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matUtils updates: new subcommand "fix"; improvements to MAT::Tree:move_node and mask --move-nodes #357

Merged
merged 3 commits into from
Nov 2, 2023
Merged

matUtils updates: new subcommand "fix"; improvements to MAT::Tree:move_node and mask --move-nodes #357

merged 3 commits into from
Nov 2, 2023

Commits on Nov 1, 2023

  1. In move_node, search for an existing child of the destination (new pa… 

    …rent) that already has the same mutation(s) as the node to be moved. If a child with the same mutations is found then merge the moved node with the existing child instead of adding it as a new separate child. Handle all combinations of leaf or internal node type for existing child and moved node. Tree::collapse_tree used a breadth-first order for nodes which caused trouble when child nodes were removed due to merging during moves, and later visited in original BFS order. I changed it to recursively descend the tree and process the deepest nodes first.
    @AngieHinrichs
    AngieHinrichs committed Nov 1, 2023
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  2. 1. Performance tweak in restrictMutationsLocally (--mask-mutations): … 

    …for each masked site, instead of copying all mutations that aren't masked, which is almost all mutations in the branch, make a usually-empty list of only the mutations that must be masked and erase those as needed.

2. In moveNodes (--move-nodes), instead of erroring out when the new parent's mutations are not exactly the same as he old parent's, also support the case of a new parent having a strict subset of the old parent's mutations.  In that case, add the mutations that the new parent doesn't have to the node and move the node to become a child of the new parent.
    @AngieHinrichs
    AngieHinrichs committed Nov 1, 2023
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  3. New matUtils subcommand fix: finds nodes whose only mutation is a rev… 

    …ersion of their grandparent's only mutation, a pattern that causes trouble for several Pango lineages, and moves those nodes to become children of their great-grandparents, having only the parent's mutation.
    @AngieHinrichs
    AngieHinrichs committed Nov 1, 2023
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