illumina::interop::logic::summary Namespace Reference

Namespaces

 detail
 
 op
 

Classes

class  error_cache_element
 
class  qval_cache
 
struct  qval_total
 
struct  read_cycle
 
class  summary_by_lane_read
 

Typedefs

typedef void(model::summary::cycle_state_summary::* set_cycle_state_func_t) (const model::run::cycle_range &)
 
typedef std::vector< std::vector< model::run::cycle_range > > cycle_range_vector2d_t
 
typedef std::vector< read_cycleread_cycle_vector_t
 

Functions

template<typename Metric >
void summarize_cycle_state (const model::metric_base::metric_set< model::metrics::tile_metric > &tile_metrics, const model::metric_base::metric_set< Metric > &cycle_metrics, const read_cycle_vector_t &cycle_to_read, set_cycle_state_func_t set_cycle_state_fun, model::summary::run_summary &run) INTEROP_THROW_SPEC((model
 
template<typename I >
void cache_error_by_lane_read (I beg, I end, const size_t max_cycle, const std::vector< read_cycle > &cycle_to_read, const constants::tile_naming_method naming_method, summary_by_lane_read< float > &read_lane_cache, summary_by_lane_read< float > &read_lane_surface_cache)
 
void error_summary_from_cache (summary_by_lane_read< float > &read_lane_cache, summary_by_lane_read< float > &read_lane_surface_cache, model::summary::run_summary &run, void(model::summary::stat_summary::*func)(const model::summary::metric_stat &), const bool skip_median=false)
 
template<typename I >
void summarize_error_metrics (I beg, I end, const read_cycle_vector_t &cycle_to_read, const constants::tile_naming_method naming_method, model::summary::run_summary &run, const bool skip_median=false) INTEROP_THROW_SPEC((model
 
template<typename I >
void summarize_extraction_metrics (I beg, I end, const read_cycle_vector_t &cycle_to_read, const size_t channel, const constants::tile_naming_method naming_method, model::summary::run_summary &run, const bool skip_median=false) INTEROP_THROW_SPEC((model
 
template<typename I , typename UnaryOp >
void map_read_to_cycle_number (I beg, I end, read_cycle_vector_t &cycle_to_read, UnaryOp op)
 
template<typename I >
void map_read_to_cycle_number (I beg, I end, read_cycle_vector_t &cycle_to_read)
 
template<class Metric >
void validate_cycle_to_read (const model::metric_base::metric_set< Metric > &set, const summary::read_cycle_vector_t &cycle_to_read)
 
template<typename I >
void summarize_phasing_metrics (I beg, I end, model::summary::run_summary &run, const constants::tile_naming_method naming_method, const bool skip_median=false) INTEROP_THROW_SPEC((model
 
template<typename I >
void summarize_collapsed_quality_metrics (I beg, I end, const read_cycle_vector_t &cycle_to_read, const constants::tile_naming_method naming_method, model::summary::run_summary &run)
 
template<typename I >
void reserve (I beg, I end, const ptrdiff_t n)
 
template<typename I , typename S >
void summarize (I beg, I end, S &stat, const bool skip_median)
 
template<typename I , typename S , typename BinaryOp , typename Compare >
void summarize (I beg, I end, S &stat, BinaryOp op, Compare comp, const bool skip_median)
 
template<typename I , typename S , typename BinaryOp , typename Compare >
size_t nan_summarize (I beg, I end, S &stat, BinaryOp op, Compare comp, const bool skip_median)
 
template<typename I , typename S , typename Op >
nan_accumulate (I beg, I end, const S init, Op op)
 
float divide (const float num, const float div)
 
template<class ExtendedTileVector >
void update_extended_tile_summary_from_cache (std::vector< ExtendedTileVector > &extended_tile_data, model::summary::stat_summary &stat_summary, const bool skip_median)
 
template<class TileVector >
void update_tile_summary_from_cache (std::vector< TileVector > &tile_data, model::summary::stat_summary &stat_summary, const bool skip_median)
 
size_t update_read_summary (summary_by_lane_read< model::metrics::read_metric >::vector_t &read_data_cache, model::summary::stat_summary &stat_summary, const bool skip_median)
 
template<typename I >
void summarize_tile_metrics (I beg, I end, const constants::tile_naming_method naming_method, model::summary::run_summary &run, const bool skip_median=false)
 
template<typename I >
void summarize_extended_tile_metrics (I beg, I end, const constants::tile_naming_method naming_method, model::summary::run_summary &run)
 
