File Changes for angie

v492_base to v493_preview (2025-12-15 to 2026-01-12) v493

• src/hg/hgVai/hgVai.c
  • lines changed 24, context: html, text, full: html, text
    63890999edbfdac428544f159a33e503618ca7f8 Wed Jan 7 13:56:43 2026 -0800
    Add support for vai.pl to accept a GenArk assembly accession as db, and for hgVai to accept a geneTrack without the hub_number_ prefix when db is a hub.
• src/hg/utils/otto/sarscov2phylo/annotatedNotDesignated
  • lines changed 1, context: html, text, full: html, text
    6847a63f394675d928eaec7dc14f8186b543b921 Thu Dec 4 15:31:22 2025 -0800
    Added BA.3.2 (back on Sep 5)
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.py
  • lines changed 29, context: html, text, full: html, text
    89f51d3b8c35a428f22c245aabc29f2461e66b62 Thu Dec 4 15:32:17 2025 -0800
    Added support for exclusions keyword (back on Oct 29)
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
  • lines changed 5, context: html, text, full: html, text
    28c91a2f0848971d9f707c0a034c48f57757a4b5 Tue Dec 2 15:32:59 2025 -0800
    Use new exclusions keyword to prevent real G23599T reversion from being masked under XFJ.3.1. Change has been in place since Oct 29, just committing it now.
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    366028b554770e59a35f881811dd006c047ce9c6 Thu Dec 4 15:32:59 2025 -0800
    Added RE.1.1 reversions and site requested by @ryhisner
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
  • lines changed 9, context: html, text, full: html, text
    b4e69d4d3191c71792bef68e94152c893a9065cf Thu Dec 4 15:45:12 2025 -0800
    Added a few more IDs that were being filtered out
• src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv
  • lines changed 1, context: html, text, full: html, text
    c8dcfe3047cce1f843f987307c989a32d38cbd32 Thu Dec 4 15:34:34 2025 -0800
    Added XFG (back on Sep 5)
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 4429, context: html, text, full: html, text
    70c31dff04e7892e0318c3380479e61cfe2d68ab Wed Jan 7 14:00:07 2026 -0800
    Major overhaul of file format now that matUtils annotate supports including mutations from parent lineage, with the addition of thousands of new lineages since the old file format made the file too large for kent repo limits.
• src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh
  • lines changed 5, context: html, text, full: html, text
    8cab21c8b8a5e84a3491b796bd6590c5d6905325 Thu Dec 4 15:45:54 2025 -0800
    Added a couple samples to spare for reversion-riddled LF.7.6.5
• src/hg/utils/vai.pl
  • lines changed 1, context: html, text, full: html, text
    63890999edbfdac428544f159a33e503618ca7f8 Wed Jan 7 13:56:43 2026 -0800
    Add support for vai.pl to accept a GenArk assembly accession as db, and for hgVai to accept a geneTrack without the hub_number_ prefix when db is a hub.