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Check for valid input in ARG likelihood #2114

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merged 1 commit into from Oct 18, 2022
Merged

Check for valid input in ARG likelihood #2114

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10 changes: 10 additions & 0 deletions msprime/likelihood.py
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Expand Up @@ -21,6 +21,8 @@
"""
import math

import numpy as np

from msprime import _msprime


Expand Down Expand Up @@ -136,6 +138,14 @@ def log_arg_likelihood(ts, recombination_rate, Ne=1):
sequence contains at least one recombination event, then returns
`-DBL_MAX`.
"""
for tree in ts.trees():
if np.any(tree.num_children_array > 2):
raise ValueError(
"ARG likelihood encountered a polytomy."
" Tree sequences must contain binary mergers only for"
" valid likelihood evaluation."
)

# Get the tables into the format we need to interchange with the low-level code.
lw_tables = _msprime.LightweightTableCollection()
lw_tables.fromdict(ts.tables.asdict())
Expand Down
27 changes: 27 additions & 0 deletions tests/test_likelihood.py
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Expand Up @@ -169,6 +169,33 @@ def test_log_likelihoods(self):
msprime.log_mutation_likelihood(arg, t),
)

def test_arg_likelihood_error_handling(self):
tables = tskit.TableCollection(sequence_length=1)
tables.nodes.add_row(
flags=tskit.NODE_IS_SAMPLE, population=0, individual=-1, time=0
)
tables.nodes.add_row(
flags=tskit.NODE_IS_SAMPLE, population=0, individual=-1, time=0
)
tables.nodes.add_row(
flags=tskit.NODE_IS_SAMPLE, population=0, individual=-1, time=0
)
tables.nodes.add_row(flags=0, population=0, individual=-1, time=1)

tables.edges.add_row(left=0, right=1, parent=3, child=0)
tables.edges.add_row(left=0, right=1, parent=3, child=1)
tables.edges.add_row(left=0, right=1, parent=3, child=2)
tables.populations.add_row()
arg = tables.tree_sequence()

with pytest.raises(
ValueError,
match="ARG likelihood encountered a polytomy."
" Tree sequences must contain binary mergers only for"
" valid likelihood evaluation.",
):
msprime.log_arg_likelihood(arg, 1)

def test_multiple_mrcas(self):
tables = tskit.TableCollection(sequence_length=1)
tables.nodes.add_row(
Expand Down