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Do not use mismatch in ancestor matching when using infer() #981

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Do not use mismatch in ancestor matching when using infer() #981

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11 changes: 11 additions & 0 deletions tests/test_inference.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4309,6 +4309,17 @@ def test_zero_recombination(self):
extended_checks=True,
)

def test_no_ancestor_mismatch_in_basic_infer(self, small_sd_anc_fixture):
# Check we are not using mismatch in match_ancestors, by
# passing a value that fails in the ma phase
sd, anc = small_sd_anc_fixture
rho = 0
with pytest.raises(_tsinfer.MatchImpossible):
# rho=0 fails if mismatch is used in match_ancestors
tsinfer.match_ancestors(sd, anc, recombination_rate=rho)
for e in [tsinfer.PY_ENGINE, tsinfer.C_ENGINE]:
tsinfer.infer(sd, recombination_rate=rho, engine=e)


class TestAlgorithmResults:
"""
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16 changes: 8 additions & 8 deletions tsinfer/inference.py
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Original file line number Diff line number Diff line change
Expand Up @@ -295,8 +295,8 @@ def infer(
and ``path_compression``.

.. note::
For finer grained control over inference, for example to set different mismatch
ratios when matching ancestors versus samples, run
For finer grained control over inference, for example to set mismatch
ratios when matching ancestors as well as when matching samples, run
:func:`tsinfer.generate_ancestors`, :func:`tsinfer.match_ancestors` and
:func:`tsinfer.match_samples` separately.

Expand All @@ -305,14 +305,14 @@ def infer(
:param recombination_rate: Either a floating point value giving a constant rate
:math:`\\rho` per unit length of genome, or an :class:`msprime.RateMap`
object. This is used to calculate the probability of recombination between
adjacent sites. If ``None``, all matching conflicts are resolved by
recombination and all inference sites will have a single mutation
(equivalent to mismatch_ratio near zero)
adjacent sites in the match_samples stage. If ``None``, all matching
conflicts are resolved by recombination and all inference sites will have
a single mutation (equivalent to mismatch_ratio near zero).
:type recombination_rate: float, msprime.RateMap
:param float mismatch_ratio: The probability of a mismatch relative to the median
probability of recombination between adjacent sites: can only be used if a
recombination rate has been set (default: ``None`` treated as 1 if
``recombination_rate`` is set).
``recombination_rate`` is set). This is only applied in the match_samples stage.
:param bool path_compression: Whether to merge edges that share identical
paths (essentially taking advantage of shared recombination breakpoints).
:param bool post_process: Whether to run the :func:`post_process` method on the
Expand Down Expand Up @@ -348,13 +348,13 @@ def infer(
progress_monitor=progress_monitor,
record_provenance=False,
)
# NB: do not pass or encourage use of the mismatch ratio / recombination rate in
# the ancestor matching phase. See https://github.com/tskit-dev/tsinfer/issues/980
ancestors_ts = match_ancestors(
sample_data,
ancestor_data,
engine=engine,
num_threads=num_threads,
recombination_rate=recombination_rate,
mismatch_ratio=mismatch_ratio,
precision=precision,
path_compression=path_compression,
progress_monitor=progress_monitor,
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