variant_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 <iosfwd>
#include <stdexcept>
#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

Typedefs
using	VariantFilterCategoryStats = FilterStats< VariantFilterTagCategory >
	Counts of how many Variants with each VariantFilterTagCategory occured in some data. More...
using	VariantFilterStats = FilterStats< VariantFilterTag >
	Counts of how many Variants with each VariantFilterTag occured in some data. More...

Enumerations
enum	VariantFilterTag : FilterStatus::IntType {   kPassed = 0, kMaskedPosition, kMaskedRegion, kMissing,   kNotPassed, kInvalid, kNoSamplePassed, kNotAllSamplesPassed,   kEmpty, kBelowMinReadDepth, kAboveMaxReadDepth, kAboveDeletionsCountLimit,   kNotSnp, kNotBiallelicSnp, kBelowSnpMinCount, kAboveSnpMaxCount,   kBelowMinAlleleFreq, kEnd }
	List of filters that we apply to a Variant, to indicate whether the Variant passed or not. More...
enum	VariantFilterTagCategory : FilterStatus::IntType {   kPassed = 0, kMasked, kMissingInvalid, kSamplesFailed,   kNumeric, kInvariant, kEnd }
	List of filter categories for a Variant. More...

Functions
std::ostream &	print_variant_filter_category_stats (std::ostream &os, VariantFilterCategoryStats const &stats, bool verbose)
std::ostream &	print_variant_filter_category_stats (std::ostream &os, VariantFilterStats const &stats, bool verbose=false)
std::string	print_variant_filter_category_stats (VariantFilterCategoryStats const &stats, bool verbose)
std::string	print_variant_filter_category_stats (VariantFilterStats const &stats, bool verbose=false)
std::ostream &	print_variant_filter_stats (std::ostream &os, VariantFilterStats const &stats, bool verbose=false)
	Print a textual representation of the counts collected. More...
std::string	print_variant_filter_stats (VariantFilterStats const &stats, bool verbose=false)
	Print a textual representation of the counts collected. More...
VariantFilterCategoryStats	variant_filter_stats_category_counts (VariantFilterStats const &stats)
	Generate summary counts for a VariantFilterStats counter. More...
size_t	variant_filter_stats_category_counts (VariantFilterStats const &stats, VariantFilterTagCategory category)
	Overload that only reports back a single category sum of the filter stats. More...
VariantFilterTagCategory	variant_filter_tag_to_category (VariantFilterTag tag)
	For a given tag, return its category tag. More...