Commits for angie

v503_preview2 to v503_base (2026-08-24 to 2026-08-31) v503

e8f2f6e391ee65e96e0a99e9a840f55db59bdb60 Fri Jun 5 15:34:13 2026 -0700

• Fixing more bugs found by Claude when Chris ran it.
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 2, context: html, text, full: html, text
  • src/hg/js/hgPhyloPlace.js - lines changed 1, context: html, text, full: html, text

186567f2a1068c3f5d804de5f0907572e91ba914 Wed Jun 10 13:08:24 2026 -0700

• Added clades 25D - 25I.
  • src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv - lines changed 6, context: html, text, full: html, text

59c6cecaf508798f9e7c4f3cda836a6f0105ad9a Wed Jun 10 13:09:00 2026 -0700

• Added new lineages up through release 1.39.
  • src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 34, context: html, text, full: html, text

de23dd389f8e8e35c41880a85d74e9838a4df8e4 Thu Jun 18 15:11:49 2026 -0700

• ssh to hgwdev for commands that need access to hgwdev-only directories, because these scripts run elsewhere now. Tweak shell variables usherDir and friends to make it easier to try out different build directories.
  • src/hg/utils/otto/dengue/buildTree.sh - lines changed 15, context: html, text, full: html, text
  • src/hg/utils/otto/measles/buildTree.sh - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/otto/mpxv/buildTree.sh - lines changed 15, context: html, text, full: html, text
  • src/hg/utils/otto/rsv/buildTree.sh - lines changed 13, context: html, text, full: html, text

e22c5be5fb552757c886e7356db9d49eca8cdedb Thu Jun 18 15:13:24 2026 -0700

• Use TMPDIR -- this no longer runs on hgwdev.
  • src/hg/utils/otto/fluA/updateAndersenLab.sh - lines changed 7, context: html, text, full: html, text

8d5f0115cf9ab2b99f18a1467c0be02a6ae55de4 Thu Jun 18 15:18:03 2026 -0700

• Use taxonium overlay html to describe the trees. Adjust filters. ssh to hgwdev for commands that need access to hgwdev-only directories, because these scripts run elsewhere now. Tweak shell variables usherDir and friends to make it easier to try out different build directories.
  • src/hg/utils/otto/fluA/buildConcatTree.sh - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/otto/fluA/buildConcatTreeD1.1.sh - lines changed 11, context: html, text, full: html, text
  • src/hg/utils/otto/fluA/buildTree.sh - lines changed 47, context: html, text, full: html, text
  • src/hg/utils/otto/fluA/taxonium_overlay.html - lines changed 52, context: html, text, full: html, text
  • src/hg/utils/otto/fluA/taxonium_overlay_b3_13.html - lines changed 89, context: html, text, full: html, text
  • src/hg/utils/otto/fluA/taxonium_overlay_d1_1.html - lines changed 89, context: html, text, full: html, text
  • src/hg/utils/otto/fluA/taxonium_overlay_h5n1_ha.html - lines changed 78, context: html, text, full: html, text
  • src/hg/utils/otto/fluA/taxonium_overlay_pb2.html - lines changed 74, context: html, text, full: html, text

f51e81544b68da673a608a8f8cb221c8f964af93 Thu Jun 18 15:20:35 2026 -0700

• Latest new lineages.
  • src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 7, context: html, text, full: html, text

0b095144508cbb36923bacffa0425003f8484042 Thu Jun 18 15:21:58 2026 -0700

• Simplify creation of pango.clade-mutations.reroot.tsv because matUtils annotate can handle multiple successive mutations at the same position now.
  • src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh - lines changed 6, context: html, text, full: html, text

8e48fb87643184fc740bb980dbccd6309fee97c6 Thu Jun 18 15:22:24 2026 -0700

• Tweak shell variables usherDir and friends to make it easier to try out different build directories.
  • src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh - lines changed 6, context: html, text, full: html, text

014bee401f2fe14c79caf74d42b5f4f6cf797dd3 Thu Jun 18 15:23:11 2026 -0700

• Loosen filters to accommodate increasingly divergent sequences. Tweak shell variables usherDir and friends to make it easier to try out different build directories.
  • src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh - lines changed 13, context: html, text, full: html, text

