feat: add example ebolavirus mutation pattern configs - #456
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Placeholder mutationPatterns configuration for BDBV, EBOV, and SUDV to demonstrate the feature; parameters are not scientifically validated. - BDBV: ADAR (A>G, T>C) and APOBEC (G>A in YGH context), window 50, cutoff 3, with synthetic example sequences - EBOV: ADAR (A>G, T>C) and APOBEC-like CpG deamination (C>T in HCG context), window 100, cutoff 5 - SUDV: ADAR (A>G, T>C), window 80, cutoff 4
…ples - Patterns use `bothStrands` and motifs with the mutated base in parentheses, so each editing signature is one event instead of hand-written complements - EBOV separates C>T in CpG context from ADAR editing, because they are different mutational processes - BDBV example sequences start from a tree node sequence, so each one shows one pattern behavior with a result known by construction
…limit - A C>T or G>A next to a TCW or WGA site must not count as APOBEC3-like, because the substituted base is not the marked base of the site - Cluster markers count toward the sequence view marker limit, so a sequence with 500 mutations and one cluster shows the coverage-only view
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- APOBEC3-like C>T in TCW context drives mpox evolution since the human outbreaks, and these mutations are scattered along the genome, so the pattern reports matches without clusters
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Placeholder
mutationPatternsconfiguration for all three Orthoebolavirus species to demonstrate the featureWork items
mutationPatternsconfig to BDBV (ADAR + APOBEC), EBOV (ADAR + APOBEC CpG), and SUDV (ADAR-only)pathogen.jsonfiles with species-specific clustering parameters