File Changes for angie

v425_preview2 to v425_base (2021-12-20 to 2022-01-10) v425

• src/hg/hgPhyloPlace/treeToAuspiceJson.c
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    1ab96609fb58d6c6053425989043e9e7c5dd9f99 Mon Jan 10 08:56:42 2022 -0800
    Update Nextstrain clade names and color spectrum in Auspice JSON output.
• src/hg/utils/otto/sarscov2phylo/getCogUk.sh
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    5b376b2547f4a5018823202b0379aad6a5d06c69 Wed Dec 15 19:27:39 2021 -0800
    The latest nextclade adds quotes around names with spaces; strip those out.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
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    5b376b2547f4a5018823202b0379aad6a5d06c69 Wed Dec 15 19:27:39 2021 -0800
    The latest nextclade adds quotes around names with spaces; strip those out.
• src/hg/utils/otto/sarscov2phylo/maskDelta.sh
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    1715fcf5e6c59c033d9f6dfb341e62b1f1b7c629 Tue Dec 7 18:38:36 2021 -0800
    Mask 21846 (S:95) in Delta branch - Cornelius Roemer and Chris Ruis pointed out phylogeny problems it caused.
• src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv
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    f19f9a980f4876f0f26668aa121b59c4ab32a046 Wed Dec 15 19:28:21 2021 -0800
    Tweak 21K (BA.1) and add 21L (BA.2).
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    922009dcce8772c595c868e9d4377d2b12e183da Tue Jan 4 12:08:24 2022 -0800
    Add Omicron label to 21L, add 21M.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    96069858e15c4e236ad4a3645d5a8c6e6ded14d0 Sat Dec 4 19:58:00 2021 -0800
    Mask out C21846T in AY lineages because we're masking 21846 (S:95) in Delta now. Remove AY.9.1 (pango-designation v1.2.104). Fix multiple appearances of 19563 in AY.34.2 path.
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    751eaf324fd6a2759f7771387f353fedb07be52c Mon Dec 6 19:49:28 2021 -0800
    Add new lineages defined in pango-designation release v1.2.105.
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    10670fc04382aaae97374b9a9a4b88c718a3d94f Tue Dec 7 18:36:52 2021 -0800
    Broaden B.1.1.529 and add new sublineages BA.1 (Omicron) and BA.2 ("outlier"/"stealth"/"Decepticron") - pango-designation v1.2.106
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    7ac562b0f61603e3c18438fde92cbe6dea73491a Thu Dec 9 19:26:28 2021 -0800
    Adjusted B.1.1.529, BA.1 and BA.2 after some more pruning/opt/adding. Added AY.124.1, B.1.637.1, B.1.640.{1,2}, renamed AY.97 to AY.5.5 - pango-designation v1.2.108.
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    cd5a3614ba723e948f1631538ab8c90b69959bda Tue Dec 14 11:59:51 2021 -0800
    Mask spurious SNVs at the deletion site found in in Alpha, Beta, Gamma and Omicron. One more tweak to BA.2. Add AY.26.1, AY.122.2; broaden AY.112 and rename old AY.112 to AY.112.1 - pango-designation v1.2.109
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    7114f0d248dde6e60e345364c1da2ec7898accb8 Tue Dec 14 12:28:45 2021 -0800
    Added AY.9.2.2, AY.119.2, AY.4.7, AY.4.8, AY.39.1.2 - pango-designation v1.2.110
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    03ea36ac4bf82b4a87a16a63c34988622e4107ea Tue Dec 14 13:00:18 2021 -0800
    Added AY.128, AY.3.2, AY.43.6, AY.102.1, AY.129, P.1.7.1; broadened AY.25.1, renamed old AY.25.1 to AY.25.1.1 - pango-designation v1.2.111
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    0a52c287f522cbe635e9479e62500b5f565fc381 Tue Dec 14 14:39:40 2021 -0800
    Added BA.3 - pango-designation v1.2.112
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    b49e29d1c9fc2d131e44db1f6f3a742367e8626b Tue Dec 14 17:50:54 2021 -0800
    Add mutations for a few lineages, and tweaking a couple existing ones, to resolve some problems turned up in a comparison between our tree's calls and pango-designation/lineages.csv.
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    ed3af61805a008c200e1f22bede2e7c69a40c4e2 Wed Dec 15 19:26:16 2021 -0800
    More B.1.1.529-tweaking
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    3cdaf3294040294806097ce9d2180f6ea0161056 Thu Dec 16 10:16:33 2021 -0800
    Since masking of 21846 (S:95) in Delta, AY.115 and AY.116 are identical, and whichever is assigned the node first in matUtils annotate wins -- not good. This hasn't been released in pango-designation yet, but since there is already an AY.116.1, AY.115 will be merged into AY.116. Make that change now so we don't produce stochastic output in the meantime.
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    5ec77175f8532e474133e5653257f4878c1e011f Wed Dec 22 15:20:28 2021 -0800
    Forgot to mask several mutations in pango-masked regions in recent new lineages. Another tweak to BA.2 mutations as nodes keep hopping around with new noisy sequences.
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    7685bc792fc8a65570eeb2e24d414a8deaf0958c Tue Jan 4 12:09:38 2022 -0800
    Add some more masked mutations to B.1.1.529 path as new sequences continue to shift around early nodes.
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    bc397b4e29e995996ef9e7f9b2f81c4e6e95002c Tue Jan 4 15:58:52 2022 -0800
    Added BB.1, BB.2, AY.102.2, AY.42.1, AY.39.1.3, AY.130 - pango-designation v1.2.113
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    1ec1f2c96c1afaedea7133c32ff179d19f9c9e09 Tue Jan 4 17:15:17 2022 -0800
    Added AY.127.1, AY.123.1, AY.3.3, AY.46.6.1, AY.33.1 and AY.122.3 - pango-designation v1.2.114
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    d74fcd0feaadd46e7042be0fe1b264a217e7f7e8 Tue Jan 4 17:35:02 2022 -0800
    Added P.1.12.1 - pango-designation v1.2.115
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    25ebd73c41dae62a2a53730e21a619a313b3ca2c Tue Jan 4 17:49:02 2022 -0800
    Added AY.131 - pango-designation v1.2.116
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    8613d8975c3f842db4516d6e127e1a7dd067f71c Tue Jan 4 19:16:05 2022 -0800
    Added AY.4.9 and AY.4.10 - pango-designation v1.2.117
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    a3a2f15ee359565a285a1706f2efe3e41e37d851 Tue Jan 4 19:39:34 2022 -0800
    Added AY.43.7 - pango-designation v1.2.118
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    71bc760d1659f6d6f77ee7ab37f3b1da25d39f93 Tue Jan 4 20:00:48 2022 -0800
    Added AY.132 - pango-designation v1.2.119
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    a7b34fd66d5f96b1fd1c78ff6d1d15b9009cd0a9 Tue Jan 4 20:24:53 2022 -0800
    Added AY.133 - pango-designation v1.2.120 [note: v1.2.121 is just an init.py tweak, no lineage changes]