vg
tools for working with variation graphs
Public Member Functions | Public Attributes | Protected Member Functions | Private Attributes | List of all members
vg::AlignerClient Class Reference

#include <aligner.hpp>

Inheritance diagram for vg::AlignerClient:
vg::BaseMapper vg::MinimizerMapper vg::Surjector vg::Mapper vg::MultipathMapper

Public Member Functions

void set_alignment_scores (int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus, uint32_t xdrop_max_gap_length=default_xdrop_max_gap_length)
 Set all the aligner scoring parameters and create the stored aligner instances. More...
 
void load_scoring_matrix (std::ifstream &matrix_stream)
 Load a scoring amtrix from a file to set scores. More...
 

Public Attributes

bool adjust_alignments_for_base_quality = false
 

Protected Member Functions

 AlignerClient (double gc_content_estimate=vg::default_gc_content)
 
const GSSWAlignerget_aligner (bool have_qualities=true) const
 
const QualAdjAlignerget_qual_adj_aligner () const
 
const Alignerget_regular_aligner () const
 

Private Attributes

unique_ptr< QualAdjAlignerqual_adj_aligner
 
unique_ptr< Alignerregular_aligner
 
double gc_content_estimate
 

Detailed Description

Holds a set of alignment scores, and has methods to produce aligners of various types on demand, using those scores. Provides a get_aligner() method to get ahold of a useful, possibly quality-adjusted Aligner. Base functionality that is shared between alignment and surjections

Constructor & Destructor Documentation

◆ AlignerClient()

AlignerClient::AlignerClient ( double  gc_content_estimate = vg::default_gc_content)
protected

Create an AlignerClient, which creates the default aligner instances, which can depend on a GC content estimate.

Member Function Documentation

◆ get_aligner()

const GSSWAligner * AlignerClient::get_aligner ( bool  have_qualities = true) const
protected

Get the appropriate aligner to use, based on adjust_alignments_for_base_quality. By setting have_qualities to false, you can force the non-quality-adjusted aligner, for reads that lack quality scores.

◆ get_qual_adj_aligner()

const QualAdjAligner * AlignerClient::get_qual_adj_aligner ( ) const
protected

◆ get_regular_aligner()

const Aligner * AlignerClient::get_regular_aligner ( ) const
protected

◆ load_scoring_matrix()

void AlignerClient::load_scoring_matrix ( std::ifstream &  matrix_stream)

Load a scoring amtrix from a file to set scores.

◆ set_alignment_scores()

void AlignerClient::set_alignment_scores ( int8_t  match,
int8_t  mismatch,
int8_t  gap_open,
int8_t  gap_extend,
int8_t  full_length_bonus,
uint32_t  xdrop_max_gap_length = default_xdrop_max_gap_length 
)

Set all the aligner scoring parameters and create the stored aligner instances.

Member Data Documentation

◆ adjust_alignments_for_base_quality

bool vg::AlignerClient::adjust_alignments_for_base_quality = false

◆ gc_content_estimate

double vg::AlignerClient::gc_content_estimate
private

◆ qual_adj_aligner

unique_ptr<QualAdjAligner> vg::AlignerClient::qual_adj_aligner
private

◆ regular_aligner

unique_ptr<Aligner> vg::AlignerClient::regular_aligner
private

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