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Author: szhan

python/tests/test_beagle.py

@@ -35,6 +35,9 @@
 the alleles in the aggregated markers form distinct allele sequences.
 Below, we do not use aggregated markers or allele sequences, which simplifies
 the implementation.
+
+Rather than trying to faithfully reimplementing the original BEAGLE 4.1 algorithm,
+the following computes Equation 1 of BB2016.
 """
 import numpy as np
 
@@ -447,6 +450,7 @@ def run_beagle(ref_h, query_h, pos):
         ref_h_genotyped, query_h_genotyped, rho, mu
     )
     assert bm.shape == (m, h)
+    # TODO: Replace this with the simpler implementation.
     # Compute HMM state probability matrix over genotyped markers
     # and forward and backward haplotype probability matrices
     sm, fwd_hap_probs, bwd_hap_probs = compute_state_probability_matrix(