#include <tile_metric.h>

Inheritance diagram for tile_metric:

Public Types
enum	{ TYPE = constants::Tile, LATEST_VERSION = 3 }

typedef std::vector< read_metric >	read_metric_vector

typedef read_metric_vector::const_iterator	const_iterator

typedef read_metric	read_metric_type

typedef tile_metric_header	header_type

Public Types inherited from base_metric
enum	{ LANE_BIT_COUNT = 6, TILE_BIT_COUNT = 26, CYCLE_BIT_COUNT = 16, READ_BIT_COUNT = 16, RESERVED_BIT_COUNT = 16, READ_BIT_SHIFT = RESERVED_BIT_COUNT, CYCLE_BIT_SHIFT = RESERVED_BIT_COUNT, TILE_BIT_SHIFT = CYCLE_BIT_SHIFT+CYCLE_BIT_COUNT, LANE_BIT_SHIFT = TILE_BIT_SHIFT+TILE_BIT_COUNT }

typedef ::uint64_t	ulong_t

typedef ulong_t	id_t

typedef ::uint16_t	ushort_t

typedef ::uint32_t	uint_t

typedef base_metric_header	header_type

typedef ::uint8_t	lane_t

typedef ::uint32_t	tile_t

typedef constants::base_tile_t	base_t

Public Types inherited from empty_metric
typedef ::uint32_t	id_t

typedef ::uint32_t	uint_t

typedef constants::base_run_t	base_t

Public Member Functions
	tile_metric ()

	tile_metric (const header_type &)

	tile_metric (const uint_t lane, const uint_t tile, const float cluster_density, const float cluster_density_pf, const float cluster_count, const float cluster_count_pf, const read_metric_vector &read_metrics=read_metric_vector())

	tile_metric (const uint_t lane, const uint_t tile, const read_metric_vector &read_metrics=read_metric_vector())

	tile_metric (const tile_metric &metric, const read_metric_vector &read_metrics=read_metric_vector())

	tile_metric (const uint_t lane, const uint_t tile, const float cluster_count, const float cluster_count_pf, const read_metric_vector &read_metrics=read_metric_vector())

float	cluster_density () const

float	cluster_density_k () const

float	cluster_density_pf () const

float	cluster_density_pf_k () const

float	cluster_count () const

float	cluster_count_k () const

float	cluster_count_m () const

float	cluster_count_pf () const

float	cluster_count_pf_k () const

float	cluster_count_pf_m () const

float	percent_pf () const

const read_metric_vector &	read_metrics () const

float	percent_aligned (const size_t n) const

float	percent_phasing (const size_t n) const

float	percent_prephasing (const size_t n) const

float	percent_aligned_at (const size_t number) const

float	percent_phasing_at (const size_t number) const

float	percent_prephasing_at (const size_t number) const

size_t	read_count () const

bool	is_dead_tile () const

void	update_phasing_if_missing (const size_t number, const float phasing, const float prephasing)

float	clusterDensity () const

float	clusterDensityPf () const

float	clusterCount () const

float	clusterCountPf () const

Public Member Functions inherited from base_metric
	base_metric (const uint_t lane=0, const uint_t tile=0)

void	set_base (const uint_t lane, const uint_t tile)

template<class BaseMetric >
void	set_base (const BaseMetric &base)

id_t	id () const

id_t	tile_hash () const

uint_t	lane () const

uint_t	tile () const

uint_t	number (const illumina::interop::constants::tile_naming_method) const

uint_t	section (const illumina::interop::constants::tile_naming_method method) const

uint_t	surface (const illumina::interop::constants::tile_naming_method method) const

uint_t	swath (const illumina::interop::constants::tile_naming_method method) const

uint_t	phyiscalLocationIndex (const illumina::interop::constants::tile_naming_method method, const uint_t section_per_lane, const uint_t tile_count, const uint_t swath_count, const bool all_surfaces) const

uint_t	phyiscalLocationColumn (const illumina::interop::constants::tile_naming_method method, const uint_t swath_count, const bool all_surfaces) const

uint_t	phyiscalLocationRow (const illumina::interop::constants::tile_naming_method method, const uint_t section_per_lane, const uint_t tile_count) const

size_t	physical_location_index (const illumina::interop::constants::tile_naming_method method, const uint_t section_per_lane, const uint_t tile_count, const uint_t swath_count, const bool all_surfaces) const

uint_t	physical_location_column (const illumina::interop::constants::tile_naming_method method, const uint_t swath_count, const bool all_surfaces) const

uint_t	physical_location_row (const illumina::interop::constants::tile_naming_method method, const uint_t section_per_lane, const uint_t tile_count) const

bool	operator< (const base_metric &metric2) const

Public Member Functions inherited from empty_metric
template<class BaseMetric >
void	set_base (const BaseMetric &)

void	set_base (const uint_t, const uint_t)

bool	operator< (const empty_metric &) const

Static Public Member Functions
static const char *	prefix ()

