File Changes for angie

v451_preview2 to v451_base (2023-07-10 to 2023-07-17) v451

• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 1, context: html, text, full: html, text
    96471ada1e945584ea0bbd8615fb1f54b743b011 Mon Jul 10 16:44:40 2023 -0700
    Add a bit more info to error message about subtree with no user sample IDs.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 8, context: html, text, full: html, text
    74badd35b7df2aef1be18519fb05beda8af1a4e4 Mon Jul 10 16:45:24 2023 -0700
    Doh, forgot to deal with strand in codonVpTxToAaChange, but MPXV has strands.
• src/hg/utils/otto/nextstrainNcov/nextstrain.py
  • lines changed 9, context: html, text, full: html, text
    f070f343168fcb94a21b832d1cb20104b0670186 Fri Jun 30 15:08:56 2023 -0700
    There really should never be a clade-defining mutation on the first or last base of the genome (low/no coverage in most genomes), but this morning it happened, so at least prevent illegal overlapping blocks in nextstrainClade bed output.
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
  • lines changed 6, context: html, text, full: html, text
    d8a34f168b65a616fb185dbff94af89c426668b6 Mon Jul 10 12:02:02 2023 -0700
    Mask position 337 in BN.1.2.3 -- noisy.
• src/hg/utils/otto/sarscov2phylo/getCncb.sh
  • lines changed 1, context: html, text, full: html, text
    6199485d849f1a1ecce4ce6f57fa01d4eb6097dd Mon Jul 10 12:02:57 2023 -0700
    No more pangolearn mode.
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
  • lines changed 2, context: html, text, full: html, text
    d746723d112678e33245af03ffd617f7076d775d Mon Jul 10 12:04:42 2023 -0700
    Adding a couple more IDs for sars-cov-2-lineages/lineage-proposals#174.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 63, context: html, text, full: html, text
    ddb2aa5ae97a44fce99c32afc22070c68deaca03 Mon Jul 10 12:01:42 2023 -0700
    Latest new lineages. Also mask 337 in descendants of BN.1.2.3 because it's masked in branchSpecificMask.yml (noisy).
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 10, context: html, text, full: html, text
    18aba4871dfccf70dabe6fc328338c1442acb2bc Mon Jul 10 11:59:23 2023 -0700
    Have been using different matOptimize args since mid-May, see comment.