vg::WFAAlignment Struct Reference

#include <gbwt_extender.hpp>

Public Types
enum	Edit { match, mismatch, insertion, deletion }

Public Member Functions
	operator bool () const
	Is this an actual alignment or a failure? More...
bool	empty () const
bool	unlocalized_insertion () const
	Returns true if the alignment is an insertion without a location. More...
int64_t	final_offset (const gbwtgraph::GBWTGraph &graph) const
void	flip (const gbwtgraph::GBWTGraph &graph, const std::string &sequence)
	Transforms the alignment to the other strand. More...
void	append (Edit edit, uint32_t length)
void	join (const WFAAlignment &second)
Path	to_path (const HandleGraph &graph, const std::string &sequence) const
	Convert the WFAAlignment into a Path. More...
std::ostream &	print (const HandleGraph &graph, std::ostream &out) const
	Prints some debug information about the alignment. More...
std::ostream &	print (std::ostream &out) const
	Prints some debug information about the alignment. More...
void	check_lengths (const HandleGraph &graph) const

Static Public Member Functions
static WFAAlignment	from_extension (const GaplessExtension &extension)
static WFAAlignment	make_unlocalized_insertion (size_t sequence_offset, size_t length, int score)
static WFAAlignment	make_empty ()
	Generate an empty WFAAlignment. More...

Public Attributes
std::vector< handle_t >	path
	Sequence of oriented nodes. More...
std::vector< std::pair< Edit, uint32_t > >	edits
	Sequence of edit operations and their lengths. More...
uint32_t	node_offset = 0
uint32_t	seq_offset = 0
	Starting offset in the sequence. More...
uint32_t	length = 0
	Length of the alignment in the sequence. More...
int32_t	score = 0
	Alignment score. More...
bool	ok = false
	Is this an actual alignment or a failure? More...

Detailed Description

An alignment found by WFAAligner, consisting of a sequence of nodes, a sequence of edits, and a starting offset in the initial node. The alignment score is computed using the match / mismatch / gap open / gap extend parameters in the Aligner object given to the WFAAligner. Full-length bonuses are not used.

Note: The aligner merges consecutive edit operations of the same type. Hence an edit may span multiple nodes.

This struct is an aggregate and can be aggregate-initialized with a brace-enclosed initializer list.

Member Enumeration Documentation

Edit

enum vg::WFAAlignment::Edit

Enumerator
match
mismatch
insertion
deletion

Member Function Documentation

append()

void vg::WFAAlignment::append	(	Edit	edit,
		uint32_t	length
	)

Appends an edit operation, merging it with the latest edit if possible. Ignores empty edits.

check_lengths()

void vg::WFAAlignment::check_lengths

(

const HandleGraph &

graph

)

const

Make sure the stored lengths, paths, and edits are accurate and consistent with each other.

empty()

bool vg::WFAAlignment::empty ( ) const

inline

Returns true if the alignment does not cover anything in the sequence and the graph.

final_offset()

int64_t vg::WFAAlignment::final_offset

(

const gbwtgraph::GBWTGraph &

graph

)

const

Computes the node offset after the alignment in the final node. Will be negative if the alignment's final node(s) are not actually used by edits.

flip()

void vg::WFAAlignment::flip	(	const gbwtgraph::GBWTGraph &	graph,
		const std::string &	sequence
	)

Transforms the alignment to the other strand.

from_extension()

WFAAlignment vg::WFAAlignment::from_extension ( const GaplessExtension &  extension )

static

Generate a WFAAlignment from a GaplessExtension. This can't be a constructor because then WFAAlignment wouldn't be able to be aggregate-initialized.

join()

void vg::WFAAlignment::join

(

const WFAAlignment &

second

)

Concatenate another WFAAlignment onto this one, assuming they abut in the read and the graph. Either may be empty, or an unlocalized insertion.

make_empty()

WFAAlignment vg::WFAAlignment::make_empty ( )

static

Generate an empty WFAAlignment.

make_unlocalized_insertion()

WFAAlignment vg::WFAAlignment::make_unlocalized_insertion ( size_t  sequence_offset, size_t  length, int  score  )

static

Generate a WFAAlignment that is an unlocalized insertion of the given length. Can also be used to represent a softclip. Length may not be 0.

operator bool()

vg::WFAAlignment::operator bool ( ) const

inline

Is this an actual alignment or a failure?

print() [1/2]

std::ostream & vg::WFAAlignment::print	(	const HandleGraph &	graph,
		std::ostream &	out
	)		const

Prints some debug information about the alignment.

print() [2/2]

std::ostream & vg::WFAAlignment::print

(

std::ostream &

out

)

const

Prints some debug information about the alignment.

to_path()

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

Convert the WFAAlignment into a Path.

unlocalized_insertion()

bool vg::WFAAlignment::unlocalized_insertion

(

)

const

Returns true if the alignment is an insertion without a location.

Member Data Documentation

edits

std::vector<std::pair<Edit, uint32_t> > vg::WFAAlignment::edits

Sequence of edit operations and their lengths.

length

uint32_t vg::WFAAlignment::length = 0

Length of the alignment in the sequence.

node_offset

uint32_t vg::WFAAlignment::node_offset = 0

Starting offset in the initial node. If there is no initial node, the value stored is undefined.

ok

bool vg::WFAAlignment::ok = false

Is this an actual alignment or a failure?

path

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

Sequence of oriented nodes.

score

int32_t vg::WFAAlignment::score = 0

Alignment score.

seq_offset

uint32_t vg::WFAAlignment::seq_offset = 0

Starting offset in the sequence.

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

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