Commits for angie

v459_preview to v459_preview2 (2023-12-18 to 2024-01-02) v459

2db23a88d1e63eb50feb97accd5ca6624021ac18 Sat Dec 23 18:24:37 2023 -0800

• Lots of new lineages and a few path updates.
  • src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 163, context: html, text, full: html, text

8206caf3deee5603597c6fdbcae1320afc37281a Sat Dec 23 18:25:37 2023 -0800

• Additional sites/ranges for BA.2.86 and XBC.
  • src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml - lines changed 6, context: html, text, full: html, text

47541d92430fc9e07cd0bab4ba386faaa1f3d76c Sat Dec 23 18:27:34 2023 -0800

• Remove duplicates between COG-UK and INSDC. Fix name format that omitted INSDC accession. Get INSDC accessions for COG-UK sequences in lineageProposalsRecombinants file.
  • src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh - lines changed 23, context: html, text, full: html, text

e14703c19576048494ee2ea07fe0e10efa67cb79 Sat Dec 23 18:29:55 2023 -0800

• Use different column for more complete Nextstrain clade labels.
  • src/hg/utils/otto/sarscov2phylo/combineMetadata.sh - lines changed 2, context: html, text, full: html, text

d4caa9d01a63434e9859ed47971217ff9a20edb9 Sat Dec 23 19:14:20 2023 -0800

• Add country and year to isolate names that don't have them, analogous to fixNcbiFastaNames.pl.
  • src/hg/utils/otto/sarscov2phylo/gbMetadataAddBioSample.pl - lines changed 7, context: html, text, full: html, text

b59b26071d63fe5cab8d3c1fc5e7892315015bd9 Sat Dec 23 19:14:50 2023 -0800

• Adding more IDs by request
  • src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv - lines changed 5, context: html, text, full: html, text

69af6ad3c35e8e4e3c11cb8290d95a394908f407 Sat Dec 23 19:16:12 2023 -0800

• Add 23G, 23H, 23I. Update labels for older clades to match current nextstrain.org labels.
  • src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv - lines changed 7, context: html, text, full: html, text

ac8238545ef1708bfafa03e6b9c7daa0352b1b76 Sat Dec 23 19:18:09 2023 -0800

• faUniqify to avoid duplicates in fasta. Use different column for more complete Nextstrain clade labels.
  • src/hg/utils/otto/sarscov2phylo/getCncb.sh - lines changed 2, context: html, text, full: html, text

a4d0ac69ad1b6dd12a46266be6d95249c405d208 Sat Dec 23 19:18:43 2023 -0800

• Remove manual patch for BioSample since records have been fixed by ENA.
  • src/hg/utils/otto/sarscov2phylo/getNcbi.sh - lines changed 7, context: html, text, full: html, text

c6d93a375ba89f43a73c00a93dd329c3f6a3d4d2 Sat Dec 23 19:19:35 2023 -0800

• Increase --max-path-length so we don't lose recent sequences with many legit mutations.
  • src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh - lines changed 1, context: html, text, full: html, text