Error rate for a spiked in PhiX control sample. More...

#include <error_metric.h>

Inheritance diagram for error_metric:

Public Types
enum	{ MAX_MISMATCH = 5, TYPE = constants::Error, LATEST_VERSION = 6 }

typedef std::vector< uint_t >	uint_array_t

typedef std::vector< float >	float_vector

typedef error_metric_header	header_type

Public Types inherited from base_cycle_metric
typedef base_cycle_metric_header	header_type

typedef constants::base_cycle_t	base_t

typedef uint16_t	cycle_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
	error_metric ()

	error_metric (const header_type &header)

	error_metric (const uint_t lane, const uint_t tile, const uint_t cycle, const float error, const float phix_adapter_rate)

	error_metric (const uint_t lane, const uint_t tile, const uint_t cycle, const float error, const float_vector &phix_adapter_rates)

float	error_rate () const

float	phix_adapter_rate () const

const float_vector &	phix_adapter_rates () const

float	phix_adapter_rate_at (const size_t n) const INTEROP_THROW_SPEC((model

size_t	phix_adapter_count () const

uint_t	mismatch_cluster_count (const size_t n) const INTEROP_THROW_SPEC((model

uint_t	mismatch_count () const

const uint_array_t &	mismatch_cluster_counts () const

float	errorRate () const

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

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 cycle)

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

uint_t	cycle () const

id_t	id () const

id_t	cycle_hash () const

bool	operator< (const base_cycle_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 const char *	prefix ()

Static Public Member Functions inherited from base_cycle_metric
static id_t	cycle_from_id (const id_t id)

static id_t	reserved_from_id (const id_t id)

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

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

Error rate for a spiked in PhiX control sample.

The error metric is the calculated error rate, as determined by a spiked in PhiX control sample. This metric is available for each lane and tile for every cycle.

Note: Supported versions: 3, 4, 5 and 6

Test:

Confirm version 3 of the metric can be written to and read from a stream

Confirm version 3 of the metric matches known binary file

Member Typedef Documentation

typedef std::vector<float> float_vector

Vector of floats points

typedef error_metric_header header_type

Error metric set header

typedef std::vector<uint_t> uint_array_t

Define a uint array using an underlying vector

Member Enumeration Documentation

anonymous enum

Enumerator
MAX_MISMATCH	Maximum number of mismatches
TYPE	Unique type code for metric
LATEST_VERSION	Latest version of the I nterOp format

Constructor & Destructor Documentation

error_metric ( )

inline

Constructor

error_metric ( const header_type & header )

inline

Constructor

error_metric	(	const uint_t	lane,
		const uint_t	tile,
		const uint_t	cycle,
		const float	error,
		const float	phix_adapter_rate
	)

inline

Constructor

Parameters

lane	lane number
tile	tile number
cycle	cycle number
error	error rate for current cycle

error_metric	(	const uint_t	lane,
		const uint_t	tile,
		const uint_t	cycle,
		const float	error,
		const float_vector &	phix_adapter_rates
	)

inline

Constructor

Parameters

lane	lane number
tile	tile number
cycle	cycle number
error	error rate for current cycle
phix_adapter_rates	rates of each adapter

Member Function Documentation

float errorRate ( ) const

inline

Calculated error rate, as determined by a spiked in PhiX control sample.

Deprecated:

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

Note: Supported by all versions

Returns: error rate

static const char* prefix ( )

inlinestatic

Get the prefix of the InterOp filename

Returns: "Error"

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/error_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