Add placeholder for implementing Equation 1

Author: szhan

python/tests/test_beagle.py

@@ -312,6 +312,24 @@ def compute_state_probability_matrix(fm, bm, ref_h, query_h, rho, mu):
     return (sm, fwd_hap_probs, bwd_hap_probs)
 
 
+def compute_state_probability_matrix_eqn1(fm, bm, ref_h, query_h, rho, mu):
+    """
+    Implement the HMM forward-backward algorithm following Equation 1 of BB2016.
+
+    This is simpler than faithfully reimplementing the original BEAGLE 4.1 algorithm.
+
+    :param numpy.ndarray fm: Forward probability matrix.
+    :param numpy.ndarray bm: Backward probability matrix.
+    :param numpy.ndarray ref_h: Reference haplotypes.
+    :param numpy.ndarray query_h: One query haplotype.
+    :param numpy.ndarray rho: Switch probabilities.
+    :param numpy.ndarray mu: Mismatch probabilities.
+    :return: HMM state probability matrix.
+    :rtype: numpy.ndarray
+    """
+    pass
+
+
 def interpolate_haplotype_probability_matrix(
     fwd_hap_probs, bwd_hap_probs, genotyped_pos, imputed_pos
 ):