Utility class to store an genomic location (Interval). More...

#include <interval.h>

Public Types
enum	IntervalType { IntervalType::GATK, IntervalType::PICARD, IntervalType::BED }
	supported output formats for an Interval More...

Public Member Functions
	Interval ()
	creates an interval with standard values More...

	Interval (const std::string &chr, const uint32_t start, const uint32_t stop, const IntervalType output_type=IntervalType::GATK)
	creates an interval with all parameters More...

	Interval (const Interval &)=default

	Interval (Interval &&)=default

Interval &	operator= (const Interval &)=default

Interval &	operator= (Interval &&)=default

bool	operator== (const Interval &rhs) const
	Checks two Intervals for equality. More...

bool	operator!= (const Interval &rhs) const
	Checks two intervals for inequality. More...

uint32_t	size () const
	calculates the number of loci in the Intervals More...

std::vector< Interval >	tile_left (const uint32_t tile_size, const uint32_t spacing) const
	Tiles an Interval with smaller Intervals anchoring (starting) on the left side (start) of the Interval. More...

std::vector< Interval >	tile_right (const uint32_t tile_size, const uint32_t spacing) const
	Tiles an Interval with smaller Intervals anchoring (starting) on the right side (stop) of the Interval. More...

std::vector< Interval >	tsca_tiling (const uint32_t spacing, const uint32_t insert_size, const uint32_t flanking) const
	creates tiling TSCA baits (small intervals with an insert in between) that tile across the entire Interval with overlaps More...

std::string	str () const
	returns a string representation of the interval More...

std::string	chr () const

uint32_t	start () const

uint32_t	stop () const

IntervalType	output_type () const

void	set_chr (const std::string &chr)

void	set_start (const uint32_t start)

void	set_stop (const uint32_t stop)

void	set_output_type (const IntervalType output_type)

Detailed Description

Utility class to store an genomic location (Interval).

An Interval can be of one or many consecutive bases in a chromosome (contig). We represent Intervals with chromosome, start and stop. A one base Interval has start == stop. No Interval can go beyond a chromosome boundary.

The Interval can be output to any output stream (e.g. stdout, file, ...) in any of the supported interval formats.

Member Enumeration Documentation

enum gamgee::Interval::IntervalType

strong

supported output formats for an Interval

Enumerator
GATK	GATK format – chr:start-stop.
PICARD	PICARD format – chr [tab] start [tab] stop [tab] strand [tab] comments.
BED	BED format – chr [tab] start [tab] stop.

Constructor & Destructor Documentation

gamgee::Interval::Interval ( )

inline

creates an interval with standard values

chromosome, start and stop are all set to 0. Output type is IntervalType::GATK.

gamgee::Interval::Interval	(	const std::string &	chr,
		const uint32_t	start,
		const uint32_t	stop,
		const IntervalType	output_type = `IntervalType::GATK`
	)

inlineexplicit

creates an interval with all parameters

Parameters

chr	chromosome
start	start location (inclusive)
stop	stop location (inclusive)
output_type	desired output format (only used if Interval is sent to output stream)

gamgee::Interval::Interval ( const Interval & )

default

gamgee::Interval::Interval ( Interval && )

default

Member Function Documentation

std::string gamgee::Interval::chr ( ) const

inline

bool gamgee::Interval::operator!= ( const Interval & rhs ) const

inline

Checks two intervals for inequality.

Implementation is the negation of operator==

Returns: true if the two intervals don't have the same values in any of their member variables

Interval& gamgee::Interval::operator= ( const Interval & )

default

Interval& gamgee::Interval::operator= ( Interval && )

default

bool gamgee::Interval::operator== ( const Interval & rhs ) const

Checks two Intervals for equality.

Parameters

rhs	the other Interval to compare to

Returns: whether or not the two Intervals have the same chromosome, start and stop. Output type is irrelevant.

IntervalType gamgee::Interval::output_type ( ) const

inline

void gamgee::Interval::set_chr ( const std::string & chr )

inline

void gamgee::Interval::set_output_type ( const IntervalType output_type )

inline

void gamgee::Interval::set_start ( const uint32_t start )

inline

void gamgee::Interval::set_stop ( const uint32_t stop )

inline

uint32_t gamgee::Interval::size ( ) const

inline

calculates the number of loci in the Intervals

Returns: stop() - start() + 1

uint32_t gamgee::Interval::start ( ) const

inline

uint32_t gamgee::Interval::stop ( ) const

inline

std::string gamgee::Interval::str ( ) const

returns a string representation of the interval

vector< Interval > gamgee::Interval::tile_left	(	const uint32_t	tile_size,
		const uint32_t	spacing
	)		const

Tiles an Interval with smaller Intervals anchoring (starting) on the left side (start) of the Interval.

Warning: by design, the Interval may or may not be covered on the right (stop) side depending on the length of the original Interval and the parameters passed.

Returns: a vector of Intervals covering the original Interval spaced by spacing loci in between them

Parameters

tile_size	size of the tiles (small Intervals) to be generated
spacing	how many loci to leave in between the tiles (small Intervals)

vector< Interval > gamgee::Interval::tile_right	(	const uint32_t	tile_size,
		const uint32_t	spacing
	)		const

Tiles an Interval with smaller Intervals anchoring (starting) on the right side (stop) of the Interval.

Warning: by design, the Interval may or may not be covered on the left (start) side depending on the length of the original Interval and the parameters passed.

Returns: a vector of Intervals covering the original Interval spaced by spacing loci in between them

Parameters

tile_size	size of the tiles (small Intervals) to be generated
spacing	how many loci to leave in between the tiles (small Intervals)

vector< Interval > gamgee::Interval::tsca_tiling	(	const uint32_t	spacing,
		const uint32_t	insert_size,
		const uint32_t	flanking
	)		const

creates tiling TSCA baits (small intervals with an insert in between) that tile across the entire Interval with overlaps

This tiling procedure will guarantee that the entire Interval is covered (tiled) by creating a list of overlapping tiles that can be used as baits if the design of the overlapping baits is split between the forward and reverse strands of the reference genome. The overlapping bait will always be centered in the spacing between the two baits in the opposite strand.

Returns: a vector of baits / tiles / small intervals that fully cover the original Interval with overlaps.

Parameters

spacing	number of loci in between the tiles
insert_size	insert size intended to be used with these baits
flanking	region before and after the target to include in the tiling

The documentation for this class was generated from the following files:

gamgee/interval.h
gamgee/interval.cpp

Public Types

Public Member Functions

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation