corrected_intensity_metric Class Reference

Intensity and count metrics for each base. More...

#include <corrected_intensity_metric.h>

Inheritance diagram for corrected_intensity_metric:

Public Types
enum	{ TYPE = constants::CorrectedInt, LATEST_VERSION = 4 }
typedef ::intptr_t	difference_type
typedef std::vector< ushort_t >	ushort_array_t
typedef std::vector< uint_t >	uint_array_t
typedef std::vector< float >	float_array_t
typedef ::uint16_t *	ushort_pointer_t
typedef ::uint32_t *	uint_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
	corrected_intensity_metric ()
	corrected_intensity_metric (const header_type &)
	corrected_intensity_metric (const uint_t lane, const uint_t tile, const uint_t cycle, const ushort_t average_cycle_intensity, const float signal_to_noise, const float_array_t &corrected_int_called, const ushort_array_t &corrected_int_all, const uint_array_t &called_counts)
	corrected_intensity_metric (const uint_t lane, const uint_t tile, const uint_t cycle, const ushort_t average_cycle_intensity, const float signal_to_noise, const float_pointer_t corrected_int_called, const ushort_pointer_t corrected_int_all, const uint_pointer_t called_counts)
	corrected_intensity_metric (const uint_t lane, const uint_t tile, const uint_t cycle, const float_array_t &corrected_int_called, const uint_array_t &called_counts)
	corrected_intensity_metric (const uint_t lane, const uint_t tile, const uint_t cycle, const ushort_pointer_t corrected_int_called, const uint_pointer_t called_counts)
	corrected_intensity_metric (const uint_t lane, const uint_t tile, const uint_t cycle, const uint_array_t &called_count)
	corrected_intensity_metric (const uint_t lane, const uint_t tile, const uint_t cycle, const ::uint32_t *called_counts, const size_t num_of_counts, const size_t, const size_t)
void	set (const uint_t lane, const uint_t tile, const uint_t cycle, const uint_array_t &called_counts)
ushort_t	average_cycle_intensity () const
ushort_t	corrected_int_all (const constants::dna_bases index) const INTEROP_THROW_SPEC((model
float	corrected_int_all_float (const constants::dna_bases index) const INTEROP_THROW_SPEC((model
float	corrected_int_called (const constants::dna_bases index) const INTEROP_THROW_SPEC((model
const uint_array_t &	called_counts_array () const
const float_array_t &	corrected_int_called_array () const
const ushort_array_t &	corrected_int_all_array () const
uint_t	called_counts (const constants::dna_bases index) const INTEROP_THROW_SPEC((model
uint_t	no_calls () const
float	signal_to_noise () const
uint_t	total_calls (const bool nocalls=false) const
uint_t	total_intensity () const
float	total_called_intensity () const
float	percent_base (const constants::dna_bases index) const INTEROP_THROW_SPEC((model
float_array_t	percent_bases () const
float	percent_nocall () const INTEROP_THROW_SPEC((model
void	corrected_int_called_array (const float_array_t &vals)
bool	any_valid_called_int () const
ushort_t	averageCycleIntensity () const
ushort_t	correctedIntAll (size_t index) const
float	correctedIntCalled (size_t index) const
const float_array_t &	correctedIntCalled () const
const ushort_array_t &	correctedIntAll () const
const uint_array_t &	calledCounts () const
uint_t	noCalls () const
float	percentBase (difference_type index) const
uint_t	calledCounts (difference_type index) const
float	signalToNoise () const
uint_t	totalCalls (const bool nocalls=false) const
uint_t	totalIntensity () const
float	totalCalledIntensity () const
float	percentIntensity (size_t index) const
float	percentCalledIntensity (const size_t index) 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

Intensity and count metrics for each base.

The corrected intensity metrics provide the percent base plot and the intensity plots.

For 4-dye systems, the intensity corrected for cross-talk between the color channels and phasing and prephasing. These are used in base calling. Note, the software generates phasing/prephasing estimates after cycle 25 (for most platforms).

For 2-dye systems, the values are calculated is another way and aid in accessing the progress of the run.

Note

Supported versions: 2, 3 and 4

Test:

Confirm version 2 of the metric matches known binary file

Confirm version 3 of the metric matches known binary file

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

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

The test, actual and expected variables are metric sets that are contained in the fixture corrected_intensity_metrics_tests.

The test variable is only set to false when the regression test is being rebaselined.

Member Typedef Documentation

typedef ::intptr_t difference_type

Define a diffference type

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 std::vector<uint_t> uint_array_t

Define a uint array using an underlying vector

typedef ::uint32_t* uint_pointer_t

Define a uint pointer to a uint array

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

Constructor & Destructor Documentation

corrected_intensity_metric ( )

inline

Constructor

corrected_intensity_metric ( const header_type &  )

inline

Constructor

corrected_intensity_metric ( const uint_t  lane, const uint_t  tile, const uint_t  cycle, const ushort_t  average_cycle_intensity, const float  signal_to_noise, const float_array_t &  corrected_int_called, const ushort_array_t &  corrected_int_all, const uint_array_t &  called_counts  )

inline

Constructor

Note

Version 2, used for unit testing

Parameters

lane	lane number
tile	tile number
cycle	cycle number
average_cycle_intensity	average intensity for the tile on that cycle
signal_to_noise	signal to noise for given tile at given cycle
corrected_int_called	average corrected intensity per PF base
corrected_int_all	average corrected intensity per base
called_counts	number of clusters called per base

corrected_intensity_metric ( const uint_t  lane, const uint_t  tile, const uint_t  cycle, const ushort_t  average_cycle_intensity, const float  signal_to_noise, const float_pointer_t  corrected_int_called, const ushort_pointer_t  corrected_int_all, const uint_pointer_t  called_counts  )

inline

Constructor

Note

Version 2, used for unit testing

Parameters

lane	lane number
tile	tile number
cycle	cycle number
average_cycle_intensity	average intensity for the tile on that cycle
signal_to_noise	signal to noise for given tile at given cycle
corrected_int_called	average corrected intensity per PF base
corrected_int_all	average corrected intensity per base
called_counts	number of clusters called per base

corrected_intensity_metric ( const uint_t  lane, const uint_t  tile, const uint_t  cycle, const float_array_t &  corrected_int_called, const uint_array_t &  called_counts  )

inline

Constructor

Note

Version 3

Parameters

lane	lane number
tile	tile number
cycle	cycle number
corrected_int_called	average corrected intensity per PF base
called_counts	number of clusters called per base

corrected_intensity_metric ( const uint_t  lane, const uint_t  tile, const uint_t  cycle, const ushort_pointer_t  corrected_int_called, const uint_pointer_t  called_counts  )

inline

Constructor

Note

Version 3

Parameters

lane	lane number
tile	tile number
cycle	cycle number
corrected_int_called	average corrected intensity per PF base
called_counts	number of clusters called per base

corrected_intensity_metric ( const uint_t  lane, const uint_t  tile, const uint_t  cycle, const uint_array_t &  called_count  )

inline

Constructor

Note

Version 4

Parameters

lane	lane number
tile	tile number
cycle	cycle number
called_count	number of clusters called per base

corrected_intensity_metric ( const uint_t  lane, const uint_t  tile, const uint_t  cycle, const ::uint32_t *  called_counts, const size_t  num_of_counts, const size_t  , const size_t    )

inline

Constructor

Note

Version 4

Parameters

lane	lane number
tile	tile number
cycle	cycle number
called_counts	number of clusters called per base
num_of_counts	number of bases

Member Function Documentation

bool any_valid_called_int ( ) const

inline

Check if there is a valid value in the called intensity array

Returns

check if there is any non-nan

ushort_t averageCycleIntensity ( ) const

inline

Average intensity over all clusters

Deprecated:

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

Note

Supported version 2, not supported by 3 or later

Returns

average intensity

const uint_array_t& calledCounts ( ) const

inline

Number of clusters called per called base (including No Calls)

Deprecated:

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

Returns

vector of called counts

uint_t calledCounts ( difference_type  index ) const

inline

Number of clusters called per called base (including No Calls)

This member accumulates cluster counts over all four bases and no calls (NC). This is used to calculate the percentage of clusters for which the selected base has been called.