void summarize_index_metrics (model::metric_base::metric_set< model::metrics::index_metric > &index_metrics, const model::metric_base::metric_set< model::metrics::tile_metric > &tile_metrics, const size_t lane, model::summary::index_lane_summary &summary)
 
void summarize_index_metrics (model::metrics::run_metrics &metrics, const size_t lane, model::summary::index_lane_summary &summary)
 
void summarize_index_metrics (model::metric_base::metric_set< model::metrics::index_metric > &index_metrics, const model::metric_base::metric_set< model::metrics::tile_metric > &tile_metrics, const size_t lane_count, model::summary::index_flowcell_summary &summary)
 
void summarize_index_metrics (model::metrics::run_metrics &metrics, model::summary::index_flowcell_summary &summary)
 
void summarize_tile_count (const model::metrics::run_metrics &metrics, model::summary::run_summary &summary)
 
void set_run_summary_metric (const model::metrics::summary_run_metric &summary_run, model::summary::metric_summary &summary)
 
void summarize_run_metrics (model::metrics::run_metrics &metrics, model::summary::run_summary &summary, const bool skip_median, const bool trim) INTEROP_THROW_SPEC((model
 

Typedef Documentation

typedef std::vector<std::vector<model::run::cycle_range> > cycle_range_vector2d_t

Vector of vectors of cycle_range objects

typedef std::vector<read_cycle> read_cycle_vector_t

Vector of read_cycle objects

typedef void(model::summary::cycle_state_summary::* set_cycle_state_func_t) (const model::run::cycle_range &)

Define a member function of cycle_state_summary that sets a cycle state

Function Documentation

void illumina::interop::logic::summary::cache_error_by_lane_read ( beg,
end,
const size_t  max_cycle,
const std::vector< read_cycle > &  cycle_to_read,
const constants::tile_naming_method  naming_method,
summary_by_lane_read< float > &  read_lane_cache,
summary_by_lane_read< float > &  read_lane_surface_cache 
)

Cache errors for all tiles up to a give max cycle

This function only includes errors from useable cycles (not the last cycle) to up the given max cycle.

Parameters
begiterator to start of a collection of error metrics
enditerator to end of a collection of error metrics
max_cyclemaximum cycle to take
cycle_to_readmap that takes a cycle and returns the read-number cycle-in-read pair
naming_methodtile naming convention
read_lane_cachedestination cache by read then by lane a collection of errors
read_lane_surface_cachesource cache by read then by lane then by surface a collection of errors
float illumina::interop::logic::summary::divide ( const float  num,
const float  div 
)
inline

Safe divide

Parameters
numnumerator
divdivisor
Returns
result of division
void illumina::interop::logic::summary::error_summary_from_cache ( summary_by_lane_read< float > &  read_lane_cache,
summary_by_lane_read< float > &  read_lane_surface_cache,
model::summary::run_summary run,
void(model::summary::stat_summary::*)(const model::summary::metric_stat &)  func,
const bool  skip_median = false 
)
inline

Calculate summary statistics for each collection of metrics organized by read and lane

Parameters
read_lane_cachesource cache by read then by lane a collection of errors
read_lane_surface_cachesource cache by read then by lane then by surface a collection of errors
rundestination run summary
funcmember function pointer to metric
skip_medianskip the median calculation
void illumina::interop::logic::summary::map_read_to_cycle_number ( beg,
end,
read_cycle_vector_t cycle_to_read,
UnaryOp  op 
)

Create a map from cycle to a pair: read number and cycle in read

Parameters
begiterator to start of a collection of read infos
enditerator to end of a collection of read infos
cycle_to_readmap that takes a cycle and returns the read-number cycle-in-read pair
opunary operator that takes some object and returns a read info
void illumina::interop::logic::summary::map_read_to_cycle_number ( beg,
end,
read_cycle_vector_t cycle_to_read 
)

Create a map from cycle to a pair: read number and cycle in read

Parameters
begiterator to start of a collection of read infos
enditerator to end of a collection of read infos
cycle_to_readmap that takes a cycle and returns the read-number cycle-in-read pair
S illumina::interop::logic::summary::nan_accumulate ( beg,
end,
const S  init,
Op  op 
)

Calculate the sum over a collection of values, ignoring NaNs

Parameters
begiterator to start of collection
enditerator to end of collection
initinitial value for accumulate call
opunary/binary operator for getting a value in a complex object
Returns
sum of init + applying op to the range [beg, end)
size_t illumina::interop::logic::summary::nan_summarize ( beg,
end,
S &  stat,
BinaryOp  op,
Compare  comp,
const bool  skip_median 
)

