Namespaces
	detail

Classes
class	linear_fit

class	metric_value

class	metric_value< model::metrics::corrected_intensity_metric >

class	metric_value< model::metrics::error_metric >

class	metric_value< model::metrics::extraction_metric >

class	metric_value< model::metrics::phasing_metric >

class	metric_value< model::metrics::q_by_lane_metric >

class	metric_value< model::metrics::q_collapsed_metric >

class	metric_value< model::metrics::tile_metric >

struct	phasing_prephasing_fit

Functions
void	populate_dynamic_phasing_metrics (model::metric_base::metric_set< model::metrics::phasing_metric > &phasing_metrics, const logic::summary::read_cycle_vector_t &cycle_to_read, model::metric_base::metric_set< model::metrics::dynamic_phasing_metric > &dynamic_phasing_metrics, model::metric_base::metric_set< model::metrics::tile_metric > &tile_metrics)

void	populate_percent_occupied (const model::metric_base::metric_set< model::metrics::tile_metric > &tile_metrics, model::metric_base::metric_set< model::metrics::extended_tile_metric > &extended_tile_metrics)

void	populate_indices (const model::metric_base::metric_set< model::metrics::tile_metric > &tile_metrics, model::metric_base::metric_set< model::metrics::index_metric > &metrics)

template<typename I >
size_t	count_q_metric_bins (I beg, I end)

size_t	count_q_metric_bins (const model::metric_base::metric_set< model::metrics::q_metric > &metric_set)

size_t	count_q_metric_bins (const model::metric_base::metric_set< model::metrics::q_by_lane_metric > &metric_set)

size_t	count_q_metric_bins (const model::metric_base::metric_set< model::metrics::q_collapsed_metric > &)

bool	requires_legacy_bins (const size_t count)

void	populate_legacy_q_score_bins (std::vector< model::metrics::q_score_bin > &q_score_bins, const constants::instrument_type instrument, const size_t count)

void	compress_q_metrics (model::metric_base::metric_set< model::metrics::q_metric > &q_metric_set)

void	compress_q_metrics (model::metric_base::metric_set< model::metrics::q_by_lane_metric > &q_metric_set)

void	populate_legacy_q_score_bins (model::metric_base::metric_set< model::metrics::q_metric > &q_metric_set, std::vector< model::metrics::q_score_bin > &q_score_bins, const constants::instrument_type instrument)

void	populate_legacy_q_score_bins (model::metric_base::metric_set< model::metrics::q_by_lane_metric > &q_metric_set, std::vector< model::metrics::q_score_bin > &q_score_bins, const constants::instrument_type instrument)

size_t	count_qvals (const model::metric_base::metric_set< model::metrics::q_metric > &q_metric_set)

size_t	count_qvals (const model::metric_base::metric_set< model::metrics::q_by_lane_metric > &q_metric_set)

size_t	count_qvals (const model::metric_base::metric_set< model::metrics::q_collapsed_metric > &)

bool	is_compressed (const model::metric_base::metric_set< model::metrics::q_metric > &q_metric_set)

bool	is_compressed (const model::metric_base::metric_set< model::metrics::q_collapsed_metric > &q_metric_set)

bool	is_compressed (const model::metric_base::metric_set< model::metrics::q_by_lane_metric > &q_metric_set)

size_t	max_qval (const model::metric_base::metric_set< model::metrics::q_metric > &q_metric_set)

size_t	max_qval (const model::metric_base::metric_set< model::metrics::q_by_lane_metric > &q_metric_set)

size_t	max_qval (const model::metric_base::metric_set< model::metrics::q_collapsed_metric > &q_metric_set)

size_t	index_for_q_value (const model::metric_base::metric_set< model::metrics::q_metric > &q_metric_set, const size_t qval)

size_t	index_for_q_value (const model::metric_base::metric_set< model::metrics::q_by_lane_metric > &q_metric_set, const size_t qval)

void	create_collapse_q_metrics (const model::metric_base::metric_set< model::metrics::q_metric > &metric_set, model::metric_base::metric_set< model::metrics::q_collapsed_metric > &collapsed)

inline::uint32_t	lane_from_name (const std::string &tile_name)

inline::uint32_t	tile_from_name (const std::string &tile_name)

constants::tile_naming_method	tile_naming_method_from_metric (const model::metric_base::base_metric &metric)

template<class Metric >
constants::tile_naming_method	tile_naming_method_from_metric (const model::metric_base::metric_set< Metric > &metric_set)

inline::uint32_t	number (const ::uint32_t tile_id, const constants::tile_naming_method)

inline::uint32_t	section (const ::uint32_t tile_id, const constants::tile_naming_method method)

inline::uint32_t	surface (const ::uint32_t tile_id, const constants::tile_naming_method method)

inline::uint32_t	swath (const ::uint32_t tile_id, const constants::tile_naming_method method)

inline::uint32_t	physical_location_column (const ::uint32_t tile_id, const constants::tile_naming_method method, const ::uint32_t swath_count, const bool all_surfaces)

inline::uint32_t	physical_location_row (const ::uint32_t tile_id, const constants::tile_naming_method method, const ::uint32_t section_per_lane, const ::uint32_t tile_count)

inline::uint32_t	physical_location_column (const ::uint32_t tile_id, const model::run::flowcell_layout &layout, const bool all_surfaces)

inline::uint32_t	physical_location_row (const ::uint32_t tile_id, const model::run::flowcell_layout &layout)

typedef	INTEROP_UNORDERED_MAP (model::metric_base::base_metric::id_t, size_t) lookup_map_t

template<typename I >
void	build_index_map (I b, I e, lookup_map_t &id_lookup_map)

void	copy_focus (const model::metric_base::metric_set< model::metrics::extraction_metric > &metrics, float *focus_scores, const size_t channel, const size_t n) INTEROP_THROW_SPEC((model

template<class QMetric >
bool	populate_cumulative_distribution_sorted (model::metric_base::metric_set< QMetric > &metric_set)

template<class QMetric >
void	populate_cumulative_distribution_t (model::metric_base::metric_set< QMetric > &metric_set)

void	populate_cumulative_distribution (model::metric_base::metric_set< model::metrics::q_by_lane_metric > &q_metric_set)

void	populate_cumulative_distribution (model::metric_base::metric_set< model::metrics::q_metric > &q_metric_set)

void	populate_cumulative_distribution (model::metric_base::metric_set< model::metrics::q_collapsed_metric > &q_metric_set)

void	create_q_metrics_by_lane_base (const model::metric_base::metric_set< model::metrics::q_metric > &metric_set, model::metric_base::metric_set< model::metrics::q_by_lane_metric > &bylane)

void	create_q_metrics_by_lane (const model::metric_base::metric_set< model::metrics::q_metric > &metric_set, model::metric_base::metric_set< model::metrics::q_by_lane_metric > &bylane, const constants::instrument_type instrument)

template<class QMetric >
void	compress_q_metrics_t (model::metric_base::metric_set< QMetric > &q_metric_set)

Variables
template<class QMetric >
void populate_cumulative_distribution(model::metric_base::metric_set< model::metrics::q_by_lane_metric > &q_metric_set) INTEROP_THROW_SPEC((model void populate_cumulative_distribution(model::metric_base::metric_set< model::metrics::q_metric > &q_metric_set) INTEROP_THROW_SPEC((model void populate_cumulative_distribution(model::metric_base::metric_set< model::metrics::q_collapsed_metric > &q_metric_set) INTEROP_THROW_SPEC((model size_t	count_legacy_q_score_bins (const model::metric_base::metric_set< QMetric > &q_metric_set)

Function Documentation

void build_index_map	(	I	b,
		I	e,
		lookup_map_t &	id_lookup_map
	)

Build a mapping from the metric ID to its position in the metric set

Template Parameters

I	iterator type

Parameters

b	iterator to start of collection
e	iterator to end of collection
id_lookup_map	map of ID to offset in collection

void compress_q_metrics ( model::metric_base::metric_set< model::metrics::q_metric > & q_metric_set )

