Namespaces
	detail

	op

Classes
class	error_cache_element

class	qval_cache

struct	qval_total

struct	read_cycle

class	summary_by_lane_read

Typedefs
typedef void(model::summary::cycle_state_summary::*	set_cycle_state_func_t) (const model::run::cycle_range &)

typedef std::vector< std::vector< model::run::cycle_range > >	cycle_range_vector2d_t

typedef std::vector< read_cycle >	read_cycle_vector_t

Functions
template<typename Metric >
void	summarize_cycle_state (const model::metric_base::metric_set< model::metrics::tile_metric > &tile_metrics, const model::metric_base::metric_set< Metric > &cycle_metrics, const read_cycle_vector_t &cycle_to_read, set_cycle_state_func_t set_cycle_state_fun, model::summary::run_summary &run) INTEROP_THROW_SPEC((model

template<typename I >
void	cache_error_by_lane_read (I beg, I end, const size_t max_cycle, const std::vector< read_cycle > &cycle_to_read, const constants::tile_naming_method naming_method, summary_by_lane_read< float > &read_lane_cache, summary_by_lane_read< float > &read_lane_surface_cache)

void	error_summary_from_cache (summary_by_lane_read< float > &read_lane_cache, summary_by_lane_read< float > &read_lane_surface_cache, model::summary::run_summary &run, void(model::summary::stat_summary::*func)(const model::summary::metric_stat &), const bool skip_median=false)

template<typename I >
void	summarize_error_metrics (I beg, I end, const read_cycle_vector_t &cycle_to_read, const constants::tile_naming_method naming_method, model::summary::run_summary &run, const bool skip_median=false) INTEROP_THROW_SPEC((model

template<typename I >
void	summarize_extraction_metrics (I beg, I end, const read_cycle_vector_t &cycle_to_read, const size_t channel, const constants::tile_naming_method naming_method, model::summary::run_summary &run, const bool skip_median=false) INTEROP_THROW_SPEC((model

template<typename I , typename UnaryOp >
void	map_read_to_cycle_number (I beg, I end, read_cycle_vector_t &cycle_to_read, UnaryOp op)

template<typename I >
void	map_read_to_cycle_number (I beg, I end, read_cycle_vector_t &cycle_to_read)

template<class Metric >
void	validate_cycle_to_read (const model::metric_base::metric_set< Metric > &set, const summary::read_cycle_vector_t &cycle_to_read)

template<typename I >
void	summarize_phasing_metrics (I beg, I end, model::summary::run_summary &run, const constants::tile_naming_method naming_method, const bool skip_median=false) INTEROP_THROW_SPEC((model

template<typename I >
void	summarize_collapsed_quality_metrics (I beg, I end, const read_cycle_vector_t &cycle_to_read, const constants::tile_naming_method naming_method, model::summary::run_summary &run)

template<typename I >
void	reserve (I beg, I end, const ptrdiff_t n)

template<typename I , typename S >
void	summarize (I beg, I end, S &stat, const bool skip_median)

template<typename I , typename S , typename BinaryOp , typename Compare >
void	summarize (I beg, I end, S &stat, BinaryOp op, Compare comp, const bool skip_median)

template<typename I , typename S , typename BinaryOp , typename Compare >
size_t	nan_summarize (I beg, I end, S &stat, BinaryOp op, Compare comp, const bool skip_median)

template<typename I , typename S , typename Op >
S	nan_accumulate (I beg, I end, const S init, Op op)

float	divide (const float num, const float div)

double	divide (const double num, const double div)

template<class ExtendedTileVector >
void	update_extended_tile_summary_from_cache (std::vector< ExtendedTileVector > &extended_tile_data, model::summary::stat_summary &stat_summary, const bool skip_median)

template<class TileVector >
void	update_tile_summary_from_cache (std::vector< TileVector > &tile_data, model::summary::stat_summary &stat_summary, const bool skip_median)

size_t	update_read_summary (summary_by_lane_read< model::metrics::read_metric >::vector_t &read_data_cache, model::summary::stat_summary &stat_summary, const bool skip_median)

template<typename I >
void	summarize_tile_metrics (I beg, I end, const constants::tile_naming_method naming_method, model::summary::run_summary &run, const bool skip_median=false)

template<typename I >
void	summarize_extended_tile_metrics (I beg, I end, const constants::tile_naming_method naming_method, model::summary::run_summary &run)

void	summarize_index_metrics (model::metric_base::metric_set< model::metrics::index_metric > &index_metrics, const model::metric_base::metric_set< model::metrics::tile_metric > &tile_metrics, const size_t lane, model::summary::index_lane_summary &summary)

void	summarize_index_metrics (model::metrics::run_metrics &metrics, const size_t lane, model::summary::index_lane_summary &summary)

void	summarize_index_metrics (model::metric_base::metric_set< model::metrics::index_metric > &index_metrics, const model::metric_base::metric_set< model::metrics::tile_metric > &tile_metrics, const size_t lane_count, model::summary::index_flowcell_summary &summary)

void	summarize_index_metrics (model::metrics::run_metrics &metrics, model::summary::index_flowcell_summary &summary)

void	summarize_tile_count (const model::metrics::run_metrics &metrics, model::summary::run_summary &summary)

void	set_run_summary_metric (const model::metrics::summary_run_metric &summary_run, model::summary::metric_summary &summary)

void	summarize_run_metrics (model::metrics::run_metrics &metrics, model::summary::run_summary &summary, const bool skip_median, const bool trim) INTEROP_THROW_SPEC((model

Typedef Documentation

typedef std::vector<std::vector<model::run::cycle_range> > cycle_range_vector2d_t

Vector of vectors of cycle_range objects

typedef std::vector<read_cycle> read_cycle_vector_t

Vector of read_cycle objects

typedef void(model::summary::cycle_state_summary::* set_cycle_state_func_t) (const model::run::cycle_range &)

Define a member function of cycle_state_summary that sets a cycle state

Function Documentation

void illumina::interop::logic::summary::cache_error_by_lane_read	(	I	beg,
		I	end,
		const size_t	max_cycle,
		const std::vector< read_cycle > &	cycle_to_read,
		const constants::tile_naming_method	naming_method,
		summary_by_lane_read< float > &	read_lane_cache,
		summary_by_lane_read< float > &	read_lane_surface_cache
	)

Cache errors for all tiles up to a give max cycle

This function only includes errors from useable cycles (not the last cycle) to up the given max cycle.

Parameters

beg	iterator to start of a collection of error metrics
end	iterator to end of a collection of error metrics
max_cycle	maximum cycle to take
cycle_to_read	map that takes a cycle and returns the read-number cycle-in-read pair
naming_method	tile naming convention
read_lane_cache	destination cache by read then by lane a collection of errors
read_lane_surface_cache	source cache by read then by lane then by surface a collection of errors

float illumina::interop::logic::summary::divide	(	const float	num,
		const float	div
	)

inline

Safe divide

Parameters

num	numerator
div	divisor

Returns: result of division

double illumina::interop::logic::summary::divide	(	const double	num,
		const double	div
	)

inline

Safe divide

Parameters

num	numerator
div	divisor

Returns: result of division

void illumina::interop::logic::summary::error_summary_from_cache	(	summary_by_lane_read< float > &	read_lane_cache,
		summary_by_lane_read< float > &	read_lane_surface_cache,
		model::summary::run_summary &	run,
		void(model::summary::stat_summary::*)(const model::summary::metric_stat &)	func,
		const bool	skip_median = `false`
	)

inline

Calculate summary statistics for each collection of metrics organized by read and lane

Parameters

read_lane_cache	source cache by read then by lane a collection of errors
read_lane_surface_cache	source cache by read then by lane then by surface a collection of errors
run	destination run summary
func	member function pointer to metric
skip_median	skip the median calculation

void illumina::interop::logic::summary::map_read_to_cycle_number	(	I	beg,
		I	end,
		read_cycle_vector_t &	cycle_to_read,
		UnaryOp	op
	)

Create a map from cycle to a pair: read number and cycle in read

Parameters

beg	iterator to start of a collection of read infos
end	iterator to end of a collection of read infos
cycle_to_read	map that takes a cycle and returns the read-number cycle-in-read pair
op	unary operator that takes some object and returns a read info

void illumina::interop::logic::summary::map_read_to_cycle_number	(	I	beg,
		I	end,
		read_cycle_vector_t &	cycle_to_read
	)

Create a map from cycle to a pair: read number and cycle in read

Parameters

beg	iterator to start of a collection of read infos
end	iterator to end of a collection of read infos
cycle_to_read	map that takes a cycle and returns the read-number cycle-in-read pair

S illumina::interop::logic::summary::nan_accumulate	(	I	beg,
		I	end,
		const S	init,
		Op	op
	)

Calculate the sum over a collection of values, ignoring NaNs

Parameters

beg	iterator to start of collection
end	iterator to end of collection
init	initial value for accumulate call
op	unary/binary operator for getting a value in a complex object

Returns: sum of init + applying op to the range [beg, end)

size_t illumina::interop::logic::summary::nan_summarize	(	I	beg,
		I	end,
		S &	stat,
		BinaryOp	op,
		Compare	comp,
		const bool	skip_median
	)

Calculate the mean, standard deviation (stddev) and median over a collection of values, ignoring NaNs

Parameters

beg	iterator to start of collection
end	iterator to end of collection
stat	object to store mean, stddev, and median
op	unary/binary operator for getting a value in a complex object
comp	comparison operator to compare a single value in a complex object
skip_median	skip the median calculation

Returns: number of non-NaN elements

void illumina::interop::logic::summary::reserve	(	I	beg,
		I	end,
		const ptrdiff_t	n
	)

Reserve space in a vector residing in another collection

Parameters

beg	iterator to start of collection containing vectors
end	iterator to end of collection containing vectors
n	number of elements to reserve

void illumina::interop::logic::summary::set_run_summary_metric	(	const model::metrics::summary_run_metric &	summary_run,
		model::summary::metric_summary &	summary
	)

void illumina::interop::logic::summary::summarize	(	I	beg,
		I	end,
		S &	stat,
		const bool	skip_median
	)

Calculate the mean, standard deviation (stddev) and median over a collection of values

Parameters

beg	iterator to start of collection
end	iterator to end of collection
stat	object to store mean, stddev, and median
skip_median	skip the median calculation

void illumina::interop::logic::summary::summarize	(	I	beg,
		I	end,
		S &	stat,
		BinaryOp	op,
		Compare	comp,
		const bool	skip_median
	)

Calculate the mean, standard deviation (stddev) and median over a collection of values

Parameters

beg	iterator to start of collection
end	iterator to end of collection
stat	object to store mean, stddev, and median
op	unary/binary operator for getting a value in a complex object
comp	comparison operator to compare a single value in a complex object
skip_median	skip the median calculation

void illumina::interop::logic::summary::summarize_collapsed_quality_metrics	(	I	beg,
		I	end,
		const read_cycle_vector_t &	cycle_to_read,
		const constants::tile_naming_method	naming_method,
		model::summary::run_summary &	run
	)

Summarize a collection collapsed quality metrics

See also: model::summary::lane_summary::percent_gt_q30; model::summary::lane_summary::yield_g; model::summary::lane_summary::projected_yield_g; model::summary::read_summary::percent_gt_q30; model::summary::read_summary::yield_g; model::summary::read_summary::projected_yield_g; model::summary::run_summary::percent_gt_q30; model::summary::run_summary::yield_g; model::summary::run_summary::projected_yield_g

Parameters

beg	iterator to start of a collection of collapsed q metrics
end	iterator to end of a collection of collapsed q metrics
cycle_to_read	map cycle to the read number and cycle within read number
naming_method	tile naming convention
run	destination run summary

void illumina::interop::logic::summary::summarize_cycle_state	(	const model::metric_base::metric_set< model::metrics::tile_metric > &	tile_metrics,
		const model::metric_base::metric_set< Metric > &	cycle_metrics,
		const read_cycle_vector_t &	cycle_to_read,
		set_cycle_state_func_t	set_cycle_state_fun,
		model::summary::run_summary &	run
	)

Summarize the cycle state for a particular metric

Parameters

tile_metrics	tile metric set
cycle_metrics	a cycle based metric set
cycle_to_read	map between the current cycle and read information
set_cycle_state_fun	callback to set the cycle state
run	run summary

void illumina::interop::logic::summary::summarize_error_metrics	(	I	beg,
		I	end,
		const read_cycle_vector_t &	cycle_to_read,
		const constants::tile_naming_method	naming_method,
		model::summary::run_summary &	run,
		const bool	skip_median = `false`
	)

Summarize a collection error metrics

See also: model::summary::stat_summary::error_rate; model::summary::stat_summary::error_rate_35; model::summary::stat_summary::error_rate_50; model::summary::stat_summary::error_rate_75; model::summary::stat_summary::error_rate_100; model::summary::read_summary::error_rate; model::summary::run_summary::error_rate

Parameters

beg	iterator to start of a collection of error metrics
end	iterator to end of a collection of error metrics
cycle_to_read	map cycle to the read number and cycle within read number
naming_method	tile naming convention
run	destination run summary
skip_median	skip the median calculation

void illumina::interop::logic::summary::summarize_extended_tile_metrics	(	I	beg,
		I	end,
		const constants::tile_naming_method	naming_method,
		model::summary::run_summary &	run
	)

Summarize a collection extended tile metrics

Note: This must be called after summarize_tile_metrics!

