Member base_metric::phyiscalLocationColumn (const illumina::interop::constants::tile_naming_method method, const uint_t swath_count, const bool all_surfaces) const

Will be removed in 1.1.x (use phyiscal_location_column instead)

Parameters

method	the tile naming method
swath_count	number of swaths
all_surfaces	layout all surfaces of the flowcell

Returns: column of the physical location within the flowcell

Member base_metric::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

Will be removed in 1.1.x (use physical_location_index instead)

Parameters

method	the tile naming method
section_per_lane	number of sections per lane
tile_count	number of tiles
swath_count	number of swaths
all_surfaces	layout all surfaces of the flowcell

Returns: index of the physical location within the flowcell

Member base_metric::phyiscalLocationRow (const illumina::interop::constants::tile_naming_method method, const uint_t section_per_lane, const uint_t tile_count) const

Will be removed in 1.1.x (use phyiscal_location_row instead)

Parameters

method	the tile naming method
section_per_lane	number of sections per lane (number of cameras that cover the lane)
tile_count	number of tiles

Returns: row of the physical location within the flowcell

Member corrected_intensity_metric::averageCycleIntensity () const

Will be removed in 1.1.x (use average_cycle_intensity instead)

Note: Supported version 2, not supported by 3 or later

Returns: average intensity

Member corrected_intensity_metric::calledCounts () const

Will be removed in 1.1.x (use called_counts_array instead)

Returns: vector of called counts

Member corrected_intensity_metric::calledCounts (difference_type index) const

Will be removed in 1.1.x (use called_counts instead)

Note: Supported by all versions

Parameters

index index of the base (NC=-1, A=0, C=1, G=2, T=3)

Returns: number of clusters called per base

Member corrected_intensity_metric::correctedIntAll () const

Will be removed in 1.1.x (use corrected_int_all_array instead)

Note: Supported version 2, not supported by 3 or later

Returns: vector of corrected called intensities

Member corrected_intensity_metric::correctedIntAll (size_t index) const

Will be removed in 1.1.x (use corrected_int_all instead)

Note: Supported version 2, not supported by 3 or later

Parameters

index index of the base (A=0, C=1, G=2, T=3)

Returns: average corrected intensity for specified base

Member corrected_intensity_metric::correctedIntCalled (size_t index) const

Will be removed in 1.1.x (use corrected_int_called instead)

Note: Supported by all versions

Parameters

index index of the base (A=0, C=1, G=2, T=3)

Returns: average corrected intensity over only base called clusters

Member corrected_intensity_metric::correctedIntCalled () const

Will be removed in 1.1.x (use corrected_int_called_array instead)

Returns: vector of corrected called intensities

Member corrected_intensity_metric::noCalls () const

Will be removed in 1.1.x (use no_calls instead)

Note: Supported by all versions

Returns: number of clusters not called

Member corrected_intensity_metric::percentBase (difference_type index) const

Will be removed in 1.1.x (use percent_base instead)

Note: Supported by all versions

Parameters

index index of the base (NC=-1, A=0, C=1, G=2, T=3)

Returns: percentage for given base

Member corrected_intensity_metric::percentCalledIntensity (const size_t index) const

Will be removed in 1.1.x

Note: Supported by all versions

Parameters

index index of the base (A=0, C=1, G=2, T=3)

Returns: percentage of intensity for each base

Member corrected_intensity_metric::percentIntensity (size_t index) const

Will be removed in 1.1.x

Note: Supported version 2, not supported by 3 or later

Parameters

index index of the base (A=0, C=1, G=2, T=3)

Returns: percentage of intensity for each base

Member corrected_intensity_metric::signalToNoise () const

Will be removed in 1.1.x (use signal_to_noise instead)

Note: Only supported by version 2, not supported by version 3 or later

Returns: signal to noise calculated from mean called intensity

Member corrected_intensity_metric::totalCalledIntensity () const

Will be removed in 1.1.x (use total_called_intensity instead)

Note: Supported by all versions

Returns: total summed intensity

Member corrected_intensity_metric::totalCalls (const bool nocalls=false) const

Will be removed in 1.1.x (use total_calls instead)

Note: Supported by all versions

Returns: total number of clusters called

Member corrected_intensity_metric::totalIntensity () const

Will be removed in 1.1.x (use total_intensity instead)

Note: Supported version 2, not supported by 3 or later

Returns: total summed intensity

Member data_point_collection< Point >::at (const size_t index) const INTEROP_THROW_SPEC((model

Will be removed in next feature version (use operator[] instead for C++ Code)

Parameters

index index of point

Returns: data point

Member error_metric::errorRate () const

Will be removed in 1.1.x (use error_rate instead)

Note: Supported by all versions

Returns: error rate

Member extraction_metric::dateTime () const

Will be removed in 1.1.x (use date_time instead)

Returns: date time code

Member extraction_metric::focusScore (size_t channel) const

Will be removed in 1.1.x (use focus_score instead)

Parameters

channel channel index

Returns: focus metric as measured by FWHM

Member extraction_metric::focusScores () const

Will be removed in 1.1.x (use focus_scores instead)

Returns: vector of focus scores

Member heatmap_data::at (const size_t idx) const INTEROP_THROW_SPEC((model

Will be removed in next feature version (use operator[] instead for C++ Code)

Parameters

idx index

Returns: value

Member heatmap_data::at (const size_t row, const size_t col) const INTEROP_THROW_SPEC((model

Will be removed in next feature version (use operator() instead for C++ Code)

