Commits for angie

6bc045a7d9e23c14433beeeaecf349ff5d5785a1 Wed Apr 15 11:03:33 2026 -0700

Use viral_usher to build daily measles tree.
- src/hg/utils/otto/measles/buildTree.sh - lines changed 89, context: html, text, full: html, text

0750648bee41e57d7f1cbc3de8e3d9177bfd4c70 Fri May 1 10:02:25 2026 -0700

Initial support for ripples seach in usher-sampled-server. Enabled by config param ripplesEnabled. If enabled, there is a new checkbox for the user to click if they want the extra search. Currently hardcoded to max of 10 sequences, otherwise extra search is not done (too slow). Ripples results, if any, are displayed in a table before the usual summary table.
- src/hg/hgPhyloPlace/hgPhyloPlace.c - lines changed 8, context: html, text, full: html, text
- src/hg/hgPhyloPlace/phyloPlace.c - lines changed 116, context: html, text, full: html, text
- src/hg/hgPhyloPlace/phyloPlace.h - lines changed 34, context: html, text, full: html, text
- src/hg/hgPhyloPlace/runUsher.c - lines changed 346, context: html, text, full: html, text

bc1dd635cfd41140693da19ddcd578ad3f5b30d6 Fri May 1 10:03:42 2026 -0700

Added new lineages.
- src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv - lines changed 17, context: html, text, full: html, text