vg::AlignerClient Class Reference

#include <aligner.hpp>

Inheritance diagram for vg::AlignerClient:

Public Member Functions
virtual void	set_alignment_scores (int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)
	Set all the aligner scoring parameters and create the stored aligner instances. More...
virtual void	set_alignment_scores (std::istream &matrix_stream, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)
virtual void	set_alignment_scores (const int8_t *score_matrix, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus)

Static Public Member Functions
static int8_t *	parse_matrix (std::istream &matrix_stream)
	Allocates an array to hold a 4x4 substitution matrix and returns it. More...

Public Attributes
bool	adjust_alignments_for_base_quality = false

Protected Member Functions
	AlignerClient (double gc_content_estimate=vg::default_gc_content)
const GSSWAligner *	get_aligner (bool have_qualities=true) const
const QualAdjAligner *	get_qual_adj_aligner () const
const Aligner *	get_regular_aligner () const

Protected Attributes
double	gc_content_estimate

Private Attributes
unique_ptr< QualAdjAligner >	qual_adj_aligner
unique_ptr< Aligner >	regular_aligner

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()

vg::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 * vg::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 * vg::AlignerClient::get_qual_adj_aligner ( ) const

protected

get_regular_aligner()

const Aligner * vg::AlignerClient::get_regular_aligner ( ) const

protected

parse_matrix()

int8_t * vg::AlignerClient::parse_matrix ( std::istream &  matrix_stream )

static

Allocates an array to hold a 4x4 substitution matrix and returns it.

set_alignment_scores() [1/3]

void vg::AlignerClient::set_alignment_scores ( const int8_t *  score_matrix, int8_t  gap_open, int8_t  gap_extend, int8_t  full_length_bonus  )

virtual

Set the algner scoring parameters and create the stored aligner instances. The score matrix should by a 4 x 4 array in the order (ACGT). Other overloads of set_alignment_scores all call this one. Note that an override of this method can't be called from the constructor, so when overriding it, make sure to also do your extra work in the constructor.

Reimplemented in vg::MultipathMapper, vg::MinimizerMapper, and vg::Surjector.

set_alignment_scores() [2/3]

void vg::AlignerClient::set_alignment_scores ( int8_t  match, int8_t  mismatch, int8_t  gap_open, int8_t  gap_extend, int8_t  full_length_bonus  )

virtual

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

set_alignment_scores() [3/3]

void vg::AlignerClient::set_alignment_scores ( std::istream &  matrix_stream, int8_t  gap_open, int8_t  gap_extend, int8_t  full_length_bonus  )

virtual

Set the algner scoring parameters and create the stored aligner instances. The stream should contain a 4 x 4 whitespace-separated substitution matrix (in the order ACGT)

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

protected

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:

• src/aligner.hpp
• src/aligner.cpp