Deprecated:

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

Note

Supported by all versions

Parameters

index

index of the base (NC=-1, A=0, C=1, G=2, T=3)

Returns

number of clusters called per base

void corrected_int_called_array ( const float_array_t &  vals )

inline

Average corrected intensity for only base called clusters: A, C, G and T

Parameters

vals	vector of corrected called intensities

ushort_t correctedIntAll ( size_t  index ) const

inline

Average corrected intensity for each type of base: A, C, G and T

Deprecated:

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

Note

Supported version 2, not supported by 3 or later

Parameters

index

index of the base (A=0, C=1, G=2, T=3)

Returns

average corrected intensity for specified base

const ushort_array_t& correctedIntAll ( ) const

inline

Average corrected intensity for each type of base: A, C, G and T

Deprecated:

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

Note

Supported version 2, not supported by 3 or later

Returns

vector of corrected called intensities

float correctedIntCalled ( size_t  index ) const

inline

Average corrected intensity for only base called clusters: A, C, G and T

Deprecated:

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

Note

Supported by all versions

Parameters

index

index of the base (A=0, C=1, G=2, T=3)

Returns

average corrected intensity over only base called clusters

const float_array_t& correctedIntCalled ( ) const

inline

Average corrected intensity for only base called clusters: A, C, G and T

Deprecated:

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

Returns

vector of corrected called intensities

uint_t noCalls ( ) const

inline

Number of clusters per no call

Deprecated:

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

Note

Supported by all versions

Returns

number of clusters not called

float percentBase ( difference_type  index ) const

inline

Get the percentage per base

Deprecated:

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

Note

Supported by all versions

Parameters

index

index of the base (NC=-1, A=0, C=1, G=2, T=3)

Returns

percentage for given base

float percentCalledIntensity ( const size_t  index ) const

inline

Get the percentage of intensity over only called clusters

Deprecated:

Will be removed in 1.1.x

Note

Supported by all versions

Parameters

index

index of the base (A=0, C=1, G=2, T=3)

Returns

percentage of intensity for each base

float percentIntensity ( size_t  index ) const

inline

Get the percentage of intensity over all clusters

Deprecated:

Will be removed in 1.1.x

Note

Supported version 2, not supported by 3 or later

Parameters

index

index of the base (A=0, C=1, G=2, T=3)

Returns

percentage of intensity for each base

static const char* prefix ( )

inlinestatic

Get the prefix of the InterOp filename

Returns

"CorrectedInt"

void set ( const uint_t  lane, const uint_t  tile, const uint_t  cycle, const uint_array_t &  called_counts  )

inline

Setter

Parameters

lane	lane number
tile	tile number
cycle	cycle number
called_counts	called base counts

float signalToNoise ( ) const

inline

The signal to noise ratio is calculated as mean called intensity divided by standard deviation of non called intensities.

Deprecated:

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

Note

Only supported by version 2, not supported by version 3 or later

Returns

signal to noise calculated from mean called intensity

float totalCalledIntensity ( ) const

inline

Get the total summed intensity for only called clusters

Deprecated:

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

Note

Supported by all versions

Returns

total summed intensity

uint_t totalCalls ( const bool  nocalls = false ) const

inline

Get the total number of clusters called

Deprecated:

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

Note

Supported by all versions

Returns

total number of clusters called

uint_t totalIntensity ( ) const

inline

Get the total summed intensity for all clusters

Deprecated:

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

Note

Supported version 2, not supported by 3 or later

Returns

total summed intensity

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/corrected_intensity_metric.h