vg::GaplessExtender Class Reference

#include <gapless_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, const std::string &sequence, size_t max_mismatches=MAX_MISMATCHES, bool trim_extensions=true) const
void	trim (std::vector< GaplessExtension > &extensions, size_t max_mismatches=MAX_MISMATCHES, const gbwt::CachedGBWT *cache=nullptr) 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...

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

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

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. All seeds in a cluster should correspond to the same alignment or positions near it. 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  )

explicit

Create a GaplessExtender using the given GBWTGraph and Aligner objects.

Member Function Documentation

extend()

std::vector< GaplessExtension > vg::GaplessExtender::extend	(	cluster_type &	cluster,
		const std::string &	sequence,
		size_t	max_mismatches = MAX_MISMATCHES,
		bool	trim_extensions = true
	)		const

Find two highest-scoring full-length alignments for the sequence within the cluster with at most max_mismatches mismatches. If that is not possible, find the set of highest-scoring maximal extensions of the seeds, allowing any number of mismatches in the seed node and max_mismatches / 2 mismatches on each flank. Flanks may have more mismatches if it does not bring the total beyond max_mismatches. Then call trim() if trim_extensions i set. The extensions are sorted by their coordinates in the sequence.

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.

trim()

void vg::GaplessExtender::trim	(	std::vector< GaplessExtension > &	extensions,
		size_t	max_mismatches = MAX_MISMATCHES,
		const gbwt::CachedGBWT *	cache = nullptr
	)		const

Try to improve the score of each extension by trimming mismatches from the flanks. Do not trim full-length alignments with <= max_mismatches mismatches. Use the provided CachedGBWT or allocate a new one. Note that extend() already calls this by default.

Member Data Documentation

aligner

const Aligner* vg::GaplessExtender::aligner

graph

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

MAX_MISMATCHES

constexpr size_t vg::GaplessExtender::MAX_MISMATCHES = 4

staticconstexpr

The default value for the maximum number of mismatches.

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

• src/gapless_extender.hpp
• src/gapless_extender.cpp