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Compression experiments - #5
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jeromekelleher merged 3 commits intoOct 16, 2026
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AncestorMatcher.viterbi_matrix runs Viterbi and also returns a CompressedMatrix of the normalised values and recombination_required flags stored in the traceback at each site, with the maximum likelihood as the normalisation factor. CompressedMatrix.dump and tsls.load_compressed_matrix save and reload matrices for a tree sequence.
experiments/compression captures exact Viterbi and forward matrices on sc2ts sub-ARGs and simulated ARGs and analyses their compression: the stored lists are already minimal, while the Viterbi traceback is dominated by repeated lists that a delta encoding would reduce 50-430x on sc2ts. Correct the sibling-merging suggestion in the thresholding README.
CI runs pytest -n 4, which requires the xdist plugin.
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