diff --git a/python/tests/beagle_numba.py b/python/tests/beagle_numba.py index 6c6fffe74d..55320f451b 100644 --- a/python/tests/beagle_numba.py +++ b/python/tests/beagle_numba.py @@ -128,9 +128,12 @@ def get_alleles_at_site(self, i): return a1, ap1, a2, ap2 +""" Helper functions. """ + + def remap_alleles(a): """ - Helper function to map an allele encoded as a character to an integer. + Map an allele encoded as a character to an integer. TODO: Move elsewhere. @@ -213,6 +216,9 @@ def convert_to_genetic_map_positions(pos, genetic_map=None): return est_cm +""" Li & Stephens HMM. """ + + def get_mismatch_probs(pos, error_rate): """ Compute mismatch probabilities at genotyped positions. @@ -363,6 +369,9 @@ def compute_state_prob_matrix(fm, bm): return sm +""" Genotype imputation. """ + + @njit def get_weights(typed_pos, untyped_pos, typed_cm, untyped_cm): """ @@ -640,6 +649,9 @@ def run_tsimpute( return (imputed_alleles, max_allele_probs) +""" Evaluation metrics and printing of results. """ + + # Individual-level data. def compute_individual_scores(alleles_1, allele_probs_1, alleles_2, allele_probs_2): """