Removing mutations above the root, and changing ancestral state accordingly #3079
hyanwong
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Here's a useful recipe, in case there are mutations above the root, which can happen when you simplify to a subset of samples (see #260). @savitakartik and I hit this problem independently recently, when testing tsdate. I have tested with some msprime-generated tree sequences and it seems to work:
E.g. test:
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