vg::GaplessExtender Class Reference

#include <gbwt_extender.hpp>

Public Types
typedef GaplessExtension::seed_type	seed_type
typedef pair_hash_set< seed_type >	cluster_type

Public Member Functions
	GaplessExtender ()
	Create an empty GaplessExtender. More...
	GaplessExtender (const gbwtgraph::GBWTGraph &graph, const Aligner &aligner)
	Create a GaplessExtender using the given GBWTGraph and Aligner objects. More...
std::vector< GaplessExtension >	extend (cluster_type &cluster, std::string sequence, const gbwtgraph::CachedGBWTGraph *cache=nullptr, size_t max_mismatches=MAX_MISMATCHES, double overlap_threshold=OVERLAP_THRESHOLD) const

Static Public Member Functions
static seed_type	to_seed (pos_t pos, size_t read_offset)
	Convert (graph position, read offset) to a seed. More...
static pos_t	get_pos (seed_type seed)
	Get the graph position from a seed. More...
static handle_t	get_handle (seed_type seed)
	Get the handle from a seed. More...
static size_t	get_node_offset (seed_type seed)
	Get the node offset from a seed. More...
static size_t	get_read_offset (seed_type seed)
	Get the read offset from a seed. More...
static bool	full_length_extensions (const std::vector< GaplessExtension > &result, size_t max_mismatches=MAX_MISMATCHES)

Public Attributes
const gbwtgraph::GBWTGraph *	graph
const Aligner *	aligner
ReadMasker	mask

Static Public Attributes
constexpr static size_t	MAX_MISMATCHES = 4
	The default value for the maximum number of mismatches. More...
constexpr static double	OVERLAP_THRESHOLD = 0.8

Detailed Description

A class that supports haplotype-consistent seed extension using GBWTGraph. Each seed is a pair of matching read/graph positions and each extension is a gapless alignment of an interval of the read to a haplotype. A cluster is an unordered set of distinct seeds. Seeds in the same node with the same (read_offset - node_offset) difference are considered equivalent. GaplessExtender also needs an Aligner object for scoring the extension candidates.

Member Typedef Documentation

cluster_type

typedef pair_hash_set<seed_type> vg::GaplessExtender::cluster_type

seed_type

typedef GaplessExtension::seed_type vg::GaplessExtender::seed_type

Constructor & Destructor Documentation

GaplessExtender() [1/2]

vg::GaplessExtender::GaplessExtender

(

)

Create an empty GaplessExtender.

GaplessExtender() [2/2]

vg::GaplessExtender::GaplessExtender	(	const gbwtgraph::GBWTGraph &	graph,
		const Aligner &	aligner
	)

Create a GaplessExtender using the given GBWTGraph and Aligner objects.

Member Function Documentation

extend()

std::vector< GaplessExtension > vg::GaplessExtender::extend	(	cluster_type &	cluster,
		std::string	sequence,
		const gbwtgraph::CachedGBWTGraph *	cache = nullptr,
		size_t	max_mismatches = MAX_MISMATCHES,
		double	overlap_threshold = OVERLAP_THRESHOLD
	)		const

Find the highest-scoring extension for each seed in the cluster. If there is a full-length extension with at most max_mismatches mismatches, sort them in descending order by score and return the best non-overlapping full-length extensions. Two extensions overlap if the fraction of identical base mappings is greater than overlap_threshold. If there are no good enough full-length extensions, trim the extensions to maximize the score and remove duplicates. In this case, the extensions are sorted by read interval. Use full_length_extensions() to determine the type of the returned extension set. The sequence that will be aligned is passed by value. All non-ACGT characters are masked with character X, which should not match any character in the graph. Allow any number of mismatches in the initial node, at least max_mismatches mismatches in the entire extension, and at least max_mismatches / 2 mismatches on each flank. Use the provided CachedGBWTGraph or allocate a new one.

full_length_extensions()

bool vg::GaplessExtender::full_length_extensions ( const std::vector< GaplessExtension > &  result, size_t  max_mismatches = MAX_MISMATCHES  )

static

Determine whether the extension set contains non-overlapping full-length extensions sorted in descending order by score. Use the same value of max_mismatches as in extend().

get_handle()

static handle_t vg::GaplessExtender::get_handle ( seed_type  seed )

inlinestatic

Get the handle from a seed.

get_node_offset()

static size_t vg::GaplessExtender::get_node_offset ( seed_type  seed )

inlinestatic

Get the node offset from a seed.

get_pos()

static pos_t vg::GaplessExtender::get_pos ( seed_type  seed )

inlinestatic

Get the graph position from a seed.

get_read_offset()

static size_t vg::GaplessExtender::get_read_offset ( seed_type  seed )

inlinestatic

Get the read offset from a seed.

to_seed()

static seed_type vg::GaplessExtender::to_seed ( pos_t  pos, size_t  read_offset  )

inlinestatic

Convert (graph position, read offset) to a seed.

Member Data Documentation

aligner

const Aligner* vg::GaplessExtender::aligner

graph

const gbwtgraph::GBWTGraph* vg::GaplessExtender::graph

mask

ReadMasker vg::GaplessExtender::mask

MAX_MISMATCHES

constexpr size_t vg::GaplessExtender::MAX_MISMATCHES = 4

staticconstexpr

The default value for the maximum number of mismatches.

OVERLAP_THRESHOLD

constexpr double vg::GaplessExtender::OVERLAP_THRESHOLD = 0.8

staticconstexpr

Two full-length alignments are distinct, if the fraction of overlapping position pairs is at most this.

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

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