Modules
	Quality Metric Header

Functions
uint_t	qscore_hist (const size_t n) const INTEROP_THROW_SPEC((model

const uint32_vector &	qscore_hist () const

size_t	size () const

uint_t	sum_qscore () const

::uint64_t	sum_qscore_cumulative () const

uint_t	total_over_qscore (const uint_t qscore, const qscore_bin_vector_type &bins) const

uint_t	total_over_qscore (const size_t qscore_index) const

::uint64_t	total_over_qscore_cumulative (const size_t qscore_index) const

float	percent_over_qscore (const size_t qscore_index) const

float	percent_over_qscore_cumulative (const size_t qscore_index) const

::uint64_t	total_over_qscore_cumulative (const uint_t qscore, const qscore_bin_vector_type &bins) const

float	percent_over_qscore (const uint_t qscore_index, const qscore_bin_vector_type &bins) const

float	percent_over_qscore_cumulative (const uint_t qscore, const qscore_bin_vector_type &bins) const

uint_t	median (const qscore_bin_vector_type &bins=qscore_bin_vector_type()) const

bool	is_cumulative_empty () const

Detailed Description

Per tile per cycle quality metrics

See full class description

Note: All metrics in this class are supported by all versions

Function Documentation

bool is_cumulative_empty ( ) const

inline

Check if the cumulative histogram has not been populated

Returns: true if cumulative histogram has not been populated

uint_t median ( const qscore_bin_vector_type & bins = qscore_bin_vector_type() ) const

inline

Get the median q-score

If the median cannot be found, return the maximum integer. This function either requires the bins from the header or the index of the q-value for the first parameter. Note that the header is apart of the metric set (q_metrics).

See also: q_score_header::bins()

Parameters

bins	header bins

Returns: median q-score

float percent_over_qscore ( const size_t qscore_index ) const

inline

Percent of clusters over the given q-score

This calculates over the local histogram. This function takes an index corresponding to the q-value of interest. This index is provided by the index_for_q_value in the metric header.

        q_metric &metric1 = q_metric_set[0];
        std::cout << "Percent >= Q30: " << metric1.percent_over_qscore(q_metric_set.index_for_q_value(30)) << std::endl;

See also: q_score_header::bins()

Parameters

qscore_index index of the q-score (for unbinned 29 is Q30)

Returns: percent of cluster over the given q-score

float percent_over_qscore	(	const uint_t	qscore_index,
		const qscore_bin_vector_type &	bins
	)		const

inline

Percent of clusters over the given q-score

This calculates over the local histogram. This function either requires the bins from the header or the index of the q-value for the first parameter. Note that the header is apart of the metric set (q_metrics).

        q_metric &metric1 = q_metric_set[0];
        std::cout << "Percent >= Q30: " << metric1.percent_over_qscore(q_metric_set.index_for_q_value(30)) << std::endl;

See also: q_score_header::bins()

Deprecated:

This function will be removed in a future version.

Parameters

qscore_index	index of the q-score (for unbinned 29 is Q30)
bins	q-score histogram bins

Returns: percent of cluster over the given q-score

float percent_over_qscore_cumulative ( const size_t qscore_index ) const

inline

Percent of clusters over the given q-score

This calculates over the local histogram. This function takes an index corresponding to the q-value of interest. This index is provided by the index_for_q_value in the metric header.

See also: q_score_header::bins()

Parameters

qscore_index index of the q-score (for unbinned 29 is Q30)

Returns: percent of cluster over the given q-score

float percent_over_qscore_cumulative	(	const uint_t	qscore,
		const qscore_bin_vector_type &	bins
	)		const

inline

Percent of clusters over the given q-score

This calculates over the cumlative histogram. This function either requires the bins from the header or the index of the q-value for the first parameter. Note that the header is apart of the metric set (q_metrics).

See also: q_score_header::bins()

Deprecated:

This function will be removed in a future version.

Parameters

qscore	percentage of clusters over the given q-score value
bins	q-score histogram bins

Returns: percent of cluster over the given q-score

uint_t qscore_hist ( const size_t n ) const

inline

Q-score value of the histogram

Returns: q-score value of the histogram

const uint32_vector& qscore_hist ( ) const

inline

Q-score histogram

Returns: q-score histogram

size_t size ( ) const

inline

Number of bins in the q-score histogram

Returns: number of bins in the q-score histogram

uint_t sum_qscore ( ) const

inline

Sum the q-score histogram

Returns: q-score histogram sum

::uint64_t sum_qscore_cumulative ( ) const

inline

Sum the cumulative q-score histogram

Returns: cumulative q-score histogram sum

uint_t total_over_qscore	(	const uint_t	qscore,
		const qscore_bin_vector_type &	bins
	)		const

inline

Number of clusters over the given q-score

This calculates over the local histogram. This function either requires the bins from the header or the index of the q-value for the first parameter. Note that the header is apart of the metric set (q_metrics).

        q_metric &metric0 = q_metric_set[0];
        std::cout << "Total >= Q30: " << metric0.total_over_qscore(q_metric_set.index_for_q_value(30)) << std::endl;

See also: q_score_header::index_for_q_value

Deprecated:

This function is deprecated in future versions

Parameters

qscore	percentage of clusters over the given q-score value
bins	q-score histogram bins

Returns: total of clusters over the given q-score

uint_t total_over_qscore ( const size_t qscore_index ) const

inline

Number of clusters over the given q-score

This calculates over the local histogram. This function takes an index corresponding to the q-value of interest. This index is provided by the index_for_q_value in the metric header.

        q_metric &metric0 = q_metric_set[0];
        std::cout << "Total >= Q30: " << metric0.total_over_qscore(q_metric_set.index_for_q_value(30)) << std::endl;

See also: q_score_header::index_for_q_value

Parameters

qscore_index index of the q-score (for unbinned 29 is Q30)

Returns: total of clusters over the given q-score

::uint64_t total_over_qscore_cumulative ( const size_t qscore_index ) const

inline

Number of clusters over the given q-score

This calculates over the local histogram. This function takes an index corresponding to the q-value of interest. This index is provided by the index_for_q_value in the metric header.

See also: q_score_header::index_for_q_value

Parameters

qscore_index index of the q-score (for unbinned 29 is Q30)

Returns: total of clusters over the given q-score

::uint64_t total_over_qscore_cumulative	(	const uint_t	qscore,
		const qscore_bin_vector_type &	bins
	)		const

inline

Number of clusters over the given q-score

This calculates over the cumlative histogram. This function either requires the bins from the header or the index of the q-value for the first parameter. Note that the header is apart of the metric set (q_metrics).

See also: q_score_header::bins()

Deprecated:

This function will be removed in future versions

Parameters

qscore	percentage of clusters over the given q-score value
bins	q-score histogram bins

Returns: total of clusters over the given q-score

Modules

Functions

Detailed Description

Function Documentation