Add threshold for state probabilities

python/tests/beagle_numba.py

@@ -391,6 +391,10 @@ def interpolate_allele_probs(sm, ref_h, typed_pos, untyped_pos, typed_cm, untype
                     else:
                         probs[i, a] += w * sm[k - 1, j]
                         probs[i, a] += (1 - w) * sm[k, j]
+    # Zero trivial probabilities.
+    # TODO: Investigate whether this arbitrary threshold matters.
+    _THRESHOLD = min(0.005, 1 / h)
+    probs[probs < _THRESHOLD] = 0
     # Rescale probabilities.
     # TODO: Check if this is necessary. Could this be a subtle source of error?
     probs_rescaled = probs / np.sum(probs, axis=1)[:, np.newaxis]
@@ -399,7 +403,7 @@ def interpolate_allele_probs(sm, ref_h, typed_pos, untyped_pos, typed_cm, untype
 
 def get_map_alleles(allele_probs):
     """
-    Compute the maximum a posteriori alleles at ungenotyped markers of a query haplotype,
+    Compute maximum a posteriori alleles at the ungenotyped markers of a query haplotype,
     based on posterior marginal allele probabilities.
 
     The imputed alleles is an array of size x.