extraction_metric Class Reference

#include <extraction_metric.h>

Inheritance diagram for extraction_metric:

Public Types
enum	{ MAX_CHANNELS = 4, TYPE = constants::Extraction, LATEST_VERSION = 3 }
typedef extraction_metric_header	header_type
typedef std::vector< ushort_t >	ushort_array_t
typedef std::vector< float >	float_array_t
typedef ::uint16_t *	ushort_pointer_t
typedef float *	float_pointer_t
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
	extraction_metric ()
	extraction_metric (const header_type &header)
	extraction_metric (const uint_t lane, const uint_t tile, const uint_t cycle, const ulong_t date_time, const ushort_array_t &intensities_p90, const float_array_t &focus_scores)
	extraction_metric (const uint_t lane, const uint_t tile, const uint_t cycle, const ulong_t date_time, const ushort_pointer_t intensities_p90, const float_pointer_t focus_scores, const uint_t channel_count=MAX_CHANNELS)
	extraction_metric (const uint_t lane, const uint_t tile, const uint_t cycle, const util::csharp_date_time date_time, const ushort_array_t &intensities_p90, const float_array_t &focus_scores)
	extraction_metric (const uint_t lane, const uint_t tile, const uint_t cycle, const util::csharp_date_time date_time, const ushort_pointer_t intensities_p90, const float_pointer_t focus_scores, const uint_t channel_count=MAX_CHANNELS)
	extraction_metric (const uint_t lane, const uint_t tile, const uint_t cycle, const ushort_array_t &max_intensity_values, const float_array_t &focus_scores)
	extraction_metric (const uint_t lane, const uint_t tile, const uint_t cycle, const ::uint16_t *intensity_values, const size_t intensity_count, const float *focus_scores, const size_t focus_count, const size_t)
void	set (const uint_t lane, const uint_t tile, const uint_t cycle, const ulong_t date_time, const ushort_array_t &max_intensity_values, const float_array_t &focus_scores)
void	set (const uint_t lane, const uint_t tile, const uint_t cycle, const ushort_array_t &max_intensity_values, const float_array_t &focus_scores)
ulong_t	date_time () const
const util::csharp_date_time &	date_time_csharp () const
ulong_t	date_time_csharp_raw () const
ushort_t	max_intensity (const size_t channel) const INTEROP_THROW_SPEC((model
float	focus_score (const size_t channel) const INTEROP_THROW_SPEC((model
const ushort_array_t &	max_intensity_values () const
const float_array_t &	focus_scores () const
size_t	channel_count () const
void	trim (const size_t channel_count)
float	focusScore (size_t channel) const
ulong_t	dateTime () const
const float_array_t &	focusScores () const
void	date_time (const ulong_t time)
bool	is_any_p90_zero () 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

Extraction metric

The extraction metrics include the max intensity and the focus score for each color channel.

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 std::vector<float> float_array_t

Define a float array using an underlying vector

typedef float* float_pointer_t

Define a float pointer to a float array

typedef extraction_metric_header header_type

Extraction metric header

typedef std::vector<ushort_t> ushort_array_t

Define a uint16_t array using an underlying vector

typedef ::uint16_t* ushort_pointer_t

Define a uint16_t pointer to a uint16_t array

Member Enumeration Documentation

anonymous enum

Enumerator
MAX_CHANNELS	Maximum number of channels
TYPE	Unique type code for metric
LATEST_VERSION	Latest version of the InterOp format

Constructor & Destructor Documentation

extraction_metric ( )

inline

Constructor

extraction_metric ( const header_type &  header )

inline

Constructor

Parameters

header

extraction metric header

extraction_metric ( const uint_t  lane, const uint_t  tile, const uint_t  cycle, const ulong_t  date_time, const ushort_array_t &  intensities_p90, const float_array_t &  focus_scores  )

inline

Constructor

Note

Version 2

Parameters

lane	lane number
tile	tile number
cycle	cycle number
date_time	time extraction was completed
intensities_p90	90th percentile of intensities for the given channel
focus_scores	focus score for the given channel

extraction_metric ( const uint_t  lane, const uint_t  tile, const uint_t  cycle, const ulong_t  date_time, const ushort_pointer_t  intensities_p90, const float_pointer_t  focus_scores, const uint_t  channel_count = MAX_CHANNELS  )

inline

Constructor

Note

Version 2

Parameters

lane	lane number
tile	tile number
cycle	cycle number
date_time	time extraction was completed
intensities_p90	90th percentile of intensities for the given channel
focus_scores	focus score for the given channel
channel_count	number of channels

extraction_metric ( const uint_t  lane, const uint_t  tile, const uint_t  cycle, const util::csharp_date_time  date_time, const ushort_array_t &  intensities_p90, const float_array_t &  focus_scores  )

inline

Constructor

Note

Version 2

Parameters

lane	lane number
tile	tile number
cycle	cycle number
date_time	time extraction was completed
intensities_p90	90th percentile of intensities for the given channel
focus_scores	focus score for the given channel

extraction_metric ( const uint_t  lane, const uint_t  tile, const uint_t  cycle, const util::csharp_date_time  date_time, const ushort_pointer_t  intensities_p90, const float_pointer_t  focus_scores, const uint_t  channel_count = MAX_CHANNELS  )

inline

Constructor

Note

Version 2

Parameters

lane	lane number
tile	tile number
cycle	cycle number
date_time	time extraction was completed
intensities_p90	90th percentile of intensities for the given channel
focus_scores	focus score for the given channel
channel_count	number of channels

extraction_metric ( const uint_t  lane, const uint_t  tile, const uint_t  cycle, const ushort_array_t &  max_intensity_values, const float_array_t &  focus_scores  )

inline

Constructor

Note

Version 3

Parameters

lane	lane number
tile	tile number
cycle	cycle number
max_intensity_values	90th percentile of intensities for the given channel
focus_scores	focus score for the given channel

extraction_metric ( const uint_t  lane, const uint_t  tile, const uint_t  cycle, const ::uint16_t *  intensity_values, const size_t  intensity_count, const float *  focus_scores, const size_t  focus_count, const size_t    )

inline

Constructor

Note

Version 3

Parameters

lane	lane number
tile	tile number
cycle	cycle number
intensity_values	90th percentile of intensities for the given channel
intensity_count	number of channels
focus_scores	focus score for the given channel
focus_count	number of channels

Member Function Documentation

void date_time ( const ulong_t  time )

inline

Set the current extraction time

Parameters

time	current time

ulong_t dateTime ( ) const

inline

Date time extraction completed

Deprecated:

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

Returns

date time code

float focusScore ( size_t  channel ) const

inline

Median Full Width Half Max (FWHM) Focus Metric

Deprecated:

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

Parameters

channel

channel index

Returns

focus metric as measured by FWHM

const float_array_t& focusScores ( ) const

inline

Get an array of focus scores

These values are estimated using full width half max (FWHM).

Deprecated:

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

Returns

vector of focus scores

bool is_any_p90_zero ( ) const

inline

Determine if any channel's P90 value is 0

Returns

true if any channel's P90 value is 0

static const char* prefix ( )

inlinestatic

Get the prefix of the InterOp filename

Returns

prefix

void set ( const uint_t  lane, const uint_t  tile, const uint_t  cycle, const ulong_t  date_time, const ushort_array_t &  max_intensity_values, const float_array_t &  focus_scores  )

inline

Setter

Note

Version 2

Parameters

lane	lane number
tile	tile number
cycle	cycle number
date_time	time extraction was completed
max_intensity_values	90th percentile of intensities for the given channel
focus_scores	focus score for the given channel

void set ( const uint_t  lane, const uint_t  tile, const uint_t  cycle, const ushort_array_t &  max_intensity_values, const float_array_t &  focus_scores  )

inline

Setter

Note

Version 3

Parameters

lane	lane number
tile	tile number
cycle	cycle number
max_intensity_values	90th percentile of intensities for the given channel
focus_scores	focus score for the given channel

void trim ( const size_t  channel_count )

inline

Trim unused channel values

Parameters

channel_count

actual number of channels

Friends And Related Function Documentation

friend struct io::generic_layout

friend

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

• /io/interop/model/metrics/extraction_metric.h