Calculate the mean, standard deviation (stddev) and median over a collection of values, ignoring NaNs

Parameters
begiterator to start of collection
enditerator to end of collection
statobject to store mean, stddev, and median
opunary/binary operator for getting a value in a complex object
compcomparison operator to compare a single value in a complex object
skip_medianskip the median calculation
Returns
number of non-NaN elements
void illumina::interop::logic::summary::reserve ( beg,
end,
const ptrdiff_t  n 
)

Reserve space in a vector residing in another collection

Parameters
begiterator to start of collection containing vectors
enditerator to end of collection containing vectors
nnumber of elements to reserve
void illumina::interop::logic::summary::set_run_summary_metric ( const model::metrics::summary_run_metric summary_run,
model::summary::metric_summary summary 
)
void illumina::interop::logic::summary::summarize ( beg,
end,
S &  stat,
const bool  skip_median 
)

Calculate the mean, standard deviation (stddev) and median over a collection of values

Parameters
begiterator to start of collection
enditerator to end of collection
statobject to store mean, stddev, and median
skip_medianskip the median calculation
void illumina::interop::logic::summary::summarize ( beg,
end,
S &  stat,
BinaryOp  op,
Compare  comp,
const bool  skip_median 
)

Calculate the mean, standard deviation (stddev) and median over a collection of values

Parameters
begiterator to start of collection
enditerator to end of collection
statobject to store mean, stddev, and median
opunary/binary operator for getting a value in a complex object
compcomparison operator to compare a single value in a complex object
skip_medianskip the median calculation
void illumina::interop::logic::summary::summarize_collapsed_quality_metrics ( beg,
end,
const read_cycle_vector_t cycle_to_read,
const constants::tile_naming_method  naming_method,
model::summary::run_summary run 
)

Summarize a collection collapsed quality metrics

See also
model::summary::lane_summary::percent_gt_q30
model::summary::lane_summary::yield_g
model::summary::lane_summary::projected_yield_g
model::summary::read_summary::percent_gt_q30
model::summary::read_summary::yield_g
model::summary::read_summary::projected_yield_g
model::summary::run_summary::percent_gt_q30
model::summary::run_summary::yield_g
model::summary::run_summary::projected_yield_g
Parameters
begiterator to start of a collection of collapsed q metrics
enditerator to end of a collection of collapsed q metrics
cycle_to_readmap cycle to the read number and cycle within read number
naming_methodtile naming convention
rundestination run summary
void illumina::interop::logic::summary::summarize_cycle_state ( const model::metric_base::metric_set< model::metrics::tile_metric > &  tile_metrics,
const model::metric_base::metric_set< Metric > &  cycle_metrics,
const read_cycle_vector_t cycle_to_read,
set_cycle_state_func_t  set_cycle_state_fun,
model::summary::run_summary run 
)

Summarize the cycle state for a particular metric

Parameters
tile_metricstile metric set
cycle_metricsa cycle based metric set
cycle_to_readmap between the current cycle and read information
set_cycle_state_funcallback to set the cycle state
runrun summary
void illumina::interop::logic::summary::summarize_error_metrics ( beg,
end,
const read_cycle_vector_t cycle_to_read,
const constants::tile_naming_method  naming_method,
model::summary::run_summary run,
const bool  skip_median = false 
)

Summarize a collection error metrics

See also
model::summary::stat_summary::error_rate
model::summary::stat_summary::error_rate_35
model::summary::stat_summary::error_rate_50
model::summary::stat_summary::error_rate_75
model::summary::stat_summary::error_rate_100
model::summary::read_summary::error_rate
model::summary::run_summary::error_rate
Parameters
begiterator to start of a collection of error metrics
enditerator to end of a collection of error metrics
cycle_to_readmap cycle to the read number and cycle within read number
naming_methodtile naming convention
rundestination run summary
skip_medianskip the median calculation
void illumina::interop::logic::summary::summarize_extended_tile_metrics ( beg,
end,
const constants::tile_naming_method  naming_method,
model::summary::run_summary run 
)

Summarize a collection extended tile metrics

Note
This must be called after summarize_tile_metrics!
Parameters
begiterator to start of a collection of extended tile metrics
enditerator to end of a collection of extended tile metrics
naming_methodtile naming convention
rundestination run summary
void illumina::interop::logic::summary::summarize_extraction_metrics ( beg,
end,
const read_cycle_vector_t cycle_to_read,
const size_t  channel,
const constants::tile_naming_method  naming_method,
model::summary::run_summary run,
const bool  skip_median = false 
)

Summarize and aggregate the first_cycle_intensity

See also
model::summary::lane_summary::first_cycle_intensity
model::summary::read_summary::first_cycle_intensity
model::summary::run_summary::first_cycle_intensity
Parameters
begiterator to start of a collection of extraction metrics
enditerator to end of a collection of extraction metrics
cycle_to_readmap cycle to the read number and cycle within read number
channelchannel to use for intensity reporting
naming_methodtile naming convention
rundestination run summary
skip_medianskip the median calculation
void illumina::interop::logic::summary::summarize_index_metrics ( model::metric_base::metric_set< model::metrics::index_metric > &  index_metrics,
const model::metric_base::metric_set< model::metrics::tile_metric > &  tile_metrics,
const size_t  lane,
model::summary::index_lane_summary summary 
)

Summarize a index metrics for a specific lane

Parameters
index_metricsset of index metrics
tile_metricssource collection of tile metrics
lanelane number
summarydestination index flowcell summary
void illumina::interop::logic::summary::summarize_index_metrics ( model::metrics::run_metrics metrics,
const size_t  lane,
model::summary::index_lane_summary summary 
)

Summarize a collection index metrics for a specific lane

Parameters
metricssource run metrics
lanelane number
summarydestination index lane summary
void illumina::interop::logic::summary::summarize_phasing_metrics ( beg,
end,
model::summary::run_summary run,
const constants::tile_naming_method  naming_method,
const bool  skip_median = false 
)

Summarize a collection of phasing metrics

See also
model::summary::lane_summary::phasing_slope
model::summary::lane_summary::phasing_offset
model::summary::lane_summary::prephasing_slope
model::summary::lane_summary::prephasing_offset
Parameters
begiterator to start of a collection of dynamic phasing metrics
enditerator to end of a collection of dynamic phasing metrics
rundestination run summary
naming_methodtile naming convention
skip_medianskip the median calculation
void illumina::interop::logic::summary::summarize_tile_count ( const model::metrics::run_metrics metrics,
model::summary::run_summary summary 
)

Determine maximum number of tiles among all metrics for each lane

Parameters
metricsrun metrics
summaryrun summary
void illumina::interop::logic::summary::summarize_tile_metrics ( beg,
end,
const constants::tile_naming_method  naming_method,
model::summary::run_summary run,
const bool  skip_median = false 
)

Summarize a collection tile metrics

See also
model::summary::lane_summary::density
model::summary::lane_summary::density_pf
model::summary::lane_summary::cluster_count
model::summary::lane_summary::cluster_count_pf
model::summary::lane_summary::percent_pf
model::summary::lane_summary::reads
model::summary::lane_summary::reads_pf
model::summary::lane_summary::percent_aligned
model::summary::lane_summary::prephasing
model::summary::lane_summary::phasing
model::summary::read_summary::percent_aligned
model::summary::run_summary::percent_aligned
Parameters
begiterator to start of a collection of tile metrics
enditerator to end of a collection of tile metrics
naming_methodtile naming convention
rundestination run summary
skip_medianskip the median calculation
void illumina::interop::logic::summary::update_extended_tile_summary_from_cache ( std::vector< ExtendedTileVector > &  extended_tile_data,
model::summary::stat_summary stat_summary,
const bool  skip_median 
)

Use the cached data to update a stat summary

Parameters
extended_tile_datacached tile data
stat_summarydestination stat summary to update
skip_medianskip the median calculation
size_t illumina::interop::logic::summary::update_read_summary ( summary_by_lane_read< model::metrics::read_metric >::vector_t &  read_data_cache,
model::summary::stat_summary stat_summary,
const bool  skip_median 
)
inline

Update the stat summary with cached read metrics

Parameters
read_data_cacheread metric cache
stat_summarystat summary
skip_medianskip the median calculation
Returns
number of non-NaN aligned entries
void illumina::interop::logic::summary::update_tile_summary_from_cache ( std::vector< TileVector > &  tile_data,
model::summary::stat_summary stat_summary,
const bool  skip_median 
)

Use the cached data to update a stat summary

Parameters
tile_datacached tile data
stat_summarydestination stat summary to update
skip_medianskip the median calculation
void illumina::interop::logic::summary::validate_cycle_to_read ( const model::metric_base::metric_set< Metric > &  set,
const summary::read_cycle_vector_t cycle_to_read 
)

Validate that the cycle to read matches the metric set

Template Parameters
Metric
Parameters
setmetric set
cycle_to_readcycle to read map