sample_counts_filter_numerical.hpp File Reference

#include "genesis/population/sample_counts.hpp"
#include "genesis/population/filter/sample_counts_filter.hpp"
#include "genesis/population/filter/variant_filter.hpp"
#include <functional>
#include <iosfwd>
#include <memory>
#include <stdexcept>
#include <string>
#include <utility>
#include <vector>

Go to the source code of this file.

Classes
struct	SampleCountsFilterNumericalParams
	Filter settings to filter and transform SampleCounts. More...

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

Functions
bool	apply_sample_counts_filter_numerical (SampleCounts &sample, SampleCountsFilterNumericalParams const &params)
	Filter a given SampleCounts based on the numerical properties of the counts. More...
bool	apply_sample_counts_filter_numerical (SampleCounts &sample, SampleCountsFilterNumericalParams const &params, SampleCountsFilterStats &stats)
	Filter a given SampleCounts based on the numerical properties of the counts. More...
bool	apply_sample_counts_filter_numerical (Variant &variant, SampleCountsFilterNumericalParams const &params, bool all_need_pass=false)
bool	apply_sample_counts_filter_numerical (Variant &variant, SampleCountsFilterNumericalParams const &params, VariantFilterStats &variant_stats, SampleCountsFilterStats &sample_count_stats, bool all_need_pass=false)
	Filter a given SampleCounts based on the numerical properties of the counts. More...
std::function< void(Variant &)>	make_sample_counts_filter_numerical_tagging (SampleCountsFilterNumericalParams const &params, bool all_need_pass=false)
	Return a functional to numerically filter the SampleCounts samples in a Variant tagging the ones that do not pass the filters, and potentially tagging the Variant. More...
std::function< void(Variant &)>	make_sample_counts_filter_numerical_tagging (SampleCountsFilterNumericalParams const &params, VariantFilterStats &variant_stats, SampleCountsFilterStats &sample_count_stats, bool all_need_pass=false)
void	transform_zero_out_by_max_count (SampleCounts &sample, size_t max_count, bool also_n_and_d_counts=true)
	Transform a SampleCounts sample by setting any nucleotide count (A, C, G, T) to zero if max_count is exceeded for that nucleotide. More...
void	transform_zero_out_by_max_count (Variant &variant, size_t max_count, bool also_n_and_d_counts=true)
	Transform a SampleCounts sample by setting any nucleotide count (A, C, G, T) to zero if max_count is exceeded for that nucleotide. More...
void	transform_zero_out_by_min_count (SampleCounts &sample, size_t min_count, bool also_n_and_d_counts=true)
	Transform a SampleCounts sample by setting any nucleotide count (A, C, G, T) to zero if min_count is not reached for that nucleotide. More...
void	transform_zero_out_by_min_count (Variant &variant, size_t min_count, bool also_n_and_d_counts=true)
	Transform a SampleCounts sample by setting any nucleotide count (A, C, G, T) to zero if min_count is not reached for that nucleotide. More...