File Changes for angie

v470_base to v471_preview (2024-08-26 to 2024-09-02) v471

• src/hg/makeDb/schema/all.joiner
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    8fd8e815893d5f97f33b065862e727273f13a7b6 Wed Aug 28 18:29:54 2024 -0700
    Add ncbiRefSeqLink.omimId to omimId rule. refs #34013
• src/hg/utils/otto/sarscov2phylo/annotatedNotDesignated
  • lines changed 2, context: html, text, full: html, text
    8e712a67beb687070337c4739f6a3664c5cc8225 Wed Aug 14 13:10:23 2024 -0700
    Fix lineage check to compare vs. lineages actually annotated on the tree, not just lineages present in pango.clade-mutations.tsv.
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
  • lines changed 2, context: html, text, full: html, text
    29784b8ab0b8c9ae4f639d4411320ca0bbb3238b Wed Aug 14 13:07:57 2024 -0700
    Added a couple JN.1 GBW artifact sites reported by @FedeGueli.
• src/hg/utils/otto/sarscov2phylo/designatedNotAnnotated
  • lines changed 32, context: html, text, full: html, text
    8e712a67beb687070337c4739f6a3664c5cc8225 Wed Aug 14 13:10:23 2024 -0700
    Fix lineage check to compare vs. lineages actually annotated on the tree, not just lineages present in pango.clade-mutations.tsv.
• src/hg/utils/otto/sarscov2phylo/getCncb.sh
  • lines changed 6, context: html, text, full: html, text
    d6e143eb6277e6a8d5ffadccbb9538325f5d86af Wed Aug 14 13:12:26 2024 -0700
    Add check for format of data returned by server (sometimes error messages are returned as text without HTTP error codes)
• src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv
  • lines changed 1, context: html, text, full: html, text
    9ea690d413932da6911d75a073d3a5d95673d7d4 Wed Aug 14 13:08:23 2024 -0700
    Added 24C (KP.3)
• src/hg/utils/otto/sarscov2phylo/updatePublic.sh
  • lines changed 19, context: html, text, full: html, text
    8e712a67beb687070337c4739f6a3664c5cc8225 Wed Aug 14 13:10:23 2024 -0700
    Fix lineage check to compare vs. lineages actually annotated on the tree, not just lineages present in pango.clade-mutations.tsv.