#include <index_metric.h>

Inheritance diagram for index_metric:

Public Types
enum { TYPE = constants::Index, LATEST_VERSION = 2 }

typedef index_metric_header header_type

typedef std::vector< index_info > index_array_t

typedef index_info index_info_t

typedef index_array_t::const_iterator const_iterator

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
index_metric ()

index_metric (const header_type &)

index_metric (uint_t lane, uint_t tile, uint_t read, const index_array_t &indices)

size_t size () const

const index_info & indices (const size_t n) const INTEROP_THROW_SPEC((model

const index_array_t & indices () const

const_iterator begin () const

const_iterator end () const

float cluster_count () const

float cluster_count_pf () const

void set_cluster_counts (const float cluster_count, const float cluster_count_pf)

float percent_demultiplexed (const std::string &sample_id) 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

Index metric

The index metric holds string information describing the indexes used in the run.

Note: Supported versions: 1 and 2

Test:

Confirm version 1 of the metric can be written to and read from a stream

Confirm version 1 of the metric matches known binary file

Member Typedef Documentation

typedef index_array_t::const_iterator const_iterator

Define a constant iterator

typedef index_metric_header header_type

Index metric header

typedef std::vector<index_info> index_array_t

Define a index array using an underlying vector

typedef index_info index_info_t

Define index info type

Member Enumeration Documentation

anonymous enum

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

Constructor & Destructor Documentation

index_metric ( )

inline

Constructor

index_metric ( const header_type & )

inline

Constructor

index_metric	(	uint_t	lane,
		uint_t	tile,
		uint_t	read,
		const index_array_t &	indices
	)

inline

Constructor

Parameters

lane	lane number
tile	tile number
read	read number
indices	array of indexes

Member Function Documentation

const_iterator begin ( ) const

inline

Get iterator to start of indices

Returns: iterator to start of indices

float cluster_count ( ) const

inline

Number of clusters for each tile

Note: Derived from tile_metric using populate_indices in run_metrics::finalize_after_load

Returns: number of clusters

float cluster_count_pf ( ) const

inline

Number of clusters passing filter for each tile

Note: Derived from tile_metric using populate_indices in run_metrics::finalize_after_load

Returns: number of clusters passing filter

const_iterator end ( ) const

inline

Get iterator to end of indices

Returns: iterator to end of indices

float percent_demultiplexed ( const std::string & sample_id ) const

inline

Percentage of PF clusters on the tile that have been demultiplexed

Dependent on tile_metric

Returns: percent of demultiplexed PF clusters

static const char* prefix ( )

inlinestatic

Get the prefix of the InterOp filename

Returns: "Index"

void set_cluster_counts	(	const float	cluster_count,
		const float	cluster_count_pf
	)

inline

Set the cluster counds dervied from tile_metric

Parameters

cluster_count	number of clusters
cluster_count_pf	number of PF clusters

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/index_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