Static Public Member Functions inherited from base_metric
static id_t	create_id (const id_t lane, const id_t tile, const id_t=0)

static id_t	lane_from_id (const id_t id)

static id_t	tile_hash_from_id (const id_t id)

static id_t	tile_from_id (const id_t id)

static const char *	suffix ()

Static Public Member Functions inherited from empty_metric
static const char *	suffix ()

static id_t	create_id (const id_t, const id_t, const id_t=0)

Friends
template<class MetricType , int Version>
struct	io::generic_layout

Detailed Description

Tile metrics

Note: Supported versions: 2 and 3

Test:

Confirm version 2 of the metric can be written to and read from a stream

Confirm version 2 of the metric matches known binary file

Member Typedef Documentation

typedef read_metric_vector::const_iterator const_iterator

Define a const read iterator

typedef tile_metric_header header_type

Define header for metric set

typedef read_metric read_metric_type

Read metric type

typedef std::vector<read_metric> read_metric_vector

Define map between read ids and read metrics

Member Enumeration Documentation

anonymous enum

Enumerator
TYPE	Unique type code for metric
LATEST_VERSION	Latest version of the InterOp format

Constructor & Destructor Documentation

tile_metric ( )

inline

Constructor

tile_metric ( const header_type & )

inline

Constructor

tile_metric	(	const uint_t	lane,
		const uint_t	tile,
		const float	cluster_density,
		const float	cluster_density_pf,
		const float	cluster_count,
		const float	cluster_count_pf,
		const read_metric_vector &	read_metrics = `read_metric_vector()`
	)

inline

Constructor

Note: Version 2, used for writing

Parameters

lane	lane number
tile	tile number
cluster_density	density of clusters for each tile (in thousands per mm2)
cluster_density_pf	density of clusters passing filter for each tile (in thousands per mm2)
cluster_count	number of clusters for each tile
cluster_count_pf	number of clusters passing filter for each tile
read_metrics	vector of metrics for each read on the tile

tile_metric	(	const uint_t	lane,
		const uint_t	tile,
		const read_metric_vector &	read_metrics = `read_metric_vector()`
	)

inline

Constructor

Note: Version 2, used for writing

Parameters

lane	lane number
tile	tile number
read_metrics	vector of metrics for each read on the tile

tile_metric	(	const tile_metric &	metric,
		const read_metric_vector &	read_metrics = `read_metric_vector()`
	)

inline

Constructor

Parameters

metric	tile metric
read_metrics	vector of metrics for each read on the tile

tile_metric	(	const uint_t	lane,
		const uint_t	tile,
		const float	cluster_count,
		const float	cluster_count_pf,
		const read_metric_vector &	read_metrics = `read_metric_vector()`
	)

inline

Constructor

Note: Version 3, used for writing

Parameters

lane	lane number
tile	tile number
cluster_count	number of clusters for each tile
cluster_count_pf	number of clusters passing filter for each tile
read_metrics	vector of metrics for each read on the tile

Member Function Documentation

float clusterCount ( ) const

inline

Number of clusters for each tile

Deprecated:

Will be removed in 1.1.x (use cluster_count instead)

Returns: number of clusters

float clusterCountPf ( ) const

inline

Number of clusters passing filter for each tile

Deprecated:

Will be removed in 1.1.x (use cluster_count_pf instead)

Returns: number of clusters passing filter

float clusterDensity ( ) const

inline

Density of clusters for each tile (in clusters per mm2)

Deprecated:

Will be removed in 1.1.x (use cluster_density instead)

Returns: cluster density

float clusterDensityPf ( ) const

inline

Density of clusters passing filter for each tile (in clusters per mm2)

Deprecated:

Will be removed in 1.1.x (use cluster_density_pf instead)

Returns: cluster density passing filter

static const char* prefix ( )

inlinestatic

Get the prefix of the InterOp filename

Returns: prefix

void update_phasing_if_missing	(	const size_t	number,
		const float	phasing,
		const float	prephasing
	)

inline

Update the phasing/prephasing slope if they don't exist

Parameters

number	read number
phasing	phasing slope
prephasing	prephasing slope

Friends And Related Function Documentation

friend struct io::generic_layout

friend

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

/io/interop/model/metrics/tile_metric.h

Public Types

Public Member Functions

Static Public Member Functions

Friends

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation