small updates to merge util, rf-sampling, and trimming

matsengrp / larch

Inference and manipulation of history DAGs

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Closed marybarker closed 3 months ago

marybarker commented 3 months ago

this branch adds functionality to the merge util so that we can:

trim a MergeDAG with respect to optimal RF distance to another provided DAG/tree.
sample a tree from the merged DAG using parsimony or RF distance, rather than saving the entire merged DAG to output. it also includes small bugfixes for sampling in larch-usher.