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Ultimately, we'd like to use Dask to run this vectorised version on chunks of sites, in parallel (although I'm not entirely clear how this would be structured)
The text was updated successfully, but these errors were encountered:
We would like a function to compute the parsimony score for each site in a dataset.
The implementation can be based on the work in the tskit-paper repository where there is a number of different versions implemented using numba.
We would return a new dataset which includes the variable
parsimony_score
, which has a value for each site in the variant data.Initially we can use a single site version, but I think we would want to use the vectorised version for better efficiency:
https://github.com/tskit-dev/tskit-paper/blob/main/tree_performance/benchmark.py#L147
Ultimately, we'd like to use Dask to run this vectorised version on chunks of sites, in parallel (although I'm not entirely clear how this would be structured)
The text was updated successfully, but these errors were encountered: