#include <aligner.hpp>

Inheritance diagram for vg::GSSWAligner:

Public Member Functions
	GSSWAligner (GSSWAligner &&)=default

GSSWAligner &	operator= (GSSWAligner &&)=default

	GSSWAligner (const GSSWAligner &)=delete

GSSWAligner &	operator= (const GSSWAligner &)=delete

virtual void	align_pinned (Alignment &alignment, const HandleGraph &g, bool pin_left, bool xdrop=false, uint16_t xdrop_max_gap_length=default_xdrop_max_gap_length) const =0

virtual void	align_pinned_multi (Alignment &alignment, vector< Alignment > &alt_alignments, const HandleGraph &g, bool pin_left, int32_t max_alt_alns) const =0

virtual void	align_global_banded (Alignment &alignment, const HandleGraph &g, int32_t band_padding=0, bool permissive_banding=true, uint64_t max_cells=std::numeric_limits< uint64_t >::max()) const =0

virtual void	align_global_banded_multi (Alignment &alignment, vector< Alignment > &alt_alignments, const HandleGraph &g, int32_t max_alt_alns, int32_t band_padding=0, bool permissive_banding=true, uint64_t max_cells=std::numeric_limits< uint64_t >::max()) const =0

virtual void	align_xdrop (Alignment &alignment, const HandleGraph &g, const vector< MaximalExactMatch > &mems, bool reverse_complemented, uint16_t max_gap_length=default_xdrop_max_gap_length) const =0
	xdrop aligner More...

virtual void	align_xdrop (Alignment &alignment, const HandleGraph &g, const vector< handle_t > &order, const vector< MaximalExactMatch > &mems, bool reverse_complemented, uint16_t max_gap_length=default_xdrop_max_gap_length) const =0

Public Member Functions inherited from vg::BaseAligner
virtual void	align (Alignment &alignment, const HandleGraph &g, bool traceback_aln) const =0

Public Attributes
std::unique_ptr< MatrixAlignmentScorer >	scorer

std::unique_ptr< MappingQualityCalculator >	mapq_calc

Protected Member Functions
	GSSWAligner (std::unique_ptr< MatrixAlignmentScorer > owned_scorer)

	~GSSWAligner ()

gssw_graph *	create_gssw_graph (const HandleGraph &g) const

unordered_set< id_t >	identify_pinning_points (const HandleGraph &graph) const

void	unreverse_graph_mapping (gssw_graph_mapping *gm) const

void	unreverse_graph (gssw_graph *graph) const

void	gssw_mapping_to_alignment (gssw_graph graph, gssw_graph_mapping gm, Alignment &alignment, bool pinned, bool pin_left) const

string	graph_cigar (gssw_graph_mapping *gm) const

Protected Attributes
DeletionAligner	deletion_aligner

Detailed Description

The basic GSSW-based core aligner implementation, which can then be quality-adjusted or not. Owns its scorer and MAPQ calculator; all scoring and MAPQ work goes through those, not through the aligner.

You aren't meant to instantiate this directly; you should have an Aligner or a QualAdjAligner as the concrete class instead.

Constructor & Destructor Documentation

◆ GSSWAligner() [1/3]

vg::GSSWAligner::GSSWAligner ( std::unique_ptr< MatrixAlignmentScorer > owned_scorer )

protected

Build a GSSWAligner around a MatrixAlignmentScorer.

This is the protected constructor meant to be called by subclasses.

◆ ~GSSWAligner()

vg::GSSWAligner::~GSSWAligner ( )

protecteddefault

◆ GSSWAligner() [2/3]

vg::GSSWAligner::GSSWAligner ( GSSWAligner && )

default

◆ GSSWAligner() [3/3]

vg::GSSWAligner::GSSWAligner ( const GSSWAligner & )

delete

Member Function Documentation

◆ align_global_banded()

virtual void vg::GSSWAligner::align_global_banded	(	Alignment &	alignment,
		const HandleGraph &	g,
		int32_t	band_padding = `0`,
		bool	permissive_banding = `true`,
		uint64_t	max_cells = `std::numeric_limits< uint64_t >::max()`
	)		const

pure virtual

Store optimal global alignment against a graph within a specified band in the Alignment object. Permissive banding auto detects the width of band needed so that paths can travel through every node in the graph.

Throws BandMatricesTooBigException if the max_cells limit on DP matric size is hit.

Implemented in vg::QualAdjAligner, and vg::Aligner.

◆ align_global_banded_multi()

virtual void vg::GSSWAligner::align_global_banded_multi	(	Alignment &	alignment,
		vector< Alignment > &	alt_alignments,
		const HandleGraph &	g,
		int32_t	max_alt_alns,
		int32_t	band_padding = `0`,
		bool	permissive_banding = `true`,
		uint64_t	max_cells = `std::numeric_limits< uint64_t >::max()`
	)		const

pure virtual

Store top scoring global alignments in the vector in descending score order up to a maximum number of alternate alignments (including the optimal alignment). If there are fewer than the maximum number of alignments in the return value, then the vector contains all possible alignments. The optimal alignment will be stored in both the vector and the original alignment object.

When multiple alignments have the same score, they are ordered deterministically but arbitrarily.

