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@benjeffery benjeffery released this 23 Feb 16:31
· 263 commits to main since this release
0.2.2
99cad13
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Learn about vigilant mode.

Bugfixes:

  • Mutations at non-inference sites are now guaranteed to be fully parsimonious.
    Previous versions required a mutation above the root when the input ancestral state
    disagreed with the ancestral state produced by the parsimony algorithm. Now fixed by
    using the new map_mutations code from tskit 0.3.7 (:pr:557, :user:hyanwong)

New Features:

Breaking changes:

  • Oldest nodes in a standard inferred tree sequence are no longer set to frequencies ~2
    and ~3 (i.e. 2 or 3 times as old as all the other nodes), but are spaced above the
    others by the mean time between unique ancestor ages (:pr:485, :user:hyanwong)

  • The tsinfer.SampleData.from_tree_sequence() function now defaults to setting
    use_sites_time and use_individuals_time to False rather than True
    (:pr:599, :user:hyanwong)

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