population/function/functions.hpp File Reference

#include "genesis/population/filter/sample_counts_filter.hpp"
#include "genesis/population/sample_counts.hpp"
#include "genesis/population/variant.hpp"
#include "genesis/sequence/reference_genome.hpp"
#include "genesis/utils/text/char.hpp"
#include <array>
#include <iosfwd>
#include <utility>
#include <string>
#include <vector>

Go to the source code of this file.

Namespaces
	genesis
	Container namespace for all symbols of genesis in order to keep them separate when used as a library.
	genesis::population

Functions
size_t	allele_count (SampleCounts const &sample)
	Return the number of alleles, that is, of non-zero nucleotide counts of the sample. More...
size_t	allele_count (SampleCounts const &sample, size_t min_count)
	Return the number of alleles, taking a min_count into consideration, that is, we compute the number of nucleotide counts of the sample that are at least the min_count. More...
size_t	allele_count (SampleCounts const &sample, size_t min_count, size_t max_count)
	Return the number of alleles, taking a min_count and max_count into consideration, that is, we compute the number of nucleotide counts of the sample that are at least min_count and at most max_count. More...
std::pair< char, double >	consensus (SampleCounts const &sample)
	Consensus character for a SampleCounts, and its confidence. More...
std::pair< char, double >	consensus (SampleCounts const &sample, bool is_covered)
	Consensus character for a SampleCounts, and its confidence. More...
SampleCounts::size_type	get_base_count (SampleCounts const &sample, char base)
	Get the count for a base given as a char. More...
char	guess_alternative_base (Variant const &variant, bool force=false, SampleCountsFilterPolicy filter_policy=SampleCountsFilterPolicy::kOnlyPassing)
	Guess the alternative base of a Variant. More...
void	guess_and_set_ref_and_alt_bases (Variant &variant, bool force=false, SampleCountsFilterPolicy filter_policy=SampleCountsFilterPolicy::kOnlyPassing)
	Guess the reference and alternative bases for a Variant, and set them. More...
void	guess_and_set_ref_and_alt_bases (Variant &variant, char ref_base, bool force=false, SampleCountsFilterPolicy filter_policy=SampleCountsFilterPolicy::kOnlyPassing)
	Guess the reference and alternative bases for a Variant, and set them, using a given reference base. More...
void	guess_and_set_ref_and_alt_bases (Variant &variant, genesis::sequence::ReferenceGenome const &ref_genome, bool force=false, SampleCountsFilterPolicy filter_policy=SampleCountsFilterPolicy::kOnlyPassing)
	Guess the reference and alternative bases for a Variant, and set them, using a given reference genme to obtain the base. More...
char	guess_reference_base (Variant const &variant, bool force=false, SampleCountsFilterPolicy filter_policy=SampleCountsFilterPolicy::kOnlyPassing)
	Guess the reference base of a Variant. More...
constexpr bool	is_valid_base (char c)
	Return whether a given base is in ACGT, case insensitive. More...
constexpr bool	is_valid_base_or_n (char c)
	Return whether a given base is in ACGTN, case insensitive. More...
SampleCounts	merge (SampleCounts const &p1, SampleCounts const &p2)
	Merge the counts of two SampleCountss. More...
SampleCounts	merge (std::vector< SampleCounts > const &p, SampleCountsFilterPolicy filter_policy)
	Merge the counts of a vector SampleCountss. More...
void	merge_inplace (SampleCounts &p1, SampleCounts const &p2)
	Merge the counts of two SampleCountss, by adding the counts of the second (p2) to the first (p1). More...
SampleCounts	merge_sample_counts (Variant const &v, SampleCountsFilterPolicy filter_policy)
	Merge the counts of a vector SampleCountss. More...
template<typename T >
std::array< size_t, 4 >	nucleotide_sorting_order (std::array< T, 4 > const &values)
	Return the sorting order of four values, for instance of the four nucleotides ACGT, in descending order (largest first). More...
constexpr size_t	nucleotide_sum (SampleCounts const &sample)
	Count of the pure nucleotide bases at this position, that is, the sum of all A, C, G, and T. More...
std::ostream &	operator<< (std::ostream &os, SampleCounts const &bs)
	Output stream operator for SampleCounts instances. More...
template<typename T >
std::array< size_t, 6 >	sample_counts_sorting_order (std::array< T, 6 > const &v)
	Return the sorting order of six values, for instance of the four nucleotides ACGT and the N and D counts of a SampleCounts object, in descending order (largest first). More...
constexpr size_t	sample_counts_sum (SampleCounts const &sample)
	Sum up all the base counts at this sample, that is, the sum of all A, C, G, T, as well as the N and D count for indetermined and deleted counts. More...
void	set_base_count (SampleCounts &sample, char base, SampleCounts::size_type value)
	Set the count for a base given as a char. More...
std::pair< SortedSampleCounts, SortedSampleCounts >	sorted_average_sample_counts (SampleCounts const &sample_a, SampleCounts const &sample_b)
	Return the sorted base counts of both input samples, orderd by the average frequencies of the nucleotide counts in the two samples. More...
SortedSampleCounts	sorted_sample_counts (SampleCounts const &sample)
	Return the order of base counts (nucleotides), largest one first. More...
SortedSampleCounts	sorted_sample_counts (Variant const &variant, bool reference_first, SampleCountsFilterPolicy filter_policy)
	Get a list of bases sorted by their counts. More...
size_t	total_nucleotide_sum (Variant const &variant, SampleCountsFilterPolicy filter_policy)
	Count of the pure nucleotide bases at this position, that is, the sum of all A, C, G, and T. More...
size_t	total_sample_counts_sum (Variant const &variant, SampleCountsFilterPolicy filter_policy)
	Sum up all the base counts at this sample, that is, the sum of all A, C, G, T, as well as the N and D count for indetermined and deleted counts. More...