Implement skip when no particular allele is observed

Author: szhan

python/tests/beagle_numba.py

@@ -561,11 +561,13 @@ def interpolate_allele_probs(
         w = weights[i]
         for a in alleles:
             is_a_in_ref_h = ref_h[i, :] == a
+            if np.sum(is_a_in_ref_h) == 0:
+                continue
             if use_threshold:
                 # TODO: Check whether this is implemented correctly. Not used by default.
                 # Threshold based on "the number of subsets in the partition Am of H".
-                threshold_Am = np.sum(is_a_in_ref_h)
-                _MIN_THRESHOLD = min(0.005, 1 / threshold_Am)
+                threshold_Am = 1 / np.sum(is_a_in_ref_h)
+                _MIN_THRESHOLD = min(0.005, threshold_Am)
             if k == 0:
                 # See 'setFirstAlleleProbs' in 'LSHapBaum.java'.
                 assert w == 1.0, "Weight should be 1.0."