GenomeRegion Struct Reference

#include <genesis/population/genome_region.hpp>

Detailed Description

A region (between two positions) on a chromosome.

This can be used to represent a gene, a feature, or just generally a region of interest, or even the whole chromosome (see special cases below). We use a simple form with a chromosome name, and a start and end position, both 1-based and inclusive (closed interval).

There are some special cases:

• We use an empty chromosome with start and end equal to 0 to denote an empty(), unspecified region.
• Another special case is a non-empty chromosome with both start and end being equal to 0, which denotes the whole chromosome as the region; this is however not considered to be a specified() region.
• All other cases are invalid, that is, an empty chromosome with non-zero start or end, or cases where start or end are zero, but not both, or where start is greather than end.

See also

GenomeLocus

GenomeLocusSet

GenomeRegionList

Definition at line 70 of file genome_region.hpp.

Public Member Functions
	GenomeRegion (std::string const &chr="", size_t s=0, size_t e=0)
bool	empty () const
bool	specified () const

Public Attributes
std::string	chromosome
size_t	end = 0
size_t	start = 0

Constructor & Destructor Documentation

GenomeRegion()

GenomeRegion ( std::string const &  chr = "", size_t  s = 0, size_t  e = 0  )

inline

Definition at line 78 of file genome_region.hpp.

Member Function Documentation

empty()

bool empty ( ) const

inline

Definition at line 86 of file genome_region.hpp.

specified()

bool specified ( ) const

inline

Definition at line 92 of file genome_region.hpp.

Member Data Documentation

chromosome

std::string chromosome

Definition at line 74 of file genome_region.hpp.

end

size_t end = 0

Definition at line 76 of file genome_region.hpp.

start

size_t start = 0

Definition at line 75 of file genome_region.hpp.

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The documentation for this struct was generated from the following file:

• genome_region.hpp