Commits for angie

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.
- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml - lines changed 5, 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/annotatedNotDesignated - lines changed 1, 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.py - lines changed 29, context: html, text, full: html, text

366028b554770e59a35f881811dd006c047ce9c6 Thu Dec 4 15:32:59 2025 -0800

Added RE.1.1 reversions and site requested by @ryhisner
- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml - lines changed 7, 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/nextstrain.clade-mutations.tsv - lines changed 1, 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/includeRecombinants.tsv - lines changed 9, 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/otto/sarscov2phylo/updateLineageTreePb.sh - lines changed 5, 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/hgVai/hgVai.c - lines changed 24, context: html, text, full: html, text
- src/hg/utils/vai.pl - lines changed 1, 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/pango.clade-mutations.tsv - lines changed 4429, context: html, text, full: html, text