#include <base_read_metric.h>

Inheritance diagram for base_read_metric:

Public Types
typedef base_read_metric_header	header_type

typedef constants::base_read_t	base_t

typedef uint8_t	read_t

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
	base_read_metric (const uint_t lane, const uint_t tile, const uint_t read)

void	set_base (const uint_t lane, const uint_t tile)

void	set_base (const uint_t lane, const uint_t tile, const uint_t read)

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

uint_t	read () const

id_t	id () const

bool	operator< (const base_read_metric &metric2) 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 id_t	create_id (const id_t lane, const id_t tile, const id_t read)

static id_t	read_from_id (const id_t id)

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)

Detailed Description

Base class for InterOp classes that contain per read tile specific metrics

These classes define both a lane, tile and read identifier.

Member Typedef Documentation

typedef constants::base_read_t base_t

Define the base type

typedef base_read_metric_header header_type

A read metric_set header

typedef uint8_t read_t

Define read type

Constructor & Destructor Documentation

base_read_metric	(	const uint_t	lane,
		const uint_t	tile,
		const uint_t	read
	)

inline

Constructor

Parameters

lane	lane number
tile	tile number
read	read number

Member Function Documentation

static id_t create_id	(	const id_t	lane,
		const id_t	tile,
		const id_t	read
	)

inlinestatic

Create unique id from the lane, tile and read

Parameters

lane	lane number
tile	tile number
read	read number

Returns: unique id

id_t id ( ) const

inline

Unique id created from the lane, tile and read

Returns: unique id

bool operator< ( const base_read_metric & metric2 ) const

inline

Comparison operator used to sort the entries in order of their IDs

Parameters

metric2 metric to compare with the current object

Returns: true if this object's ID is less than metric2's ID

uint_t read ( ) const

inline

Read number

Returns: read number

static id_t read_from_id ( const id_t id )

inlinestatic

Get the read from the unique lane/tile/read id

Parameters

id	unique lane/tile/read id

Returns: read number

void set_base	(	const uint_t	lane,
		const uint_t	tile
	)

inline

Set id

Note: This is only supported to enable easier unit testing, this should not be used.

Parameters

lane	lane number
tile	tile number

void set_base	(	const uint_t	lane,
		const uint_t	tile,
		const uint_t	read
	)

inline

Sets ID given lane-tile-read as opposed to the BaseReadMetric

Parameters

lane	lane number
tile	tile number
read	read number

void set_base ( const BaseReadMetric & base )

inline

Set the base metric identifiers

Parameters

base	layout base

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

/io/interop/model/metric_base/base_read_metric.h

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation