyloPlace doesn't have to read in protobuf to get names for matching uploaded names/IDs.
  • src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh - lines changed 18, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh - lines changed 21, context: html, text, full: html, text

7c9ef333258146c91b2abba00508a7d76b44b080 Mon Jan 9 18:00:56 2023 -0800

• Adding some recently proposed recombinants
  • src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv - lines changed 15, context: html, text, full: html, text

e174398ee58fcdd6fb59b393ac7af1c59645ab53 Mon Jan 9 18:01:23 2023 -0800

• Save failed .zip files for reporting to NCBI.
  • src/hg/utils/otto/sarscov2phylo/getNcbi.sh - lines changed 2, context: html, text, full: html, text

edc4389658f330657da35d00e56837afdc95c4a7 Mon Jan 9 18:02:05 2023 -0800

• Use as many threads as possible on the ku nodes, with current memory requirements.
  • src/hg/utils/otto/sarscov2phylo/runPangolin.sh - lines changed 1, context: html, text, full: html, text