Throws BandMatricesTooBigException if the max_cells limit on DP matric size is hit.

Implemented in vg::QualAdjAligner, and vg::Aligner.

◆ align_pinned()

virtual void vg::GSSWAligner::align_pinned	(	Alignment &	alignment,
		const HandleGraph &	g,
		bool	pin_left,
		bool	xdrop = `false`,
		uint16_t	xdrop_max_gap_length = `default_xdrop_max_gap_length`
	)		const

pure virtual

store optimal alignment against a graph in the Alignment object with one end of the sequence guaranteed to align to a source/sink node. if xdrop is selected, use the xdrop heuristic, which does not guarantee an optimal alignment.

pinning left means that that the alignment starts with the first base of the read sequence and the first base of a source node sequence, pinning right means that the alignment starts with the final base of the read sequence and the final base of a sink node sequence

Gives the full length bonus only on the non-pinned end of the alignment.

Implemented in vg::QualAdjAligner, and vg::Aligner.

◆ align_pinned_multi()

virtual void vg::GSSWAligner::align_pinned_multi	(	Alignment &	alignment,
		vector< Alignment > &	alt_alignments,
		const HandleGraph &	g,
		bool	pin_left,
		int32_t	max_alt_alns
	)		const

pure virtual

store the top scoring pinned alignments in the vector in descending score order up to a maximum number of alignments (including the optimal one). if there are fewer than the maximum number in the return value, then it includes all alignments with a positive score. the optimal alignment will be stored in both the vector and in the main alignment object

Implemented in vg::QualAdjAligner, and vg::Aligner.

◆ align_xdrop() [1/2]

virtual void vg::GSSWAligner::align_xdrop	(	Alignment &	alignment,
		const HandleGraph &	g,
		const vector< handle_t > &	order,
		const vector< MaximalExactMatch > &	mems,
		bool	reverse_complemented,
		uint16_t	max_gap_length = `default_xdrop_max_gap_length`
	)		const

pure virtual

xdrop aligner, but with a precomputed topological order on the graph, which need not include all of the graph's handles and which may contain both orientations of a handle

Implemented in vg::QualAdjAligner, and vg::Aligner.

◆ align_xdrop() [2/2]

virtual void vg::GSSWAligner::align_xdrop	(	Alignment &	alignment,
		const HandleGraph &	g,
		const vector< MaximalExactMatch > &	mems,
		bool	reverse_complemented,
		uint16_t	max_gap_length = `default_xdrop_max_gap_length`
	)		const

pure virtual

xdrop aligner

Implemented in vg::QualAdjAligner, and vg::Aligner.

◆ create_gssw_graph()

gssw_graph * vg::GSSWAligner::create_gssw_graph ( const HandleGraph & g ) const

protected

◆ graph_cigar()

string vg::GSSWAligner::graph_cigar ( gssw_graph_mapping * gm ) const

protected

◆ gssw_mapping_to_alignment()

void vg::GSSWAligner::gssw_mapping_to_alignment	(	gssw_graph *	graph,
		gssw_graph_mapping *	gm,
		Alignment &	alignment,
		bool	pinned,
		bool	pin_left
	)		const

protected

◆ identify_pinning_points()

unordered_set< vg::id_t > vg::GSSWAligner::identify_pinning_points ( const HandleGraph & graph ) const

protected

◆ operator=() [1/2]

GSSWAligner& vg::GSSWAligner::operator= ( const GSSWAligner & )

delete

◆ operator=() [2/2]

GSSWAligner& vg::GSSWAligner::operator= ( GSSWAligner && )

default

◆ unreverse_graph()

void vg::GSSWAligner::unreverse_graph ( gssw_graph * graph ) const

protected

◆ unreverse_graph_mapping()

void vg::GSSWAligner::unreverse_graph_mapping ( gssw_graph_mapping * gm ) const

protected

Member Data Documentation

◆ deletion_aligner

DeletionAligner vg::GSSWAligner::deletion_aligner

protected

Widget for producing alignments that we know in advance will be complete deletions.

◆ mapq_calc

std::unique_ptr<MappingQualityCalculator> vg::GSSWAligner::mapq_calc

Mapping quality calculator for computing mapping qualities under the scoring scheme we use. Not used internally, but exposed so that aligner clients have easy access to a MAPQ calculator for free and don't need to build their own.

◆ scorer

std::unique_ptr<MatrixAlignmentScorer> vg::GSSWAligner::scorer

Alignment scorer that represents the scoring scheme used for computing alignments.

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

src/aligner.hpp
src/aligner.cpp

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ GSSWAligner() [1/3]

◆ ~GSSWAligner()

◆ GSSWAligner() [2/3]

◆ GSSWAligner() [3/3]

Member Function Documentation

◆ align_global_banded()

◆ align_global_banded_multi()

◆ align_pinned()

◆ align_pinned_multi()

◆ align_xdrop() [1/2]

◆ align_xdrop() [2/2]

◆ create_gssw_graph()

◆ graph_cigar()

◆ gssw_mapping_to_alignment()

◆ identify_pinning_points()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ unreverse_graph()

◆ unreverse_graph_mapping()

Member Data Documentation

◆ deletion_aligner

◆ mapq_calc

◆ scorer