function/genome_region.hpp File Reference

#include "genesis/population/genome_locus_set.hpp"
#include "genesis/population/genome_region_list.hpp"
#include "genesis/population/genome_region.hpp"
#include "genesis/population/format/vcf_record.hpp"
#include <iosfwd>
#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
bool	is_covered (GenomeLocusSet const &loci, std::string const &chromosome, size_t position)
	Test whether the chromosome/position is within a given GenomeLocusSet. More...
template<class T >
bool	is_covered (GenomeLocusSet const &loci, T const &locus)
	Test whether the chromosome/position of a locus is within a given GenomeLocusSet. More...
bool	is_covered (GenomeLocusSet const &loci, VcfRecord const &variant)
bool	is_covered (GenomeRegion const &region, std::string const &chromosome, size_t position)
	Test whether the chromosome/position is within a given genomic region. More...
template<class T >
bool	is_covered (GenomeRegion const &region, T const &locus)
	Test whether the chromosome/position of a locus is within a given genomic region. More...
bool	is_covered (GenomeRegion const &region, VcfRecord const &variant)
bool	is_covered (GenomeRegionList const &regions, std::string const &chromosome, size_t position)
	Test whether the chromosome/position is within a given list of genomic regions. More...
template<class T >
bool	is_covered (GenomeRegionList const &regions, T const &locus)
	Test whether the chromosome/position of a locus is within a given list of genomic regions. More...
bool	is_covered (GenomeRegionList const &regions, VcfRecord const &variant)
bool	operator!= (GenomeRegion const &a, GenomeRegion const &b)
	Inequality comparison (!=) for two GenomeRegions. More...
std::ostream &	operator<< (std::ostream &os, GenomeRegion const &region)
bool	operator== (GenomeRegion const &a, GenomeRegion const &b)
	Equality comparison (!=) for two GenomeRegions. More...
GenomeRegion	parse_genome_region (std::string const &region, bool zero_based=false, bool end_exclusive=false)
	Parse a genomic region. More...
GenomeRegionList	parse_genome_regions (std::string const &regions, bool zero_based=false, bool end_exclusive=false)
	Parse a set/list of genomic regions. More...
std::string	to_string (GenomeRegion const &region)