Commits for angie

5dd22774eea1a954815f0a32797d5a1dbfdcecc8 Tue Sep 10 14:01:20 2024 -0700

When writing the auspice JSON tree, if a sample is found in the optional config file anchorSamples, then add an empty 'vaccine' attribute to get the X icon in auspice display.
- src/hg/hgPhyloPlace/treeToAuspiceJson.c - lines changed 31, context: html, text, full: html, text

9804a48d4ee019ce876c5eb2f98239830a2ef766 Tue Sep 10 14:03:32 2024 -0700

Mask artifactual reversions in KP.3.1.1.
- src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml - lines changed 9, context: html, text, full: html, text

466d876c3308a789b3abd3e2ae559d1413ea5fc5 Thu Sep 12 10:01:15 2024 -0700

nextclade sort's scoring function, for short similar reference sequences, gives too much weight to reference sequence length and not enough to numHits. So, instead of using nextclade sort's top-scoring match for each input sequence, run nextclade sort --all-matches and choose the ref with the highest (score * numHits). This does a better job when distinguishing between 7 RefSeq assemblies for influenza A segments.
- src/hg/hgPhyloPlace/phyloPlace.c - lines changed 49, context: html, text, full: html, text

e4e4f9d3a53e8bc8b1354be2267031d392d09886 Fri Sep 13 12:57:40 2024 -0700

Fix the way basesAligned is calculated: insBases were never part of (tEnd - tStart).
- src/hg/hgPhyloPlace/vcfFromFasta.c - lines changed 1, context: html, text, full: html, text

6b482d67559bf0e2f7c27eed5182a18f85f0db2b Fri Sep 13 13:55:38 2024 -0700

Add config setting enableOptimization (for small trees). Since there are now too many configurable usher-sampled options to handle by truncating a list, instead we now add options if configured.
- src/hg/hgPhyloPlace/runUsher.c - lines changed 30, context: html, text, full: html, text