Parameters

beg	iterator to start of a collection of extended tile metrics
end	iterator to end of a collection of extended tile metrics
naming_method	tile naming convention
run	destination run summary

void illumina::interop::logic::summary::summarize_extraction_metrics	(	I	beg,
		I	end,
		const read_cycle_vector_t &	cycle_to_read,
		const size_t	channel,
		const constants::tile_naming_method	naming_method,
		model::summary::run_summary &	run,
		const bool	skip_median = `false`
	)

Summarize and aggregate the first_cycle_intensity

See also: model::summary::lane_summary::first_cycle_intensity; model::summary::read_summary::first_cycle_intensity; model::summary::run_summary::first_cycle_intensity

Parameters

beg	iterator to start of a collection of extraction metrics
end	iterator to end of a collection of extraction metrics
cycle_to_read	map cycle to the read number and cycle within read number
channel	channel to use for intensity reporting
naming_method	tile naming convention
run	destination run summary
skip_median	skip the median calculation

void illumina::interop::logic::summary::summarize_index_metrics	(	model::metric_base::metric_set< model::metrics::index_metric > &	index_metrics,
		const model::metric_base::metric_set< model::metrics::tile_metric > &	tile_metrics,
		const size_t	lane,
		model::summary::index_lane_summary &	summary
	)

Summarize a index metrics for a specific lane

Parameters

index_metrics	set of index metrics
tile_metrics	source collection of tile metrics
lane	lane number
summary	destination index flowcell summary

void illumina::interop::logic::summary::summarize_index_metrics	(	model::metrics::run_metrics &	metrics,
		const size_t	lane,
		model::summary::index_lane_summary &	summary
	)

Summarize a collection index metrics for a specific lane

Parameters

metrics	source run metrics
lane	lane number
summary	destination index lane summary

void illumina::interop::logic::summary::summarize_phasing_metrics	(	I	beg,
		I	end,
		model::summary::run_summary &	run,
		const constants::tile_naming_method	naming_method,
		const bool	skip_median = `false`
	)

Summarize a collection of phasing metrics

See also: model::summary::lane_summary::phasing_slope; model::summary::lane_summary::phasing_offset; model::summary::lane_summary::prephasing_slope; model::summary::lane_summary::prephasing_offset

Parameters

beg	iterator to start of a collection of dynamic phasing metrics
end	iterator to end of a collection of dynamic phasing metrics
run	destination run summary
naming_method	tile naming convention
skip_median	skip the median calculation

void illumina::interop::logic::summary::summarize_tile_count	(	const model::metrics::run_metrics &	metrics,
		model::summary::run_summary &	summary
	)

Determine maximum number of tiles among all metrics for each lane

Parameters

metrics	run metrics
summary	run summary

void illumina::interop::logic::summary::summarize_tile_metrics	(	I	beg,
		I	end,
		const constants::tile_naming_method	naming_method,
		model::summary::run_summary &	run,
		const bool	skip_median = `false`
	)

Summarize a collection tile metrics

See also: model::summary::lane_summary::density; model::summary::lane_summary::density_pf; model::summary::lane_summary::cluster_count; model::summary::lane_summary::cluster_count_pf; model::summary::lane_summary::percent_pf; model::summary::lane_summary::reads; model::summary::lane_summary::reads_pf; model::summary::lane_summary::percent_aligned; model::summary::lane_summary::prephasing; model::summary::lane_summary::phasing; model::summary::read_summary::percent_aligned; model::summary::run_summary::percent_aligned

Parameters

beg	iterator to start of a collection of tile metrics
end	iterator to end of a collection of tile metrics
naming_method	tile naming convention
run	destination run summary
skip_median	skip the median calculation

void illumina::interop::logic::summary::update_extended_tile_summary_from_cache	(	std::vector< ExtendedTileVector > &	extended_tile_data,
		model::summary::stat_summary &	stat_summary,
		const bool	skip_median
	)

Use the cached data to update a stat summary

Parameters

extended_tile_data	cached tile data
stat_summary	destination stat summary to update
skip_median	skip the median calculation

size_t illumina::interop::logic::summary::update_read_summary	(	summary_by_lane_read< model::metrics::read_metric >::vector_t &	read_data_cache,
		model::summary::stat_summary &	stat_summary,
		const bool	skip_median
	)

inline

Update the stat summary with cached read metrics

Parameters

read_data_cache	read metric cache
stat_summary	stat summary
skip_median	skip the median calculation

Returns: number of non-NaN aligned entries

void illumina::interop::logic::summary::update_tile_summary_from_cache	(	std::vector< TileVector > &	tile_data,
		model::summary::stat_summary &	stat_summary,
		const bool	skip_median
	)

Use the cached data to update a stat summary

Parameters

tile_data	cached tile data
stat_summary	destination stat summary to update
skip_median	skip the median calculation

void illumina::interop::logic::summary::validate_cycle_to_read	(	const model::metric_base::metric_set< Metric > &	set,
		const summary::read_cycle_vector_t &	cycle_to_read
	)

Validate that the cycle to read matches the metric set

Template Parameters

Metric

Parameters

set	metric set
cycle_to_read	cycle to read map

Namespaces

Classes

Typedefs

Functions

Typedef Documentation

Function Documentation