Compress the q-metric set using the bins in the header

Parameters

q_metric_set q-metric set

void compress_q_metrics ( model::metric_base::metric_set< model::metrics::q_by_lane_metric > & q_metric_set )

Compress the q-metric set using the bins in the header

Parameters

q_metric_set q-metric set

void illumina::interop::logic::metric::compress_q_metrics_t ( model::metric_base::metric_set< QMetric > & q_metric_set )

Compress the q-metric set using the bins in the header

Parameters

q_metric_set q-metric set

void illumina::interop::logic::metric::copy_focus	(	const model::metric_base::metric_set< model::metrics::extraction_metric > &	metrics,
		float *	focus_scores,
		const size_t	channel,
		const size_t	n
	)

size_t illumina::interop::logic::metric::count_q_metric_bins	(	I	beg,
		I	end
	)

Count the number of bins in the q metric

Parameters

beg	iterator to start of q_metric collection
end	iterator to end of q_metric collection

Returns: number of bins

size_t illumina::interop::logic::metric::count_q_metric_bins ( const model::metric_base::metric_set< model::metrics::q_metric > & metric_set )

inline

Count the number of bins in the q metric

Parameters

metric_set q-metric set

Returns: number of bins

size_t illumina::interop::logic::metric::count_q_metric_bins ( const model::metric_base::metric_set< model::metrics::q_by_lane_metric > & metric_set )

inline

Count the number of bins in the q metric

Parameters

metric_set q-metric set

Returns: number of bins

size_t illumina::interop::logic::metric::count_q_metric_bins ( const model::metric_base::metric_set< model::metrics::q_collapsed_metric > & )

inline

Count the number of bins in the q metric

Note: Always returns 0

Returns: 0

size_t illumina::interop::logic::metric::count_qvals ( const model::metric_base::metric_set< model::metrics::q_metric > & q_metric_set )

inline

Test whether the q-values are compressed

Parameters

q_metric_set q-metric set

Returns: number of q-vals

size_t illumina::interop::logic::metric::count_qvals ( const model::metric_base::metric_set< model::metrics::q_by_lane_metric > & q_metric_set )

inline

Test whether the q-values are compressed

Parameters

q_metric_set by lane q-metric set

Returns: number of q-vals

size_t illumina::interop::logic::metric::count_qvals ( const model::metric_base::metric_set< model::metrics::q_collapsed_metric > & )

inline

Test whether the q-values are compressed

Note: This always returns 0

Returns: 0

void create_collapse_q_metrics	(	const model::metric_base::metric_set< model::metrics::q_metric > &	metric_set,
		model::metric_base::metric_set< model::metrics::q_collapsed_metric > &	collapsed
	)

Generate collapsed Q-metric data from Q-metrics

Parameters

metric_set	q-metric set
collapsed	collapsed Q-metrics

void illumina::interop::logic::metric::create_q_metrics_by_lane	(	const model::metric_base::metric_set< model::metrics::q_metric > &	metric_set,
		model::metric_base::metric_set< model::metrics::q_by_lane_metric > &	bylane,
		const constants::instrument_type	instrument
	)

Generate by lane Q-metric data from Q-metrics

Parameters

metric_set	Q-metrics
bylane	bylane Q-metrics
instrument	instrument type

Exceptions

index_out_of_bounds_exception

void illumina::interop::logic::metric::create_q_metrics_by_lane_base	(	const model::metric_base::metric_set< model::metrics::q_metric > &	metric_set,
		model::metric_base::metric_set< model::metrics::q_by_lane_metric > &	bylane
	)

Generate by lane Q-metric data from Q-metrics

Note: This function is only used for unit testing

Parameters

metric_set	Q-metrics
bylane	bylane Q-metrics

Exceptions

index_out_of_bounds_exception

size_t illumina::interop::logic::metric::index_for_q_value	(	const model::metric_base::metric_set< model::metrics::q_metric > &	q_metric_set,
		const size_t	qval
	)

inline

Get the index for the given q-value

Parameters

q_metric_set	q-metric set
qval	threshold

Returns: index of q-val above given threshold

size_t illumina::interop::logic::metric::index_for_q_value	(	const model::metric_base::metric_set< model::metrics::q_by_lane_metric > &	q_metric_set,
		const size_t	qval
	)

inline

Get the index for the given q-value

Parameters

q_metric_set	by lane q-metric set
qval	threshold

Returns: index of q-val above given threshold

typedef INTEROP_UNORDERED_MAP	(	model::metric_base::base_metric::id_t	,
		size_t
	)

Look up map type for id to offset mapping

bool illumina::interop::logic::metric::is_compressed ( const model::metric_base::metric_set< model::metrics::q_metric > & q_metric_set )

inline

Test whether the q-values are compressed

Parameters

q_metric_set q-metric set

Returns: true if the histogram is compressed (no all zero columns)

bool illumina::interop::logic::metric::is_compressed ( const model::metric_base::metric_set< model::metrics::q_collapsed_metric > & q_metric_set )

inline

Test whether the q-values are compressed

Parameters

q_metric_set collapsed q-metric set

Returns: true if the histogram is compressed (no all zero columns)

bool illumina::interop::logic::metric::is_compressed ( const model::metric_base::metric_set< model::metrics::q_by_lane_metric > & q_metric_set )

inline

Test whether the q-values are compressed

Parameters

q_metric_set by lane q_metric set

Returns: true if the histogram is compressed (no all zero columns)

inline ::uint32_t illumina::interop::logic::metric::lane_from_name ( const std::string & tile_name )

Convert string lane/tile identifier (1_1111) to lane number

Parameters

tile_name lane/tile identifier (1_1111)

Returns: lane number (1)

size_t illumina::interop::logic::metric::max_qval ( const model::metric_base::metric_set< model::metrics::q_metric > & q_metric_set )

inline

Determine the maximum Q-value

Parameters

q_metric_set q-metric set

Returns: the maximum Q-value

size_t illumina::interop::logic::metric::max_qval ( const model::metric_base::metric_set< model::metrics::q_by_lane_metric > & q_metric_set )

inline

Determine the maximum Q-value

Parameters

q_metric_set by lane q-metric set

Returns: the maximum Q-value

size_t illumina::interop::logic::metric::max_qval ( const model::metric_base::metric_set< model::metrics::q_collapsed_metric > & q_metric_set )

inline

Determine the maximum Q-value

Parameters

q_metric_set collapsed q-metric set

Returns: the maximum Q-value

inline ::uint32_t illumina::interop::logic::metric::number	(	const ::uint32_t	tile_id,
		const constants::tile_naming_method
	)

Tile number

Calculates the number of the tile from the tile id.

Returns: number of the tile.

inline ::uint32_t illumina::interop::logic::metric::physical_location_column	(	const ::uint32_t	tile_id,
		const constants::tile_naming_method	method,
		const ::uint32_t	swath_count,
		const bool	all_surfaces
	)

Determine the physical location (in terms of its column number) of the tile on the flow cell

Parameters

tile_id	tile id
method	tile naming method (4-digit or 5-digit or Absolute)
swath_count	number of swathes per lane
all_surfaces	if true, then find the proper column assuming all surfaces are being displayed

Returns: physical location of the tile in terms of its column number

inline ::uint32_t illumina::interop::logic::metric::physical_location_column	(	const ::uint32_t	tile_id,
		const model::run::flowcell_layout &	layout,
		const bool	all_surfaces
	)

Determine the physical location (in terms of its column number) of the tile on the flow cell

Parameters

tile_id	tile id
layout	flow cell layout
all_surfaces	if true, then find the proper column assuming all surfaces are being displayed

Returns: physical location of the tile in terms of its column number

inline ::uint32_t illumina::interop::logic::metric::physical_location_row	(	const ::uint32_t	tile_id,
		const constants::tile_naming_method	method,
		const ::uint32_t	section_per_lane,
		const ::uint32_t	tile_count
	)

