#include <extended_tile_metric.h>

Inheritance diagram for extended_tile_metric:
base_metric empty_metric

Public Types

enum  { TYPE = constants::ExtendedTile, LATEST_VERSION = 3 }
 
- 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

 extended_tile_metric ()
 
 extended_tile_metric (const header_type &)
 
 extended_tile_metric (const uint_t lane, const uint_t tile, const float occupied, const point2d &upper_left=point2d())
 
void set (const uint_t lane, const uint_t tile, const float occupied, const point2d &upper_left=point2d())
 
float cluster_count_occupied () const
 
float cluster_count_occupied_k () const
 
float percent_occupied () const
 
const point2dupper_left () const
 
void set_cluster_count_k (const float cluster_count_k)
 
- 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_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

Extended tile metric

The extended tile metric reports tile metrics such as the occupancy aka number of empty wells on a tile.

Note
Supported versions: 2 and 3
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 Enumeration Documentation

anonymous enum
Enumerator
TYPE 

Unique type code for metric

LATEST_VERSION 

Latest version of the InterOp format

Constructor & Destructor Documentation

Constructor

extended_tile_metric ( const header_type )
inline

Constructor

extended_tile_metric ( const uint_t  lane,
const uint_t  tile,
const float  occupied,
const point2d upper_left = point2d() 
)
inline

Constructor

Parameters
lanelane number
tiletile number
occupiednumber of occupied wells
upper_leftcoordinate of upper left fiducial

Member Function Documentation

static const char* prefix ( )
inlinestatic

Get the prefix of the InterOp filename

Returns
"ExtendedTile"
void set ( const uint_t  lane,
const uint_t  tile,
const float  occupied,
const point2d upper_left = point2d() 
)
inline

Setter

Note
Version 1 and 2
Parameters
lanelane number
tiletile number
occupiednumber of occupied wells
upper_leftcoordinate of upper left fiducial
void set_cluster_count_k ( const float  cluster_count_k)
inline

Set the cluster count in kilo bases

Derived from tile_metric using populate_percent_occupied in run_metrics::finalize_after_load

Parameters
cluster_count_kcluster count in kilo bases

Friends And Related Function Documentation

friend struct io::generic_layout
friend

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