#include <dynamic_phasing_metric.h>

Inheritance diagram for dynamic_phasing_metric:

Public Types
enum { TYPE = constants::DynamicPhasing, LATEST_VERSION = 1 }

Public Types inherited from base_read_metric
typedef base_read_metric_header header_type

typedef constants::base_read_t base_t

typedef uint8_t read_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
dynamic_phasing_metric ()

dynamic_phasing_metric (const header_type &)

dynamic_phasing_metric (const uint_t lane, const uint_t tile, const uint_t read, const float phasing_slope, const float phasing_offset, const float prephasing_slope, const float prephasing_offset)

float phasing_slope () const

float prephasing_slope () const

float phasing_offset () const

float prephasing_offset () const

Public Member Functions inherited from base_read_metric
base_read_metric (const uint_t lane, const uint_t tile, const uint_t read)

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 read)

template<class BaseReadMetric >
void	set_base (const BaseReadMetric &base)

uint_t read () const

id_t id () const

bool operator< (const base_read_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_read_metric
static id_t create_id (const id_t lane, const id_t tile, const id_t read)

static id_t read_from_id (const id_t id)

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

Dynamic phasing metric

The dynamic phasing metric contains the estimated phasing and prephasing slope/offsets learned for each tile and read.

Note: This is not actually an InterOp written to disk, but is calculated from EmpiricalPhasingMetricsOut.bin; Supported versions: 1

Member Enumeration Documentation

anonymous enum

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

Constructor & Destructor Documentation

dynamic_phasing_metric ( )

inline

Constructor

dynamic_phasing_metric ( const header_type & )

inline

Constructor

dynamic_phasing_metric	(	const uint_t	lane,
		const uint_t	tile,
		const uint_t	read,
		const float	phasing_slope,
		const float	phasing_offset,
		const float	prephasing_slope,
		const float	prephasing_offset
	)

inline

Constructor

Parameters

lane	lane number
tile	tile number
read	read number
phasing_slope	phasing slope for current read
phasing_offset	phasing offset for current read
prephasing_slope	prephasing slope for current read
prephasing_offset	prephasing offset for current read

Member Function Documentation

static const char* prefix ( )

inlinestatic

Get the prefix of the InterOp filename

Returns: "DynamicPhasing"

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/dynamic_phasing_metric.h

Public Types

Public Member Functions

Static Public Member Functions

Friends

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation