#include <aligner.hpp>

Inheritance diagram for vg::QualAdjAligner:

Public Member Functions
	QualAdjAligner (const int8_t *score_matrix=default_score_matrix, int8_t gap_open=default_gap_open, int8_t gap_extension=default_gap_extension, int8_t full_length_bonus=default_full_length_bonus, double gc_content=default_gc_content)

	QualAdjAligner (QualAdjAligner &&)=default

QualAdjAligner &	operator= (QualAdjAligner &&)=default

void	align (Alignment &alignment, const HandleGraph &g, bool traceback_aln) const override

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 override

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 override

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 override

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

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 override
	xdrop aligner More...

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 override

Public Member Functions inherited from vg::GSSWAligner
	GSSWAligner (GSSWAligner &&)=default

GSSWAligner &	operator= (GSSWAligner &&)=default

	GSSWAligner (const GSSWAligner &)=delete

GSSWAligner &	operator= (const GSSWAligner &)=delete

Protected Member Functions
void	align_internal (Alignment &alignment, vector< Alignment > *multi_alignments, const HandleGraph &g, bool pinned, bool pin_left, int32_t max_alt_alns, bool traceback_aln) const
	Internal function interacting with gssw for pinned and local alignment. More...

Protected Member Functions inherited from vg::GSSWAligner
	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
vector< QualAdjXdropAligner >	xdrops

Protected Attributes inherited from vg::GSSWAligner
DeletionAligner	deletion_aligner

Additional Inherited Members
Public Attributes inherited from vg::GSSWAligner
std::unique_ptr< MatrixAlignmentScorer >	scorer

std::unique_ptr< MappingQualityCalculator >	mapq_calc

Detailed Description

An aligner that uses read base qualities to adjust its scores and alignments.

Constructor & Destructor Documentation

◆ QualAdjAligner() [1/2]

vg::QualAdjAligner::QualAdjAligner	(	const int8_t *	score_matrix = `default_score_matrix`,
		int8_t	gap_open = `default_gap_open`,
		int8_t	gap_extension = `default_gap_extension`,
		int8_t	full_length_bonus = `default_full_length_bonus`,
		double	gc_content = `default_gc_content`
	)

◆ QualAdjAligner() [2/2]

vg::QualAdjAligner::QualAdjAligner ( QualAdjAligner && )

default

Member Function Documentation

◆ align()

void vg::QualAdjAligner::align	(	Alignment &	alignment,
		const HandleGraph &	g,
		bool	traceback_aln
	)		const

overridevirtual

Store optimal local alignment against a graph in the Alignment object. Gives the full length bonus separately on each end of the alignment.

Implements vg::BaseAligner.

◆ align_global_banded()

void vg::QualAdjAligner::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

overridevirtual

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.

Implements vg::GSSWAligner.

◆ align_global_banded_multi()

void vg::QualAdjAligner::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

overridevirtual

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.

Implements vg::GSSWAligner.

◆ align_internal()

void vg::QualAdjAligner::align_internal	(	Alignment &	alignment,
		vector< Alignment > *	multi_alignments,
		const HandleGraph &	g,
		bool	pinned,
		bool	pin_left,
		int32_t	max_alt_alns,
		bool	traceback_aln
	)		const

protected

Internal function interacting with gssw for pinned and local alignment.

we didn't get any alignments either because the graph was empty and we couldn't run

◆ align_pinned()

void vg::QualAdjAligner::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

overridevirtual

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.

Implements vg::GSSWAligner.

◆ align_pinned_multi()

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

overridevirtual

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

Implements vg::GSSWAligner.

◆ align_xdrop() [1/2]

void vg::QualAdjAligner::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

overridevirtual

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

Implements vg::GSSWAligner.

◆ align_xdrop() [2/2]

void vg::QualAdjAligner::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

overridevirtual

xdrop aligner

Implements vg::GSSWAligner.

◆ operator=()

QualAdjAligner& vg::QualAdjAligner::operator= ( QualAdjAligner && )

default

Member Data Documentation

◆ xdrops

vector<QualAdjXdropAligner> vg::QualAdjAligner::xdrops

protected

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

src/aligner.hpp
src/aligner.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ QualAdjAligner() [1/2]

◆ QualAdjAligner() [2/2]

Member Function Documentation

◆ align()

◆ align_global_banded()

◆ align_global_banded_multi()

◆ align_internal()

◆ align_pinned()

◆ align_pinned_multi()

◆ align_xdrop() [1/2]

◆ align_xdrop() [2/2]

◆ operator=()

Member Data Documentation

◆ xdrops