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tsdate.preprocess_ts() should split root nodes when their children change #452

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hyanwong opened this issue Jan 20, 2025 · 0 comments
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@hyanwong
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In tsinfer, by defaults we split the "ultimate root" (the one that is all-ancestral states) into separate segments when any of its children change. However, we do not split local root nodes. This might improve dating (see tskit-dev/tsinfer#850). I see this as quite similar to the split_disjoint routine, so maybe we should make it part of tsdate.preprocess_ts, rather than a default for tsinfer. We could simply add a split_roots option too.

In the long term, this may not matter as:

  1. @duncanMR is likely to change the ancestor-generating process so that ancient topology is resolved using neighbour-joining, which may lead to roots being split up anyway.
  2. We are thinking of combining tsdate into the tsinfer pathway, so maybe it's not important where it gets put?
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