Add --maintain-topo and --no-simplify options to grg convert #14
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Conversion from TS to GRG previously ignored topology changes below a mutation _IF_ that topology change did not impact the sample set of the mutation. This manifests when the break and join point of a recombination both occur entirely below a mutation. You can no run `grg convert --maintain-topo` if you want to instead retain such topology changes. The algorithm change is quite simple: instead of traversing from added/removed edges to their MRCA we instead just traverse all the way to the root(s). The nodes along the way are marked to be split next time they are encountered by a mutation. On a reasonably large Tree-Seq file (500k samples, 100Mbp len), there is no noticeable timing difference between the two versions of the algorithm. GRG file size is pretty much the same as well; when you look at the edges/nodes you see the minimal difference: Original algorithm == Nodes: 3998656, Edges: 13190551 Maintain topo == Nodes: 4011727, Edges: 13245575 But both files are 140Mb Additionally I exposed the already existing "--no-simplify" option to "grg convert". When you turn off simplification you DO see the size difference: Maintain topo + no simplify == Nodes: 10648753, Edges: 19297506 File size = 201Mb vs. 140Mb
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Conversion from TS to GRG previously ignored topology changes below a mutation IF that topology change did not impact the sample set of the mutation. This manifests when the break and join point of a recombination both occur entirely below a mutation.
You can now run
grg convert --maintain-topoif you want to instead retain such topology changes. The algorithm change is quite simple: instead of traversing from added/removed edges to their MRCA we instead just traverse all the way to the root(s). The nodes along the way are marked to be split next time they are encountered by a mutation.On a reasonably large Tree-Seq file (500k samples, 100Mbp len), there is no noticeable timing difference between the two versions of the algorithm.
GRG file size is pretty much the same as well; when you look at the edges/nodes you see the minimal difference:
But both files are 140Mb
Additionally I exposed the already existing "--no-simplify" option to "grg convert". When you turn off simplification you DO see the size difference:
File size = 201Mb vs. 140Mb