#include <mapping_quality_calculator.hpp>

Public Member Functions
template<typename ScorerT >
	MappingQualityCalculator (const ScorerT &scorer)

void	compute_mapping_quality (std::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 (std::pair< std::vector< Alignment >, std::vector< Alignment >> &alignment_pairs, const std::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

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

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

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

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

double	mapping_quality_score_diff (double mapping_quality) const

double	score_to_unnormalized_likelihood_ln (double score) const
	Convert a score to an unnormalized log likelihood for the sequence. More...

double	max_possible_mapping_quality (int length) const

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

double	estimate_next_best_score (int length, double min_diffs) const

Static Public Member Functions
static double	maximum_mapping_quality_exact (const std::vector< double > &scaled_scores, size_t max_idx_out, const std::vector< double > multiplicities=nullptr)

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

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

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

Private Member Functions
double	group_mapping_quality_exact (const std::vector< double > &scaled_scores, const std::vector< size_t > &group, const std::vector< double > *multiplicities=nullptr) const

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

Private Attributes
double	rep_match

double	rep_mismatch

double	log_base

Detailed Description

Widget for computing mapping qualities from collections of alignment scores.

Constructable from any AlignmentScorer that also exposes arithmetic match and mismatch members. No reference to the scorer is retained after construction.

TODO: This stores (a forgery of) the scorer's log_base instead of the whole scorer. Should we keep a reference to the scorer and get the log base from it on demand instead?

Constructor & Destructor Documentation

◆ MappingQualityCalculator()

template<typename ScorerT >

vg::MappingQualityCalculator::MappingQualityCalculator ( const ScorerT & scorer )

inline

Member Function Documentation

◆ all_mapping_qualities_exact()

vector< double > vg::MappingQualityCalculator::all_mapping_qualities_exact	(	const std::vector< double > &	scaled_scores,
		const std::vector< double > *	multiplicities = `nullptr`
	)		const

private

◆ compute_all_mapping_qualities()

vector< int32_t > vg::MappingQualityCalculator::compute_all_mapping_qualities	(	const std::vector< double > &	scores,
		const std::vector< double > *	multiplicities = `nullptr`
	)		const

Computes mapping quality for all of a vector of scores. Optionally includes a vector of implicit counts >= 1 for the scores, but only 1 count can apply toward the mapping quality.

◆ compute_first_mapping_quality()

int32_t vg::MappingQualityCalculator::compute_first_mapping_quality	(	const std::vector< double > &	scores,
		bool	fast_approximation,
		const std::vector< double > *	multiplicities = `nullptr`
	)		const

Computes mapping quality for the first score in a vector of scores. Optionally includes a vector of implicit counts >= 1 for the scores, but only 1 count can apply toward the mapping quality.

◆ compute_group_mapping_quality()

int32_t vg::MappingQualityCalculator::compute_group_mapping_quality	(	const std::vector< double > &	scores,
		const std::vector< size_t > &	group,
		const std::vector< double > *	multiplicities = `nullptr`
	)		const

Computes mapping quality for a group of scores. Optionally includes a vector of implicit counts >= 1 for the score, but the mapping quality is always calculated as if each member of the group has a count of 1.

◆ compute_mapping_quality()

void vg::MappingQualityCalculator::compute_mapping_quality	(	std::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

Stores -10 * log_10(P_err) in alignment mapping_quality field where P_err is the probability that the alignment is not the correct one (assuming that one of the alignments in the vector is correct).

◆ compute_max_mapping_quality()

int32_t vg::MappingQualityCalculator::compute_max_mapping_quality	(	const std::vector< double > &	scores,
		bool	fast_approximation,
		const std::vector< double > *	multiplicities = `nullptr`
	)		const

Computes mapping quality for the optimal score in a vector of scores. Optionally includes a vector of implicit counts >= 1 for the scores, but only 1 count can apply toward the mapping quality.

◆ compute_paired_mapping_quality()

void vg::MappingQualityCalculator::compute_paired_mapping_quality	(	std::pair< std::vector< Alignment >, std::vector< Alignment >> &	alignment_pairs,
		const std::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

Stores mapoping qualities in paired reads' mapping quality fields. Mapping qualities are stored in both alignments.

◆ estimate_max_possible_mapping_quality()

double vg::MappingQualityCalculator::estimate_max_possible_mapping_quality	(	int	length,
		double	min_diffs,
		double	next_min_diffs
	)		const

◆ estimate_next_best_score()

double vg::MappingQualityCalculator::estimate_next_best_score	(	int	length,
		double	min_diffs
	)		const

◆ first_mapping_quality_approx()

double vg::MappingQualityCalculator::first_mapping_quality_approx	(	const std::vector< double > &	scaled_scores,
		const std::vector< double > *	multiplicities = `nullptr`
	)

static

Same as maximum_mapping_quality_approx except alway s computes mapping quality for the first score

◆ first_mapping_quality_exact()

double vg::MappingQualityCalculator::first_mapping_quality_exact	(	const std::vector< double > &	scaled_scores,
		const std::vector< double > *	multiplicities = `nullptr`
	)

static

Same as maximum_mapping_quality_exact except always computes mapping quality for the first score

◆ group_mapping_quality_exact()

double vg::MappingQualityCalculator::group_mapping_quality_exact	(	const std::vector< double > &	scaled_scores,
		const std::vector< size_t > &	group,
		const std::vector< double > *	multiplicities = `nullptr`
	)		const

private

◆ mapping_quality_score_diff()

double vg::MappingQualityCalculator::mapping_quality_score_diff ( double mapping_quality ) const

Returns the difference between an optimal and second-best alignment scores that would result in this mapping quality using the fast mapping quality approximation

◆ max_possible_mapping_quality()

double vg::MappingQualityCalculator::max_possible_mapping_quality ( int length ) const

◆ maximum_mapping_quality_approx()

double vg::MappingQualityCalculator::maximum_mapping_quality_approx	(	const std::vector< double > &	scaled_scores,
		size_t *	max_idx_out,
		const std::vector< double > *	multiplicities = `nullptr`
	)

static

Given a nonempty vector of nonnegative scaled alignment scores, approximate the mapping quality of the maximal score in the vector. Sets max_idx_out to the index of that score in the vector. Optionally includes a vector of implicit counts >= 1 for the scores, but the mapping quality is always calculated as if its multiplicity is 1.

◆ maximum_mapping_quality_exact()

double vg::MappingQualityCalculator::maximum_mapping_quality_exact	(	const std::vector< double > &	scaled_scores,
		size_t *	max_idx_out,
		const std::vector< double > *	multiplicities = `nullptr`
	)

static

Given a nonempty vector of nonnegative scaled alignment scores, compute the mapping quality of the maximal score in the vector. Sets max_idx_out to the index of that score in the vector. Optionally includes a vector of implicit counts >= 1 for the scores, but the mapping quality is always calculated as if its multiplicity is 1.

◆ score_to_unnormalized_likelihood_ln()

double vg::MappingQualityCalculator::score_to_unnormalized_likelihood_ln ( double score ) const

Convert a score to an unnormalized log likelihood for the sequence.

Member Data Documentation

◆ log_base

double vg::MappingQualityCalculator::log_base

private

◆ rep_match

double vg::MappingQualityCalculator::rep_match

private

◆ rep_mismatch

double vg::MappingQualityCalculator::rep_mismatch

private

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

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MappingQualityCalculator()

Member Function Documentation

◆ all_mapping_qualities_exact()

◆ compute_all_mapping_qualities()

◆ compute_first_mapping_quality()

◆ compute_group_mapping_quality()

◆ compute_mapping_quality()

◆ compute_max_mapping_quality()

◆ compute_paired_mapping_quality()

◆ estimate_max_possible_mapping_quality()

◆ estimate_next_best_score()

◆ first_mapping_quality_approx()

◆ first_mapping_quality_exact()

◆ group_mapping_quality_exact()

◆ mapping_quality_score_diff()

◆ max_possible_mapping_quality()

◆ maximum_mapping_quality_approx()

◆ maximum_mapping_quality_exact()

◆ score_to_unnormalized_likelihood_ln()

Member Data Documentation

◆ log_base

◆ rep_match

◆ rep_mismatch