#include <q_collapsed_metric.h>

Inheritance diagram for q_collapsed_metric:

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

typedef ::uint64_t ulong_t

typedef q_collapsed_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
q_collapsed_metric ()

q_collapsed_metric (const header_type &)

q_collapsed_metric (const uint_t lane, const uint_t tile, const uint_t cycle, const uint_t q20, const uint_t q30, const uint_t total, const uint_t median_qscore)

uint_t q20 () const

uint_t q30 () const

uint_t total () const

uint_t median_qscore () const

float median_qscore_flt () const

ulong_t cumulative_q20 () const

ulong_t cumulative_q30 () const

ulong_t cumulative_total () const

float percent_over_q20 () const

float percent_over_q30 () const

float cumulative_percent_over_q20 () const

float cumulative_percent_over_q30 () const

void accumulate (const q_collapsed_metric &metric)

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 const char * suffix ()

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

Pre-calculated Q20 and Q30 counts for each tile/cycle

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

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_collapsed_header header_type

Q-score metric header

typedef ::uint64_t ulong_t

Define a unsigned long 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_collapsed_metric ( )

inline

Constructor

q_collapsed_metric ( const header_type & )

inline

Constructor

q_collapsed_metric	(	const uint_t	lane,
		const uint_t	tile,
		const uint_t	cycle,
		const uint_t	q20,
		const uint_t	q30,
		const uint_t	total,
		const uint_t	median_qscore
	)

inline

Constructor

Parameters

lane	lane number
tile	tile number
cycle	cycle number
q20	Q20 cluster count
q30	Q30 cluster count
total	total clusters
median_qscore	median q-score

Member Function Documentation

void accumulate ( const q_collapsed_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

static const char* prefix ( )

inlinestatic

Get the prefix of the InterOp filename

Returns: prefix

static const char* suffix ( )

inlinestatic

Get the suffix of the InterOp filename

Returns: suffix

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/q_collapsed_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