Explicitly guard against > 2 alleles in HMM.

Closes tskit-dev#415

tests/test_inference.py

@@ -492,6 +492,23 @@ def verify_data_round_trip(
                 ts, genotypes, positions, alleles, sample_data.sequence_length
             )
 
+    # Skipping these tests as the HMM is currently not working properly
+    # for > 2 alleles, and we we have a guard on this just to make
+    # sure that no user-data uses the faulty engine. Renable these
+    # when the HMM is fixed.
+
+    @pytest.mark.skip("Not currently working for > 2 alleles; #415")
+    def test_triallelic(self):
+        pass
+
+    @pytest.mark.skip("Not currently working for > 2 alleles; #415")
+    def test_n_allelic(self):
+        pass
+
+    @pytest.mark.skip("Not currently working for > 2 alleles; #415")
+    def test_not_all_alleles_in_genotypes(self):
+        pass
+
 
 class TestMissingDataRoundTrip(TestRoundTrip):
     """

tsinfer/inference.py

@@ -1113,6 +1113,8 @@ def __init__(
         # quickly be big enough even for very large instances.
         max_edges = 64 * 1024
         max_nodes = 64 * 1024
+        if np.any(num_alleles > 2):
+            raise ValueError("Cannot currently match with > 2 alleles.")
         self.tree_sequence_builder = self.tree_sequence_builder_class(
             num_alleles=num_alleles, max_nodes=max_nodes, max_edges=max_edges
         )