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Initial tsls engine - #3
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jeromekelleher merged 1 commit intoOct 16, 2026
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A single Li and Stephens HMM engine based on the tsinfer matcher. Every node in the tree at a position is a state (isolated nodes cannot be copied), any topology is supported, and the engine provides the Viterbi algorithm (with tsinfer's find_path interface) and the forward and backward algorithms, returning compressed matrices. It uses tsinfer's compression, likelihood threshold and weight_by_n, and supports multiple mutations per site. The tests compare against a dense implementation on small hand-built examples. Add tsls engine to the benchmarks
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