Searched refs:allele_counts (Results 1 – 5 of 5) sorted by relevance
15 def hwe_expectation(genotype, allele_counts): argument18 population_total_alleles = sum(allele_counts)21 allele_frequencies = [count / float(population_total_alleles) for count in allele_counts]41 allele_counts = fold(add_tuple, [[a * g[1] for a in g[0]] for g in genotypes])49 …angements_of_alleles_in_sample = multinomial_coefficientln(population_total_alleles, allele_counts)62 allele_counts = fold(add_tuple, [[a * g[1] for a in g[0]] for g in genotypes])65 expected = hwe_expectation(genotype, allele_counts) * population_total_genotypes
795 vector<int> allele_counts; in filter_sites_by_frequency_and_call_rate() local796 get_allele_counts(allele_counts, N_non_missing_chr); in filter_sites_by_frequency_and_call_rate()803 freq = allele_counts[ui] / (double)N_non_missing_chr; in filter_sites_by_frequency_and_call_rate()896 vector<int> allele_counts; in filter_sites_by_allele_count() local897 get_allele_counts(allele_counts, N_non_missing_chr); in filter_sites_by_allele_count()904 mac = min(allele_counts[ui], mac); in filter_sites_by_allele_count()905 if ((ui > 0) && ((allele_counts[ui] < min_non_ref_ac) || (allele_counts[ui] > max_non_ref_ac))) in filter_sites_by_allele_count()908 …if ((ui > 0) && ((allele_counts[ui] < min_non_ref_ac_any) || (allele_counts[ui] > max_non_ref_ac_a… in filter_sites_by_allele_count()
50 vector<int> allele_counts; in output_frequency() local199 vector<int> allele_counts; in output_het() local324 vector<int> allele_counts; in output_hwe() local529 vector<int> allele_counts; in output_indv_freq_burden() local2740 vector<int> allele_counts; in output_singletons() local3167 vector<int> allele_counts; in output_TsTv_by_count() local3896 vector<int> allele_counts; in output_per_site_nucleotide_diversity() local3977 vector<int> allele_counts; in output_Tajima_D() local4104 vector<int> allele_counts; in output_windowed_nucleotide_diversity() local4602 vector<int> allele_counts; in output_indv_relatedness_Manichaikul() local[all …]
398 vector<int> allele_counts(get_N_alleles(), 0); in get_allele_counts() local411 allele_counts[genotype.first]++; in get_allele_counts()416 allele_counts[genotype.second]++; in get_allele_counts()421 out = allele_counts; in get_allele_counts()
367 Counts<Nt2> allele_counts = tally_allele_counts(sample_calls()); in filter_mac() local368 if (allele_counts.sorted()[1].first < min_mac) in filter_mac()