Determine the physical location (in terms of its row number) of the tile on the flow cell

Parameters

tile_id	tile id
method	tile naming method (4-digit or 5-digit or Absolute)
section_per_lane	number of sections per lane (5-digit only)
tile_count	number of tiles per swath

Returns: physical location of the tile in terms of its row number

inline ::uint32_t illumina::interop::logic::metric::physical_location_row	(	const ::uint32_t	tile_id,
		const model::run::flowcell_layout &	layout
	)

Determine the physical location (in terms of its row number) of the tile on the flow cell

Parameters

tile_id	tile id
layout	flow cell layout

Returns: physical location of the tile in terms of its row number

void illumina::interop::logic::metric::populate_cumulative_distribution ( model::metric_base::metric_set< model::metrics::q_by_lane_metric > & q_metric_set )

Populate cumulative by lane q-metric distribution

Parameters

q_metric_set q-metric set

void illumina::interop::logic::metric::populate_cumulative_distribution ( model::metric_base::metric_set< model::metrics::q_metric > & q_metric_set )

Populate cumulative q-metric distribution

Note: This can exist here or in SWIG. This is a swig interface function.

Parameters

q_metric_set q-metric set

void illumina::interop::logic::metric::populate_cumulative_distribution ( model::metric_base::metric_set< model::metrics::q_collapsed_metric > & q_metric_set )

Populate cumulative cpllapsed q-metric distribution

Note: This can exist here or in SWIG. This is a swig interface function.

Parameters

q_metric_set q-metric set

bool illumina::interop::logic::metric::populate_cumulative_distribution_sorted ( model::metric_base::metric_set< QMetric > & metric_set )

Populate cumulative q-metric distribution

Parameters

metric_set q-metric set

void illumina::interop::logic::metric::populate_cumulative_distribution_t ( model::metric_base::metric_set< QMetric > & metric_set )

Populate cumulative q-metric distribution

Parameters

metric_set q-metric set

void populate_dynamic_phasing_metrics	(	model::metric_base::metric_set< model::metrics::phasing_metric > &	phasing_metrics,
		const logic::summary::read_cycle_vector_t &	cycle_to_read,
		model::metric_base::metric_set< model::metrics::dynamic_phasing_metric > &	dynamic_phasing_metrics,
		model::metric_base::metric_set< model::metrics::tile_metric > &	tile_metrics
	)

Populate the dynamic phasing metrics (slope & offset for phasing & prephasing) data structure given the phasing metrics data

Parameters

phasing_metrics	phasing metric set
cycle_to_read	map of cycle to read information
dynamic_phasing_metrics	dynamic phasing metric set (to be populated)
tile_metrics	tile metric set (to be populated)

Populate the dynamic phasing metrics (slope & offset for phasing/prephasing) data structure given the phasing metrics data

Parameters

phasing_metrics	phasing metric set
cycle_to_read	map of cycle to read information
dynamic_phasing_metrics	dynamic phasing metric set (to be populated)

void populate_indices	(	const model::metric_base::metric_set< model::metrics::tile_metric > &	tile_metrics,
		model::metric_base::metric_set< model::metrics::index_metric > &	metrics
	)

Populate the unique index sequences while maintaining the order

Parameters

tile_metrics	tile metric set
metrics	index metric set

void populate_legacy_q_score_bins	(	std::vector< model::metrics::q_score_bin > &	q_score_bins,
		const constants::instrument_type	instrument,
		const size_t	count
	)

Populate the q-score header bins from the data

This only for legacy platforms that use older q-metric formats, which do not include bin information in the header.

Parameters

q_score_bins	vector of q-score bins
instrument	instrument type
count	number of bins

void illumina::interop::logic::metric::populate_legacy_q_score_bins	(	model::metric_base::metric_set< model::metrics::q_metric > &	q_metric_set,
		std::vector< model::metrics::q_score_bin > &	q_score_bins,
		const constants::instrument_type	instrument
	)

inline

Populate the q-score header bins from the data

This only for legacy platforms that use older q-metric formats, which do not include bin information in the header.

