sample_counts_filter.hpp File Reference

#include "genesis/population/sample_counts.hpp"
#include "genesis/population/filter/filter_stats.hpp"
#include "genesis/population/filter/filter_status.hpp"
#include "genesis/population/variant.hpp"
#include <array>
#include <cassert>
#include <iosfwd>
#include <stdexcept>
#include <string>
#include <type_traits>
#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

Typedefs
using	SampleCountsFilterCategoryStats = FilterStats< SampleCountsFilterTagCategory >
	Counts of how many SampleCounts with each SampleCountsFilterTagCategory occured in some data. More...
using	SampleCountsFilterStats = FilterStats< SampleCountsFilterTag >
	Counts of how many SampleCountss with each SampleCountsFilterTag occured in some data. More...

Enumerations
enum	SampleCountsFilterPolicy { kAll, kOnlyPassing }
	Policy helper to decide how to treat filtered SampleCounts. More...
enum	SampleCountsFilterTag : FilterStatus::IntType {   kPassed = 0, kMaskedPosition, kMaskedRegion, kMissing,   kNotPassed, kInvalid, kEmpty, kBelowMinReadDepth,   kAboveMaxReadDepth, kAboveDeletionsCountLimit, kNotSnp, kNotBiallelicSnp,   kEnd }
enum	SampleCountsFilterTagCategory : FilterStatus::IntType {   kPassed = 0, kMasked, kMissingInvalid, kNumeric,   kEnd }
	List of filter categories for a SampleCounts. More...

Functions
std::string	print_sample_counts_filter_category_stats (SampleCountsFilterCategoryStats const &stats, bool verbose)
std::string	print_sample_counts_filter_category_stats (SampleCountsFilterStats const &stats, bool verbose=false)
std::ostream &	print_sample_counts_filter_category_stats (std::ostream &os, SampleCountsFilterCategoryStats const &stats, bool verbose)
std::ostream &	print_sample_counts_filter_category_stats (std::ostream &os, SampleCountsFilterStats const &stats, bool verbose=false)
std::string	print_sample_counts_filter_stats (SampleCountsFilterStats const &stats, bool verbose=false)
	Print a textual representation of the counts collected. More...
std::ostream &	print_sample_counts_filter_stats (std::ostream &os, SampleCountsFilterStats const &stats, bool verbose=false)
	Print a textual representation of the counts collected. More...
SampleCountsFilterCategoryStats	sample_counts_filter_stats_category_counts (SampleCountsFilterStats const &stats)
	Generate summary counts for a SampleCountsFilterStats counter. More...
size_t	sample_counts_filter_stats_category_counts (SampleCountsFilterStats const &stats, SampleCountsFilterTagCategory category)
	Overload that only reports back a single category sum of the filter stats. More...
SampleCountsFilterTagCategory	sample_counts_filter_tag_to_category (SampleCountsFilterTag tag)
	For a given tag, return its category tag. More...