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Tidy extend_haplotypes docstring #3315

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Nov 10, 2025
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Tidy extend_haplotypes docstring #3315

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13 changes: 8 additions & 5 deletions c/tskit/trees.h
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Expand Up @@ -933,17 +933,20 @@ path from `p` to `c`. For instance, if `p` is the parent of `n` and `n`
is the parent of `c`, then the span of the edges from `p` to `n` and
`n` to `c` are extended, and the span of the edge from `p` to `c` is
reduced. However, any edges whose child node is a sample are not
modified. The `node` of certain mutations may also be remapped; to do this
modified. See Fritze et al. (2025):
https://doi.org/10.1093/genetics/iyaf198 for more details.

The method works by iterating over the genome to look for edges that can
be extended in this way; the maximum number of such iterations is
controlled by ``max_iter``.

The `node` of certain mutations may also be remapped; to do this
unambiguously we need to know mutation times. If mutations times are unknown,
use `tsk_table_collection_compute_mutation_times` first.

The method will not affect any tables except the edge table, or the node
column in the mutation table.

The method works by iterating over the genome to look for edges that can
be extended in this way; the maximum number of such iterations is
controlled by ``max_iter``.

@rst

**Options**: None currently defined.
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18 changes: 10 additions & 8 deletions python/tskit/trees.py
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Expand Up @@ -7395,7 +7395,9 @@ def extend_haplotypes(self, max_iter=10):
`n` to `c` are extended, and the span of the edge from `p` to `c` is
reduced. Thus, the ancestral haplotype represented by `n` is extended
to a longer span of the genome. However, any edges whose child node is
a sample are not modified.
a sample are not modified. See
`Fritze et al. (2025) <https://doi.org/10.1093/genetics/iyaf198>`_
for more details.

Since some edges may be removed entirely, this process usually reduces
the number of edges in the tree sequence.
Expand All @@ -7418,15 +7420,15 @@ def extend_haplotypes(self, max_iter=10):
known mutation times. See :meth:`.impute_unknown_mutations_time` if
mutation times are not known.

The method will not affect the marginal trees (so, if the original tree
sequence was simplified, then following up with `simplify` will recover
the original tree sequence, possibly with edges in a different order).
It will also not affect the genotype matrix, or any of the tables other
than the edge table or the node column in the mutation table.
.. note::
The method will not affect the marginal trees (so, if the original tree
sequence was simplified, then following up with `simplify` will recover
the original tree sequence, possibly with edges in a different order).
It will also not affect the genotype matrix, or any of the tables other
than the edge table or the node column in the mutation table.

:param int max_iters: The maximum number of iterations over the tree
:param int max_iter: The maximum number of iterations over the tree
sequence. Defaults to 10.

:return: A new tree sequence with unary nodes extended.
:rtype: tskit.TreeSequence
"""
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