Parameters

q_metric_set	q-metric set
q_score_bins	vector of q-score bins
instrument	type

void illumina::interop::logic::metric::populate_legacy_q_score_bins	(	model::metric_base::metric_set< model::metrics::q_by_lane_metric > &	q_metric_set,
		std::vector< model::metrics::q_score_bin > &	q_score_bins,
		const constants::instrument_type	instrument
	)

inline

Populate the q-score header bins from the data

This only for legacy platforms that use older q-metric formats, which do not include bin information in the header.

Parameters

q_metric_set	q-metric set
q_score_bins	vector of q-score bins
instrument	type

void populate_percent_occupied	(	const model::metric_base::metric_set< model::metrics::tile_metric > &	tile_metrics,
		model::metric_base::metric_set< model::metrics::extended_tile_metric > &	extended_tile_metrics
	)

Populate percent occupied in extended tile metrics

Parameters

tile_metrics	tile metric set
extended_tile_metrics	destination extended tile metric set

bool illumina::interop::logic::metric::requires_legacy_bins ( const size_t count )

inline

Test if legacy binning should be performed

Parameters

count number of bins

Returns: true if determining the bins is required

inline ::uint32_t illumina::interop::logic::metric::section	(	const ::uint32_t	tile_id,
		const constants::tile_naming_method	method
	)

Section number

Calculates the section of the tile from the tile id.

Returns: section of the tile.

inline ::uint32_t illumina::interop::logic::metric::surface	(	const ::uint32_t	tile_id,
		const constants::tile_naming_method	method
	)

Surface number

Calculates the surface of the tile from the tile id.

Returns: surface of the tile.

inline ::uint32_t illumina::interop::logic::metric::swath	(	const ::uint32_t	tile_id,
		const constants::tile_naming_method	method
	)

Swath number

Calculates the surface of the tile from the tile id.

Returns: surface of the tile.

inline ::uint32_t illumina::interop::logic::metric::tile_from_name ( const std::string & tile_name )

Convert string lane/tile identifier (1_1111) to tile hash

Parameters

tile_name lane/tile identifier (1_1111)

Returns: tile hash (1111)

constants::tile_naming_method illumina::interop::logic::metric::tile_naming_method_from_metric ( const model::metric_base::base_metric & metric )

inline

Determine the tile naming method from a metric tile ID

Parameters

metric tile metric

Returns: tile_naming_method

constants::tile_naming_method illumina::interop::logic::metric::tile_naming_method_from_metric ( const model::metric_base::metric_set< Metric > & metric_set )

Determine the tile naming method from a metric set

Parameters

metric_set metric set

Returns: tile_naming_method

Variable Documentation

void populate_cumulative_distribution (model::metric_base::metric_set<model::metrics::q_by_lane_metric>& q_metric_set) INTEROP_THROW_SPEC(( model void populate_cumulative_distribution (model::metric_base::metric_set<model::metrics::q_metric>& q_metric_set) INTEROP_THROW_SPEC(( model void populate_cumulative_distribution (model::metric_base::metric_set<model::metrics::q_collapsed_metric>& q_metric_set) INTEROP_THROW_SPEC(( model size_t count_legacy_q_score_bins(const model::metric_base::metric_set< QMetric > &q_metric_set)

Populate cumulative by lane q-metric distribution

Parameters

q_metric_set q-metric set Populate cumulative q-metric distribution

Note: This can exist here or in SWIG. This is a swig interface function.

Parameters

q_metric_set q-metric set Populate cumulative cpllapsed q-metric distribution

Note: This can exist here or in SWIG. This is a swig interface function.

Parameters

q_metric_set q-metric set Count number of unique counts to determine number of unique bins for legacy binning

Note: , if the number of bins is greater than 7, than this function stops counting!

Parameters

q_metric_set q-metric set

Returns: number of unique bins

Namespaces

Classes

Functions

Variables

Function Documentation

Variable Documentation