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Missingness support in alignments #3317

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Merged
merged 1 commit into from
Nov 12, 2025
Merged

Missingness support in alignments #3317

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9 changes: 9 additions & 0 deletions c/CHANGELOG.rst
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Unreleased
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- ``tsk_variant_init`` and associated variant decoding methods now
fully support TSK_ISOLATED_NOT_MISSING not being set for internal nodes.
(:user:`benjeffery`, :pr:`3313`)


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[1.2.0] - 2025-09-24
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17 changes: 17 additions & 0 deletions python/CHANGELOG.rst
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@@ -1,3 +1,20 @@
----------
Unreleased
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**Features**

- ``TreeSequence.variants``, ``.genotype_matrix``, ``.haplotypes``, and ``.alignments`` methods
now fully support ``isolated_as_missing`` behaviour with internal nodes.
(:user:`benjeffery`, :pr:`3313`, :pr:`3317`, :issue:`1896`)

**Breaking Changes**

- The ``reference_sequence`` argument to ``TreeSequence.alignments`` is now required
to be the same length as the tree sequence. Previously it was required to be the length
of the requested interval.
(:user:`benjeffery`, :pr:`3317`)

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[1.0.0b3] - 2025-10-15
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