#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 (void)

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

void	align_global_banded (Alignment &alignment, const HandleGraph &g, int32_t band_padding=0, bool permissive_banding=true) const

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

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) const

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

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
	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

int32_t	score_exact_match (const Alignment &aln, size_t read_offset, size_t length) const

int32_t	score_exact_match (const string &sequence, const string &base_quality) const

int32_t	score_exact_match (string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const

int32_t	score_mismatch (string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const

int32_t	score_full_length_bonus (bool left_side, string::const_iterator seq_begin, string::const_iterator seq_end, string::const_iterator base_qual_begin) const

int32_t	score_full_length_bonus (bool left_side, const Alignment &alignment) const

int32_t	score_partial_alignment (const Alignment &alignment, const HandleGraph &graph, const path_t &path, string::const_iterator seq_begin, bool no_read_end_scoring=false) const
	Compute the score of a path against the given range of subsequence with the given qualities. More...

Public Member Functions inherited from vg::GSSWAligner
double	max_possible_mapping_quality (int length) const

double	estimate_max_possible_mapping_quality (int length, double min_diffs, double next_min_diffs) const

int32_t	score_gap (size_t gap_length) const
	Returns the score of an insert or deletion of the given length. More...

void	compute_mapping_quality (vector< Alignment > &alignments, int max_mapping_quality, bool fast_approximation, double cluster_mq, bool use_cluster_mq, int overlap_count, double mq_estimate, double maybe_mq_threshold, double identity_weight) const

void	compute_paired_mapping_quality (pair< vector< Alignment >, vector< Alignment >> &alignment_pairs, const vector< double > &frag_weights, int max_mapping_quality1, int max_mapping_quality2, bool fast_approximation, double cluster_mq, bool use_cluster_mq, int overlap_count1, int overlap_count2, double mq_estimate1, double mq_estimate2, double maybe_mq_threshold, double identity_weight) const
	same function for paired reads, mapping qualities are stored in both alignments in the pair More...

int32_t	compute_first_mapping_quality (const vector< double > &scores, bool fast_approximation, const vector< double > *multiplicities=nullptr) const

int32_t	compute_max_mapping_quality (const vector< double > &scores, bool fast_approximation, const vector< double > *multiplicities=nullptr) const

int32_t	compute_group_mapping_quality (const vector< double > &scores, const vector< size_t > &group, const vector< double > *multiplicities=nullptr) const

vector< int32_t >	compute_all_mapping_qualities (const vector< double > &scores, const vector< double > *multiplicities=nullptr) const

double	mapping_quality_score_diff (double mapping_quality) const

double	score_to_unnormalized_likelihood_ln (double score) const

size_t	longest_detectable_gap (const Alignment &alignment, const string::const_iterator &read_pos) const
	The longest gap detectable from a read position without soft-clipping. More...

size_t	longest_detectable_gap (size_t read_length, size_t read_pos) const
	The longest gap detectable from a read position without soft-clipping, for a generic read. More...

size_t	longest_detectable_gap (const Alignment &alignment) const
	The longest gap detectable from any read position without soft-clipping. More...

size_t	longest_detectable_gap (size_t read_length) const
	The longest gap detectable from any read position without soft-clipping, for a generic read. More...

virtual int32_t	score_discontiguous_alignment (const Alignment &aln, const function< size_t(pos_t, pos_t, size_t)> &estimate_distance, bool strip_bonuses=false) const

virtual int32_t	score_contiguous_alignment (const Alignment &aln, bool strip_bonuses=false) const

virtual int32_t	remove_bonuses (const Alignment &aln, bool pinned=false, bool pin_left=false) const

Protected Member Functions
int8_t *	qual_adjusted_matrix (const int8_t *score_matrix, double gc_content, uint32_t max_qual) const

int8_t *	qual_adjusted_bonuses (int8_t _full_length_bonus, uint32_t max_qual) const

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

Protected Member Functions inherited from vg::GSSWAligner
	GSSWAligner ()=default

	GSSWAligner (const int8_t *_score_matrix, int8_t _gap_open, int8_t _gap_extension, int8_t _full_length_bonus, double _gc_content)

	~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

double	group_mapping_quality_exact (const vector< double > &scaled_scores, const vector< size_t > &group, const vector< double > *multiplicities=nullptr) const

double	estimate_next_best_score (int length, double min_diffs) const

double	recover_log_base (const int8_t *score_matrix, double gc_content, double tol) const

bool	verify_valid_log_odds_score_matrix (const int8_t score_matrix, const double nt_freqs) const

double	alignment_score_partition_function (double lambda, const int8_t score_matrix, const double nt_freqs) const

vector< double >	all_mapping_qualities_exact (const vector< double > &scaled_scores, const vector< double > *multiplicities=nullptr) const