6091af3e8fff91595ab6361974787afef032a342 Thu Jun 25 11:03:38 2026 -0700

• Fix second filtering to match first. Extract tree of sequences from the past year plus sequences within a radius of 5 edges of those.
  • src/hg/utils/otto/sarscov2phylo/find_recent_samples.py - lines changed 69, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/prune_to_radius.py - lines changed 129, context: html, text, full: html, text
  • src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh - lines changed 24, context: html, text, full: html, text

c210683fd63e352426e983f869c6c9aa389da3e1 Wed Aug 26 16:59:09 2026 -0700

• Add exceptions for some XFJ and XFG branches.
  • src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml - lines changed 8, context: html, text, full: html, text

d433a2f3c25a7364956f5904c9e391d93eb3a3c8 Wed Aug 26 17:01:55 2026 -0700

• Many new lineages and a few tweaks.
  • src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 96, context: html, text, full: html, text

9949a453819bff3ae00234d5f65b73c903ea4b2f Fri Aug 28 08:13:40 2026 -0700

• Replace non-Pango extra labels with Pango labels before pangolin test runs because some new extra labels on older split lineages were causing regex failure in pangolin. Remove the BA.5.1_no29666 branch because it's always problematic.
  • src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh - lines changed 29, context: html, text, full: html, text

ad81d8de49a9c061fb50958f72a017ae1436497d Fri Aug 28 08:17:19 2026 -0700

• Fix regex for rerooting pango.clade-mutations.tsv to also match B's empty mutation list. Bug caught by Claude automated review of 0b09514. Fortunately masked in latest pangolin-data release because the lineage B annotation was preserved when rerooting the tree and did not need re-annotating.
  • src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh - lines changed 1, context: html, text, full: html, text

92ed679e589bc5f2f4bcc78dd89584e67e496cfc Fri Aug 28 08:20:24 2026 -0700

• Support representativeBacktrack for exclusions too. It occurs to me that if a representative is used in multiple places and has representativeBacktrack in any of them, the one that the script finds first will be applied to all. Pressed for time and not yet sure what to do about that. Probably should at least detect & warn.
  • src/hg/utils/otto/sarscov2phylo/branchSpecificMask.py - lines changed 8, context: html, text, full: html, text

61e501ff1e558ceb89d89ce46acb8fae1cb46cfc Fri Aug 28 08:23:02 2026 -0700

• Add representativeBacktrack: 1 for exclusion of 23599 for XFJ.3.1 because representative was removed and added back with another masked mut putting it one node deeper in the pre-masking tree which caused the exclusion to be applied only to that little branch.
  • src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml - lines changed 1, context: html, text, full: html, text

b9f2ec794548c0db212574a8172c27d32ed47026 Fri Aug 28 08:24:26 2026 -0700

• Use csvtk grep because we hit a wall with grep -Fwf performance.
  • src/hg/utils/otto/sarscov2phylo/combineMetadata.sh - lines changed 1, context: html, text, full: html, text

637a3d134a395adf8eb77c177ff11aa6972146c0 Fri Aug 28 08:25:27 2026 -0700

• Use csvtk grep because we hit a wall with grep -Fwf performance.
  • src/hg/utils/otto/sarscov2phylo/makeNewMaskedMaple.sh - lines changed 22, context: html, text, full: html, text

d3954606ff07dd6169919e7059e53bc0d7e98b06 Fri Aug 28 08:27:34 2026 -0700

• Now that XFJ.3.1 is excluded from masking of 21617 (in JN.1), we can include A21617G in descendants of XFJ.3.1.
  • src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 4, context: html, text, full: html, text

d0ed6814b11e78dfd69dbe071b296acf46b8e24a Fri Aug 28 08:28:16 2026 -0700

• If split lineages were found, report them.
  • src/hg/utils/otto/sarscov2phylo/updatePublic.sh - lines changed 3, context: html, text, full: html, text

efdf71bc99d33cb9fc9327b8b8e05244dab81e08 Fri Aug 28 08:29:52 2026 -0700

• Scan the tree for split lineages, excluding some highly recurrent mutations.
  • src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh - lines changed 12, context: html, text, full: html, text

d356fdc7acdc6b715b559ad6cd8a72d651c282ee Fri Aug 28 08:31:06 2026 -0700

• Add genotype and None to colorByOptions -- they're not automatically included.
  • src/hg/utils/otto/mtb/taxonium.annotated.config.json - lines changed 2, context: html, text, full: html, text

23d1d4ea2a7caf6ecc1c7f3c4e3b730e25456e63 Fri Aug 28 08:36:57 2026 -0700

• Fixing typo found by Claude.
  • src/hg/utils/otto/fluA/taxonium_overlay_b3_13.html - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/fluA/taxonium_overlay_d1_1.html - lines changed 1, context: html, text, full: html, text