Parameters

row	row index
col	column index

Returns: value

Member image_metric::channelCount () const

Will be removed in 1.1.x (use channel_count instead)

Returns: number of channels

Member image_metric::maxContrast (size_t channel) const

Will be removed in 1.1.x (use max_contrast instead)

Returns: maximum contrast intensity

Member image_metric::maxContrast () const

Will be removed in 1.1.x (use max_contrast_array instead)

Returns: maximum contrast intensity

Member image_metric::minContrast (size_t channel) const

Will be removed in 1.1.x (use min_contrast instead)

Returns: minimum contrast intensity

Member image_metric::minContrast () const

Will be removed in 1.1.x (use min_contrast_array instead)

Returns: minimum contrast intensity

Member image_metric_header::channelCount () const

Use channel_count() instead

Returns: number of channels

Member index_flowcell_summary::at (const size_type n) const INTEROP_THROW_SPEC((model

Will be removed in next feature version (use operator[] instead for C++ Code)

Parameters

n index

Returns: constant reference to lane summary

Member index_flowcell_summary::at (const size_t n) INTEROP_THROW_SPEC((model

Will be removed in next feature version (use operator[] instead for C++ Code)

Parameters

n index

Returns: reference to lane summary

Member index_lane_summary::at (const size_t n) INTEROP_THROW_SPEC((model

Will be removed in next feature version (use operator[] instead for C++ Code)

Parameters

n index

Returns: reference to lane summary

Member index_lane_summary::at (const size_type n) const INTEROP_THROW_SPEC((model

Will be removed in next feature version (use operator[] instead for C++ Code)

Parameters

n index

Returns: constant reference to lane summary

Member lane_summary::at (const size_type n) const INTEROP_THROW_SPEC((model

Will be removed in next feature version (use operator[] instead for C++ Code)

Parameters

n index

Returns: constant reference to lane_summary

Member lane_summary::at (const size_t n) INTEROP_THROW_SPEC((model

Will be removed in next feature version (use operator[] instead for C++ Code)

Parameters

n index

Returns: reference to lane_summary

Member metric_set< T >::at (const size_t n) const INTEROP_THROW_SPEC((model

Will be removed in next feature version (use operator[] instead for C++ Code)

Parameters

n index

Returns: metric

Member metric_set< T >::at (const size_t n) INTEROP_THROW_SPEC((model

Will be removed in next feature version (use operator[] instead for C++ Code)

Parameters

n index

Returns: metric

Member plot_data< Point >::at (const size_t index) const INTEROP_THROW_SPEC((model

Will be removed in next feature version (use operator[] instead for C++ Code)

Parameters

index index of point

Returns: data point

Member q_metric::percent_over_qscore (const uint_t qscore_index, const qscore_bin_vector_type &bins) const

This function will be removed in a future version.

Parameters

qscore_index	index of the q-score (for unbinned 29 is Q30)
bins	q-score histogram bins

Returns: percent of cluster over the given q-score

Member q_metric::percent_over_qscore_cumulative (const uint_t qscore, const qscore_bin_vector_type &bins) const

This function will be removed in a future version.

Parameters

qscore	percentage of clusters over the given q-score value
bins	q-score histogram bins

Returns: percent of cluster over the given q-score

Member q_metric::qscoreHist () const

Will be removed in 1.1.x (use qscore_hist instead)

Returns: q-score histogram

Member q_metric::qscoreHist (const size_t n) const

Will be removed in 1.1.x (use qscore_hist instead)

Returns: q-score value of the histogram

Member q_metric::total_over_qscore (const uint_t qscore, const qscore_bin_vector_type &bins) const

This function is deprecated in future versions

Parameters

qscore	percentage of clusters over the given q-score value
bins	q-score histogram bins

Returns: total of clusters over the given q-score

Member q_metric::total_over_qscore_cumulative (const uint_t qscore, const qscore_bin_vector_type &bins) const

This function will be removed in future versions

Parameters

qscore	percentage of clusters over the given q-score value
bins	q-score histogram bins

Returns: total of clusters over the given q-score

Member q_score_header::binAt (const size_t n) const

Will be removed in 1.1.x (use bin_at instead)

Returns: q-score bin

Member q_score_header::binCount () const

Will be removed in 1.1.x (use bin_count instead)

Returns: number of bins in header

Member read_summary::at (const size_type n) const INTEROP_THROW_SPEC((model

Will be removed in next feature version (use operator[] instead for C++ Code)

Parameters

n index

Returns: constant reference to lane_summary

Member read_summary::at (const size_type n) INTEROP_THROW_SPEC((model

Will be removed in next feature version (use operator[] instead for C++ Code)

Parameters

n index

Returns: reference to lane_summary

Member run_summary::at (const size_type n) const INTEROP_THROW_SPEC((model

Will be removed in next feature version (use operator[] instead for C++ Code)

Parameters

n index

Returns: constant reference to read_summary

Member run_summary::at (const size_t n) INTEROP_THROW_SPEC((model

Will be removed in next feature version (use operator[] instead for C++ Code)

Parameters

n index

Returns: reference to read_summary

Member tile_metric::clusterCount () const

Will be removed in 1.1.x (use cluster_count instead)

Returns: number of clusters

Member tile_metric::clusterCountPf () const

Will be removed in 1.1.x (use cluster_count_pf instead)

Returns: number of clusters passing filter

Member tile_metric::clusterDensity () const

Will be removed in 1.1.x (use cluster_density instead)

Returns: cluster density

Member tile_metric::clusterDensityPf () const

Will be removed in 1.1.x (use cluster_density_pf instead)

Returns: cluster density passing filter