File Changes for angie

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

• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
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    8206caf3deee5603597c6fdbcae1320afc37281a Sat Dec 23 18:25:37 2023 -0800
    Additional sites/ranges for BA.2.86 and XBC.
• src/hg/utils/otto/sarscov2phylo/combineMetadata.sh
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    e14703c19576048494ee2ea07fe0e10efa67cb79 Sat Dec 23 18:29:55 2023 -0800
    Use different column for more complete Nextstrain clade labels.
• src/hg/utils/otto/sarscov2phylo/gbMetadataAddBioSample.pl
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    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/getCncb.sh
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    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/getNcbi.sh
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    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/includeRecombinants.tsv
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    b59b26071d63fe5cab8d3c1fc5e7892315015bd9 Sat Dec 23 19:14:50 2023 -0800
    Adding more IDs by request
• src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
  • lines changed 23, 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/nextstrain.clade-mutations.tsv
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    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/pango.clade-mutations.tsv
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    2db23a88d1e63eb50feb97accd5ca6624021ac18 Sat Dec 23 18:24:37 2023 -0800
    Lots of new lineages and a few path updates.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
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    c6d93a375ba89f43a73c00a93dd329c3f6a3d4d2 Sat Dec 23 19:19:35 2023 -0800
    Increase --max-path-length so we don't lose recent sequences with many legit mutations.