vg::GaplessExtension Struct Reference

#include <gbwt_extender.hpp>

Public Types
typedef std::pair< handle_t, int64_t >	seed_type

Public Member Functions
size_t	length () const
	Length of the extension. More...
bool	empty () const
	Is the extension empty? More...
bool	full () const
	Is the extension a full-length alignment? More...
bool	exact () const
	Is the extension an exact match? More...
size_t	mismatches () const
	Number of mismatches in the extension. More...
bool	contains (const HandleGraph &graph, seed_type seed) const
	Does the extension contain the seed? More...
Position	starting_position (const HandleGraph &graph) const
	Return the starting position of the extension. More...
Position	tail_position (const HandleGraph &graph) const
	Return the position after the extension. More...
size_t	tail_offset (const HandleGraph &graph) const
	Return the node offset after the extension. More...
size_t	overlap (const HandleGraph &graph, const GaplessExtension &another) const
	Number of shared (read position, graph position) pairs in the extensions. More...
GaplessExtension	prefix (size_t prefix_length) const
	Take a prefix of the extension as a new GaplessExtension object. More...
Path	to_path (const HandleGraph &graph, const std::string &sequence) const
	Convert the extension into a Path. The sequence should be the full read-space sequence. More...
bool	operator< (const GaplessExtension &another) const
	For priority queues. More...
bool	operator== (const GaplessExtension &another) const
bool	operator!= (const GaplessExtension &another) const
	Two extensions are not equal if the state, the read interval, or the node offset is different. More...

Public Attributes
std::vector< handle_t >	path
size_t	offset
gbwt::BidirectionalState	state
std::pair< size_t, size_t >	read_interval
std::vector< size_t >	mismatch_positions
int32_t	score
bool	left_full
bool	right_full
bool	left_maximal
bool	right_maximal
uint32_t	internal_score
uint32_t	old_score

Detailed Description

A result of the gapless extension of a seed.

• The extension is a path starting from offset 'offset' of node path.front().
• Search state 'state' corresponds to the path.
• The extension covers semiopen interval [read_interval.first, read_interval.second) of the read.
• Vector 'mismatch_positions' contains the mismatching read positions in sorted order.
• 'score' is an alignment score (bigger is better).
• Flags 'left_full' and 'right_full' indicate whether the extension covers the start/end of the read.

Member Typedef Documentation

seed_type

typedef std::pair<handle_t, int64_t> vg::GaplessExtension::seed_type

Member Function Documentation

contains()

bool vg::GaplessExtension::contains	(	const HandleGraph &	graph,
		seed_type	seed
	)		const

Does the extension contain the seed?

empty()

bool vg::GaplessExtension::empty ( ) const

inline

Is the extension empty?

exact()

bool vg::GaplessExtension::exact ( ) const

inline

Is the extension an exact match?

full()

bool vg::GaplessExtension::full ( ) const

inline

Is the extension a full-length alignment?

length()

size_t vg::GaplessExtension::length ( ) const

inline

Length of the extension.

mismatches()

size_t vg::GaplessExtension::mismatches ( ) const

inline

Number of mismatches in the extension.

operator!=()

bool vg::GaplessExtension::operator!= ( const GaplessExtension &  another ) const

inline

Two extensions are not equal if the state, the read interval, or the node offset is different.

operator<()

bool vg::GaplessExtension::operator< ( const GaplessExtension &  another ) const

inline

For priority queues.

operator==()

bool vg::GaplessExtension::operator== ( const GaplessExtension &  another ) const

inline

Two extensions are equal if the same read interval matches the same search state with the same node offset.

overlap()

size_t vg::GaplessExtension::overlap	(	const HandleGraph &	graph,
		const GaplessExtension &	another
	)		const

Number of shared (read position, graph position) pairs in the extensions.

prefix()

GaplessExtension vg::GaplessExtension::prefix

(

size_t

prefix_length

)

const

Take a prefix of the extension as a new GaplessExtension object.

starting_position()

Position vg::GaplessExtension::starting_position

(

const HandleGraph &

graph

)

const

Return the starting position of the extension.

tail_offset()

size_t vg::GaplessExtension::tail_offset

(

const HandleGraph &

graph

)

const

Return the node offset after the extension.

tail_position()

Position vg::GaplessExtension::tail_position

(

const HandleGraph &

graph

)

const

Return the position after the extension.

to_path()

Path vg::GaplessExtension::to_path	(	const HandleGraph &	graph,
		const std::string &	sequence
	)		const

Convert the extension into a Path. The sequence should be the full read-space sequence.

Member Data Documentation

internal_score

uint32_t vg::GaplessExtension::internal_score

left_full

bool vg::GaplessExtension::left_full

left_maximal

bool vg::GaplessExtension::left_maximal

mismatch_positions

std::vector<size_t> vg::GaplessExtension::mismatch_positions

offset

size_t vg::GaplessExtension::offset

old_score

uint32_t vg::GaplessExtension::old_score

path

std::vector<handle_t> vg::GaplessExtension::path

read_interval

std::pair<size_t, size_t> vg::GaplessExtension::read_interval

right_full

bool vg::GaplessExtension::right_full

right_maximal

bool vg::GaplessExtension::right_maximal

score

int32_t vg::GaplessExtension::score

state

gbwt::BidirectionalState vg::GaplessExtension::state

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

• src/gbwt_extender.hpp
• src/gbwt_extender.cpp