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

Private Attributes
unique_ptr< QualAdjAligner >	qual_adj_aligner
unique_ptr< Aligner >	regular_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()

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.

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

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

private

qual_adj_aligner

unique_ptr<QualAdjAligner> vg::AlignerClient::qual_adj_aligner

private

regular_aligner

unique_ptr<Aligner> vg::AlignerClient::regular_aligner

private

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

• src/aligner.hpp
• src/aligner.cpp