#include <q_by_lane_metric.h>

Inheritance diagram for q_by_lane_metric:

Public Types
enum	{ TYPE = constants::QByLane, LATEST_VERSION = 6 }

typedef constants::base_lane_t	base_t

Public Types inherited from q_metric
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_by_lane_metric ()

	q_by_lane_metric (const header_type &header)

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

void	accumulate_by_lane (const q_metric &metric)

Public Member Functions inherited from q_metric
	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 *	suffix ()

Static Public Member Functions inherited from q_metric
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)

Additional Inherited Members
Protected Attributes inherited from q_metric
uint32_vector	m_qscore_hist

Detailed Description

Total histogram by lane

Member Typedef Documentation

typedef constants::base_lane_t base_t

Define the base type

Member Enumeration Documentation

anonymous enum

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

Constructor & Destructor Documentation

q_by_lane_metric ( )

inline

Constructor

q_by_lane_metric ( const header_type & header )

inline

Constructor

Parameters

header header of q-metric set

q_by_lane_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

Member Function Documentation

void accumulate_by_lane ( const q_metric & metric )

inline

Accummulate another q_metric from the same lane/cycle

Parameters

metric q_metric from same lane/cycle

static const char* suffix ( )

inlinestatic

Get the suffix of the InterOp filename

Returns: suffix

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

/io/interop/model/metrics/q_by_lane_metric.h

Public Types

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation