#include <q_metric.h>

Inheritance diagram for q_metric:

Public Types
enum	{ TYPE = constants::Q, LATEST_VERSION = 7 }

enum	{ MAX_Q_BINS = q_score_header::MAX_Q_BINS }

typedef q_score_header	header_type

typedef header_type::qscore_bin_vector_type	qscore_bin_vector_type

typedef std::vector< ::uint32_t >	uint32_vector

typedef std::vector< ::uint32_t >	uint_vector

typedef std::vector< ::uint64_t >	uint64_vector

typedef ::uint32_t *	uint_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
	q_metric ()

	q_metric (const header_type &header)

	q_metric (const uint_t lane, const uint_t tile, const uint_t cycle, const uint32_vector &qscore_hist)

	q_metric (const uint_t lane, const uint_t tile, const uint_t cycle, const uint_pointer_t qscore_hist, const uint_t count)

void	set (const uint_t lane, const uint_t tile, const uint_t cycle, const uint32_vector &qscore_hist)

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

const uint32_vector &	qscore_hist () const

size_t	size () const

uint_t	sum_qscore () const

::uint64_t	sum_qscore_cumulative () const

uint_t	total_over_qscore (const uint_t qscore, const qscore_bin_vector_type &bins) const

uint_t	total_over_qscore (const size_t qscore_index) const

::uint64_t	total_over_qscore_cumulative (const size_t qscore_index) const

float	percent_over_qscore (const size_t qscore_index) const

float	percent_over_qscore_cumulative (const size_t qscore_index) const

::uint64_t	total_over_qscore_cumulative (const uint_t qscore, const qscore_bin_vector_type &bins) const

float	percent_over_qscore (const uint_t qscore_index, const qscore_bin_vector_type &bins) const

float	percent_over_qscore_cumulative (const uint_t qscore, const qscore_bin_vector_type &bins) const

uint_t	median (const qscore_bin_vector_type &bins=qscore_bin_vector_type()) const

bool	is_cumulative_empty () const

void	accumulate (const q_metric &metric)

template<typename T >
void	accumulate_into (std::vector< T > &distribution) const

void	compress (const header_type &header)

uint_t	qscoreHist (const size_t n) const

const uint32_vector &	qscoreHist () 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)

Protected Attributes
uint32_vector	m_qscore_hist

Friends
template<class MetricType , int Version>
struct	io::generic_layout

Detailed Description

Q-score metric

The QMetricsOut.bin InterOp file contains a histogram of the counts of PF clusters at each quality value ranging from 1 to 50 for each lane, tile, and cycle. % >= Q30 is calculated as the sum of the populations in bins with a quality value of 30 or greater divided by the total non-N basecalls (sum of the population over all bins times) 100.

Note: Supported versions: 4, 5, 6 and 7

Test:

Confirm version 4 of the metric can be written to and read from a stream

Confirm version 4 of the metric matches known binary file

Confirm version 5 of the metric can be written to and read from a stream

Confirm version 5 of the metric matches known binary file

Confirm version 6 of the metric can be written to and read from a stream

Confirm version 6 of the metric matches known binary file

Member Typedef Documentation

typedef q_score_header header_type

Q-score metric header

typedef header_type::qscore_bin_vector_type qscore_bin_vector_type

Vector of q-scores type

typedef std::vector< ::uint32_t > uint32_vector

Defines a vector of unsigned 32-bit ints

typedef std::vector< ::uint64_t > uint64_vector

Defines a vector of unsigned 64-bit ints

typedef ::uint32_t* uint_pointer_t

Define a uint pointer to a uint array

typedef std::vector< ::uint32_t > uint_vector

Defines a vector of unsigned 32-bit ints (TODO: remove this def)

Member Enumeration Documentation

anonymous enum

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

anonymous enum

Enumerator
MAX_Q_BINS	Maximum number of q-score bins

Constructor & Destructor Documentation

q_metric ( )

inline

Constructor

q_metric ( const header_type & header )

inline

Constructor

Parameters

header q-metric set header

q_metric	(	const uint_t	lane,
		const uint_t	tile,
		const uint_t	cycle,
		const uint32_vector &	qscore_hist
	)

inline

Constructor

Parameters

lane	lane number
tile	tile number
cycle	cycle number
qscore_hist	q-score histogram

q_metric	(	const uint_t	lane,
		const uint_t	tile,
		const uint_t	cycle,
		const uint_pointer_t	qscore_hist,
		const uint_t	count
	)

inline

Constructor

Parameters

lane	lane number
tile	tile number
cycle	cycle number
qscore_hist	q-score histogram
count	number of elements in the histogram

Member Function Documentation

void accumulate ( const q_metric & metric )

inline

Accumulate q-score histogram from last cycle

This helper function also allocates memory for the cumulative q-score histogram.

Parameters

metric last cycle q-metric

void accumulate_into ( std::vector< T > & distribution ) const

inline

Accumulate q-score histogram into the destination distribution

Parameters

distribution overall distribution

void compress ( const header_type & header )

inline

Compress bins

Parameters

header binned header

static const char* prefix ( )

inlinestatic

Get the prefix of the InterOp filename

Returns: prefix

uint_t qscoreHist ( const size_t n ) const

inline

Q-score value of the histogram

Deprecated:

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

Returns: q-score value of the histogram

const uint32_vector& qscoreHist ( ) const

inline

Q-score histogram

Deprecated:

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

Returns: q-score histogram

void set	(	const uint_t	lane,
		const uint_t	tile,
		const uint_t	cycle,
		const uint32_vector &	qscore_hist
	)

inline

Setter

Parameters

lane	lane number
tile	tile number
cycle	cycle number
qscore_hist	Q-score histogram

Friends And Related Function Documentation

friend struct io::generic_layout

friend

Member Data Documentation

uint32_vector m_qscore_hist

protected

Unsigned int vector for q-score histogram

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

/io/interop/model/metrics/q_metric.h

Public Types

Public Member Functions

Static Public Member Functions

Protected Attributes

Friends

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation