File Changes for angie

v450_preview2 to v450_base (2023-06-20 to 2023-06-26) v450

• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
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    8a1149c22482aaa4787bb02799a62f348c5dc2b2 Thu Jun 22 10:17:38 2023 -0700
    Send verbose usher_to_taxonium output to log
• src/hg/utils/otto/sarscov2phylo/getCncb.sh
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    ba4425b7d509f2d52bec87b22c3cd8a6802ef3db Thu Jun 22 10:17:25 2023 -0700
    Not making full nextalign.fa.xz at this point, just incrementals.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
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    e2df9883de70a2ab2d08b96aaec1a62f916a426a Thu Jun 22 10:17:09 2023 -0700
    Update datasets command line options and biosample filename for latest version. pangoLEARN has been discontinued so use default usher mode in pangolin and skip scorpio for speed.
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
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    2f86bf00b7eff014176677a0bfb4fdaaf9ad842f Thu Jun 22 10:17:15 2023 -0700
    Added recombinant spotted by @aviczhl2 in sars-cov-2-variants/lineage-proposals#174
• src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
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    9011b709f1fa87332b94a5920062582f5a725f68 Thu Jun 22 10:17:30 2023 -0700
    Watch out for empty name and date columns for COG-UKs in GenBank
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    5d6035bbe436dacd64aeb482b8b45669f1cbdf49 Thu Jun 22 09:34:26 2023 -0700
    Many new lineages (and a few tweaks). pango-designation v1.21
• src/hg/utils/otto/sarscov2phylo/runPangolin.sh
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    5dd7dc49abd77ba2cbbebba8d818cdacf5d00af8 Thu Jun 22 10:17:00 2023 -0700
    pangoLEARN has been discontinued so use default usher mode in pangolin and skip scorpio for speed.