From 6ca83716e1394022f2fe988655c22b1d7da345be Mon Sep 17 00:00:00 2001 From: Shing Zhan Date: Wed, 30 Aug 2023 13:56:11 +0100 Subject: [PATCH] Add notes --- python/tests/test_beagle.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/python/tests/test_beagle.py b/python/tests/test_beagle.py index eddd86c3b4..3f6adc6a04 100644 --- a/python/tests/test_beagle.py +++ b/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(