Protected Attributes
int8_t *	qual_adj_full_length_bonuses = nullptr

vector< QualAdjXdropAligner >	xdrops

Additional Inherited Members
Static Public Member Functions inherited from vg::GSSWAligner
static double	maximum_mapping_quality_exact (const vector< double > &scaled_scores, size_t max_idx_out, const vector< double > multiplicities=nullptr)

static double	maximum_mapping_quality_approx (const vector< double > &scaled_scores, size_t max_idx_out, const vector< double > multiplicities=nullptr)

static double	first_mapping_quality_exact (const vector< double > &scaled_scores, const vector< double > *multiplicities=nullptr)

static double	first_mapping_quality_approx (const vector< double > &scaled_scores, const vector< double > *multiplicities=nullptr)

Public Attributes inherited from vg::GSSWAligner
DeletionAligner	deletion_aligner

int8_t *	nt_table = nullptr

int8_t *	score_matrix = nullptr

int8_t	match

int8_t	mismatch

int8_t	gap_open

int8_t	gap_extension

int8_t	full_length_bonus

double	log_base = 0.0

Detailed Description

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

Constructor & Destructor Documentation

◆ QualAdjAligner()

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()

vg::QualAdjAligner::~QualAdjAligner ( void )

Member Function Documentation

◆ align()

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

virtual

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`
	)		const

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

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`
	)		const

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

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

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

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.

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

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

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

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

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

virtual

xdrop aligner

Implements vg::GSSWAligner.

◆ qual_adjusted_bonuses()

int8_t * vg::QualAdjAligner::qual_adjusted_bonuses	(	int8_t	_full_length_bonus,
		uint32_t	max_qual
	)		const

protected

◆ qual_adjusted_matrix()

int8_t * vg::QualAdjAligner::qual_adjusted_matrix	(	const int8_t *	score_matrix,
		double	gc_content,
		uint32_t	max_qual
	)		const

protected

◆ score_exact_match() [1/3]

int32_t vg::QualAdjAligner::score_exact_match	(	const Alignment &	aln,
		size_t	read_offset,
		size_t	length
	)		const

virtual

Compute the score of an exact match in the given alignment, from the given offset, of the given length.

Implements vg::GSSWAligner.

◆ score_exact_match() [2/3]

int32_t vg::QualAdjAligner::score_exact_match	(	const string &	sequence,
		const string &	base_quality
	)		const

virtual

Compute the score of an exact match of the given sequence with the given qualities. Qualities may be ignored by some implementations.

Implements vg::GSSWAligner.

◆ score_exact_match() [3/3]

int32_t vg::QualAdjAligner::score_exact_match	(	string::const_iterator	seq_begin,
		string::const_iterator	seq_end,
		string::const_iterator	base_qual_begin
	)		const

virtual

Compute the score of an exact match of the given range of sequence with the given qualities. Qualities may be ignored by some implementations.

Implements vg::GSSWAligner.

◆ score_full_length_bonus() [1/2]

int32_t vg::QualAdjAligner::score_full_length_bonus	(	bool	left_side,
		const Alignment &	alignment
	)		const

virtual

Implements vg::GSSWAligner.

◆ score_full_length_bonus() [2/2]

int32_t vg::QualAdjAligner::score_full_length_bonus	(	bool	left_side,
		string::const_iterator	seq_begin,
		string::const_iterator	seq_end,
		string::const_iterator	base_qual_begin
	)		const

virtual

Implements vg::GSSWAligner.

◆ score_mismatch()

int32_t vg::QualAdjAligner::score_mismatch	(	string::const_iterator	seq_begin,
		string::const_iterator	seq_end,
		string::const_iterator	base_qual_begin
	)		const

virtual

Compute the score of a mismatch of the given range of sequence with the given qualities. Qualities may be ignored by some implementations. Note that the return value is SIGNED, and almost certainly NEGATIVE, because mismatches are bad.

Implements vg::GSSWAligner.

◆ score_partial_alignment()

int32_t vg::QualAdjAligner::score_partial_alignment	(	const Alignment &	alignment,
		const HandleGraph &	graph,
		const path_t &	path,
		string::const_iterator	seq_begin,
		bool	no_read_end_scoring = `false`
	)		const

virtual

Compute the score of a path against the given range of subsequence with the given qualities.

Implements vg::GSSWAligner.

Member Data Documentation

◆ qual_adj_full_length_bonuses

int8_t* vg::QualAdjAligner::qual_adj_full_length_bonuses = nullptr

protected

◆ 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()

◆ ~QualAdjAligner()

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]

◆ qual_adjusted_bonuses()

◆ qual_adjusted_matrix()

◆ score_exact_match() [1/3]

◆ score_exact_match() [2/3]

◆ score_exact_match() [3/3]

◆ score_full_length_bonus() [1/2]

◆ score_full_length_bonus() [2/2]

◆ score_mismatch()

◆ score_partial_alignment()

Member Data Documentation

◆ qual_adj_full_length_bonuses

◆ xdrops