vg
tools for working with variation graphs
Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | Static Public Attributes | List of all members
vg::GaplessExtender Class Reference

#include <gapless_extender.hpp>

Public Types

typedef GaplessExtension::seed_type seed_type
 
typedef pair_hash_set< seed_typecluster_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< GaplessExtensionextend (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 Aligneraligner
 

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

◆ 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.


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