File Changes for angie

v428_preview2 to v428_base (2022-03-07 to 2022-03-14) v428

• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
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    df04c1f66cdd6895471998c6d9c70b1a413f7d4e Sat Mar 12 20:33:25 2022 -0800
    Use new --include-nt option when generating taxonium protobufs. Also watch out for EPI_ISL as part of GenBank name.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
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    baa98a4c7bb930fd0bf6365f92436eb900ade8e3 Sat Mar 12 20:31:52 2022 -0800
    Prevent duplicate lines in ncbi_dataset.plusBioSample.tsv.
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
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    914fa0581c7c17a37b1d598c92a4e42e427d1bcb Sun Feb 27 12:02:01 2022 -0800
    Adding more IDs from pango-designation issues.
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    0b90c5052025ceeea65ca83ee8440c681206d170 Tue Mar 1 09:53:52 2022 -0800
    Added more IDs from pango-designation
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    9d334a5f23ebdd944e0a2591f484c06ce0229537 Thu Mar 3 09:56:42 2022 -0800
    More updates from pango-designation issues
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    fc65b0a377a7cda3f03078dd255d5c8d6933a5b4 Thu Mar 3 18:33:07 2022 -0800
    More updates from pango-designation
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    f488be28f1793410327aa93ac1ba01982b37f260 Sat Mar 12 20:34:27 2022 -0800
    Adding lots of updates from pango-designation; also COG-UK names because not all are in GenBank downloads yet.
• src/hg/utils/otto/sarscov2phylo/maskDelta.sh
  • lines changed 44, context: html, text, full: html, text
    3bdcfd94b4905ad578c1ae99c9bb47fbb937893c Sat Mar 12 20:35:04 2022 -0800
    Mask out deleted sites in BA.1 and BA.2
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 21, context: html, text, full: html, text
    847e5bdd773beb9f499db99b1f03ff57c95ca586 Mon Feb 28 15:38:51 2022 -0800
    Added BA.1.16, BA.1.16.1, BA.1.17, BA.1.17.1, BA.1.1.[1-16] and BC.1 -- pango-designation v1.2.130
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    d07abd6a8dabab3342586f2be472c4ae4a8ad32f Sat Mar 12 20:38:50 2022 -0800
    Added AY.36.1, BA.2.1-3, removed BC.1 -- pango-designation v1.2.131
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 1, context: html, text, full: html, text
    df04c1f66cdd6895471998c6d9c70b1a413f7d4e Sat Mar 12 20:33:25 2022 -0800
    Use new --include-nt option when generating taxonium protobufs. Also watch out for EPI_ISL as part of GenBank name.