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szhan committed Aug 30, 2023
1 parent 3465301 commit 6ca8371
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4 changes: 4 additions & 0 deletions python/tests/test_beagle.py
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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

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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(
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