File Changes for angie

v423_preview2 to v423_base (2021-11-01 to 2021-11-09) v423

• src/hg/makeDb/doc/wuhCor1/phylogenetics.txt
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    999310144add887891307673ea81cadc756fdac8 Tue Nov 2 13:08:38 2021 -0700
    Updated Problematic Sites track.
• src/hg/utils/otto/sarscov2phylo/combineMetadata.sh
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    2c3a1d65d38fbd4b75eb55b3f8e854a452254459 Tue Nov 2 12:58:07 2021 -0700
    Crank down on duplicate lines of metadata (reported by Theo Sanderson IIRC).
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
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    75d8863314800ba0199291f101308dc2e52435be Tue Nov 2 12:53:58 2021 -0700
    Add the new -M (--clade-mutations) option to matUtils annotate for precise (yet hopefully more stable than --clade-paths) identification of lineage root nodes.
• src/hg/utils/otto/sarscov2phylo/kuRunMatOptimize.sh
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    dab60a7ef0dc81b9ef5992d26cced0a5b7fa1435 Tue Nov 2 12:59:25 2021 -0700
    Helper script for running matOptimize on the cluster
• src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv
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    07cbdefa64e387ad41f07f6c900a058cfbbe118c Tue Nov 2 12:50:50 2021 -0700
    Adding mutation sets for Nextstrain Clades and selected Pango lineages (mostly VoCs) for use with matUtils annotate --clade-mutations. These are based on paths in the current tree, but with forward & back-mutations removed or changed to N. AY.* path ends checked vs. table in https://www.pango.network/summary-of-designated-ay-lineages/ .
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    07cbdefa64e387ad41f07f6c900a058cfbbe118c Tue Nov 2 12:50:50 2021 -0700
    Adding mutation sets for Nextstrain Clades and selected Pango lineages (mostly VoCs) for use with matUtils annotate --clade-mutations. These are based on paths in the current tree, but with forward & back-mutations removed or changed to N. AY.* path ends checked vs. table in https://www.pango.network/summary-of-designated-ay-lineages/ .
• src/hg/utils/otto/sarscov2phylo/runPangolin.sh
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    b2702356792837c28408c0dc239c42f066f02e06 Tue Nov 2 13:03:26 2021 -0700
    Helper script for running Pangolin on the cluster.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
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    543b4946d460da38fd7dae2c3bfb3ece9af03218 Tue Nov 2 12:53:34 2021 -0700
    Add the new -M (--clade-mutations) option to matUtils annotate for precise (yet hopefully more stable than --clade-paths) identification of lineage root nodes. Also clip input columns when tacking on clade & lineage from tree at end, so we can run multiple times without gaining extra columns.
• src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh
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    921f73e5adb3b42171efedb00a795fa4651655a7 Tue Nov 2 13:07:42 2021 -0700
    Use the new --clade-mutations option for matUtils annotate (but adjust mutations to be rooted in lineage A instead of B). The simplified trees always win, so don't bother testing unsimplified trees, saves ~1.5 hours.
• src/hg/utils/otto/sarscov2phylo/usherClusterRun.sh
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    0b7dfc66c9f922d96a37066655a01299a3c70de0 Tue Nov 2 12:56:59 2021 -0700
    Run matOptimize on the cluster. It uses MPI for job management; reserve cluster nodes with a fake parasol job and specify those nodes for MPI.