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

Fixes #980

Author: hyanwong

CHANGELOG.md

@@ -7,6 +7,11 @@
 - Document that the `zarr-vcf` dataset can be either a path or an in-memory zarr group.
   (feature introduced in {pr}`966`, documented in {pr}`974`, {user}`hyanwong`)
 
+**Breaking Changes**
+
+- If a mismatch ratio is provided to the `infer` command, it only applies during the
+  `match_samples` phase ({issue}`980`, {pr}`981`, {user}`hyanwong`)
+
 **Fixes**
 
 - Properly account for "N" as an unknown ancestral state, and ban "" from being

tests/test_inference.py

@@ -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:
     """

tsinfer/inference.py

@@ -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.
 
@@ -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
@@ -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,