#include <extended_tile_metric.h>

Inheritance diagram for extended_tile_metric:

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

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
	extended_tile_metric ()

	extended_tile_metric (const header_type &)

	extended_tile_metric (const uint_t lane, const uint_t tile, const float occupied, const point2d &upper_left=point2d())

void	set (const uint_t lane, const uint_t tile, const float occupied, const point2d &upper_left=point2d())

float	cluster_count_occupied () const

float	cluster_count_occupied_k () const

float	percent_occupied () const

const point2d &	upper_left () const

void	set_cluster_count_k (const float cluster_count_k)

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

Extended tile metric

The extended tile metric reports tile metrics such as the occupancy aka number of empty wells on a tile.

Note: Supported versions: 2 and 3

Test:

Confirm version 1 of the metric can be written to and read from a stream

Confirm version 1 of the metric matches known binary file

Member Enumeration Documentation

anonymous enum

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

Constructor & Destructor Documentation

extended_tile_metric ( )

inline

Constructor

extended_tile_metric ( const header_type & )

inline

Constructor

extended_tile_metric	(	const uint_t	lane,
		const uint_t	tile,
		const float	occupied,
		const point2d &	upper_left = `point2d()`
	)

inline

Constructor

Parameters

lane	lane number
tile	tile number
occupied	number of occupied wells
upper_left	coordinate of upper left fiducial

Member Function Documentation

static const char* prefix ( )

inlinestatic

Get the prefix of the InterOp filename

Returns: "ExtendedTile"

void set	(	const uint_t	lane,
		const uint_t	tile,
		const float	occupied,
		const point2d &	upper_left = `point2d()`
	)

inline

Setter

Note: Version 1 and 2

Parameters

lane	lane number
tile	tile number
occupied	number of occupied wells
upper_left	coordinate of upper left fiducial

void set_cluster_count_k ( const float cluster_count_k )

inline

Set the cluster count in kilo bases

Derived from tile_metric using populate_percent_occupied in run_metrics::finalize_after_load

Parameters

cluster_count_k cluster count in kilo bases

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/extended_tile_metric.h

Public Types

Public Member Functions

Static Public Member Functions

Friends

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation