feat: add recombination parameter estimator#464
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Python mirror of the Rust estimator for freezing reviewed HMM parameters into datasets. Computes gamma, muW, muR from the reference tree using the same algorithm as the run-time estimator: substitutions and insertions counted, deletions excluded, muR from inter-clade leaf distances.
Parity tests transcribe the Rust unit-test fixtures as the oracle. CLI smoke tests verify the --pathogen write-back and stdout modes.
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Mirror the Rust estimator change: count a branch mutation only when both its reference and query bases are present (non-gap), so neither insertions ("-10A", gap reference) nor deletions ("A15-", gap query) contribute to muW/muR. The decoder scores substitutions only, so calibrating against indels would inflate both rates on externally produced trees (augur/TreeTime) that carry insertion tokens.
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nextclade: #1774A dataset can freeze reviewed HMM parameter values as explicit
pathogen.jsonoverrides, so that the model a reviewer signed off on is not silently shifted by a later tree update. This PR adds the Python helper that computes them.The script mirrors the Rust run-time estimator: it computes$\gamma$ , $\mu_w$ , $\mu_r$ from the reference tree using the same definitions (substitutions and insertions counted, deletions excluded, $\mu_r$ from inter-clade leaf distances). With
--pathogen, the estimates are written into the file'srecombinationobject in place; without it, they are printed to stdout for inspection. Parity is guarded by tests that transcribe the Rust unit-test fixtures as the oracle.Work items
scripts/recombination_paramswith tree-based estimation matching the Rust algorithm