enums.h File Reference
#include <climits>
#include <limits>
#include <string>
#include "interop/util/cstdint.h"

Go to the source code of this file.

Namespaces

 illumina
 
 illumina::interop
 
 illumina::interop::constants
 

Macros

#define INTEROP_UNKNOWN   0x800
 
#define INTEROP_ENUM_METRIC_FEATURE_TYPE
 
#define INTEROP_ENUM_METRIC_TYPES
 
#define INTEROP_ENUM_METRIC_GROUPS
 
#define INTEROP_ENUM_METRIC_DATA_TYPES
 
#define INTEROP_ENUM_TILE_NAMING_METHODS
 
#define INTEROP_ENUM_DNA_BASE_TYPES
 
#define INTEROP_ENUM_SURFACE_TYPES
 
#define INTEROP_ENUM_INSTRUMENT_TYPES
 
#define INTEROP_ENUM_METRIC_BASE_TYPES
 
#define INTEROP_ENUM_PLOT_COLORS
 
#define INTEROP_ENUM_PLOT_TYPES
 
#define INTEROP_ENUM_BAR_PLOT_OPTIONS
 
#define INTEROP_TUPLE7(X, Unused1, Unused2, Unused3, Unused4, Unused5, Unused6)   X,
 
#define INTEROP_TUPLE4(X, Y, Z, A)   X,
 
#define INTEROP_TUPLE3(X, Y, Z)   X
 
#define INTEROP_TUPLE1(X)   X
 
#define INTEROP_TUPLE2(X, V)   X
 
#define INTEROP_TUPLE_ASSIGN(X, V)   X=V
 

Enumerations

enum  common { Unknown = 0x800 }
 
enum  metric_type {
  Intensity, FWHM, BasePercent, PercentNoCall,
  Q20Percent, Q30Percent, AccumPercentQ20, AccumPercentQ30,
  QScore, Clusters, ClustersPF, ClusterCount,
  ClusterCountPF, ErrorRate, PercentPhasing, PercentPrephasing,
  PercentAligned, Phasing, PrePhasing, CorrectedIntensity,
  CalledIntensity, SignalToNoise, OccupiedCountK, PercentOccupied,
  PercentPF, MetricTypeCount, UnknownMetricType = 0x800
}
 
enum  metric_group {
  CorrectedInt, Error, Extraction, Image,
  Index, Q, Tile, QByLane,
  QCollapsed, EmpiricalPhasing, DynamicPhasing, ExtendedTile,
  SummaryRun, MetricCount, UnknownMetricGroup = 0x800
}
 
enum  tile_naming_method {
  FourDigit, FiveDigit, Absolute, TileNamingMethodCount,
  UnknownTileNamingMethod = 0x800
}
 
enum  dna_bases {
  NC = -1, A, C, G,
  T, NUM_OF_BASES, NUM_OF_BASES_AND_NC, UnknownBase = 0x800
}
 
enum  surface_type { SentinelSurface, Top, Bottom, UnknownSurface = 0x800 }
 
enum  instrument_type {
  HiSeq, HiScan, MiSeq, NextSeq,
  MiniSeq, NovaSeq, iSeq, NextSeq1k2k,
  InstrumentCount, UnknownInstrument = 0x800
}
 
enum  metric_base_type {
  BaseTileType, BaseCycleType, BaseReadType, BaseLaneType,
  BaseRunType, BaseMetricCount, UnknownBaseType = 0x800
}
 
enum  plot_colors {
  Red, Green, Blue, Black,
  PlotColorCount, UnknownColor = 0x800
}
 
enum  bar_plot_options { Centered, Shifted, UnknownBarPlotOption = 0x800 }
 
enum  metric_data {
  IdType, ValueType, StructType, ChannelArray,
  BaseArray, MetricDataCount, UnknownMetricData = 0x800
}
 
enum  metric_feature_type {
  TileFeature = 0x01, CycleFeature = 0x02, ReadFeature = 0x04, BaseFeature = 0x08,
  ChannelFeature = 0x10, LaneFeature = 0x20, DiskFeature = 0x400, UnknownMetricFeature = 0x800
}
 
enum  plot_types {
  FlowcellPlot, ByCyclePlot, ByLanePlot, QHistogramPlot,
  QHeatmapPlot, SampleQCPlot, UnknownPlotType = 0x800
}
 

Detailed Description

Enumeration constants used throughout InterOp

Date
9/27/15
Version
1.0

Macro Definition Documentation

#define INTEROP_ENUM_BAR_PLOT_OPTIONS
Value:
\
INTEROP_TUPLE1(Centered), \\
INTEROP_TUPLE1(Shifted), \
INTEROP_TUPLE1(UnknownBarPlotOption)

Enumeration of bar plot options

Note
This macro requires the macro INTEROP_TUPLE1 to be defined before use
See also
illumina::interop::constants::bar_plot_options
#define INTEROP_ENUM_DNA_BASE_TYPES
Value:
\
INTEROP_TUPLE_ASSIGN(NC, -1), \ \
INTEROP_TUPLE1(A), \ \
INTEROP_TUPLE1(C), \ \
INTEROP_TUPLE1(G), \ \
INTEROP_TUPLE1(T), \ \
INTEROP_TUPLE1(NUM_OF_BASES), \ \
INTEROP_TUPLE1(NUM_OF_BASES_AND_NC), \ \
INTEROP_TUPLE1(UnknownBase)
Definition: enums.h:301
Definition: enums.h:301
Definition: enums.h:301
Definition: enums.h:301
Definition: enums.h:301

Enumeration of DNA bases

Note
This macro requires the macro INTEROP_TUPLE1 to be defined before use
This macro requires the macro INTEROP_TUPLE_ASSIGN to be defined before use
See also
illumina::interop::constants::dna_bases
#define INTEROP_ENUM_INSTRUMENT_TYPES
Value:
INTEROP_TUPLE1(HiScan), \
INTEROP_TUPLE1(MiSeq), \
INTEROP_TUPLE1(NextSeq), \
INTEROP_TUPLE1(MiniSeq), \
INTEROP_TUPLE1(NovaSeq), \
INTEROP_TUPLE1(iSeq), \
INTEROP_TUPLE1(NextSeq1k2k), \
INTEROP_TUPLE1(InstrumentCount), \
INTEROP_TUPLE1(UnknownInstrument)
Definition: enums.h:311
#define INTEROP_TUPLE1(X)
Definition: enums.h:260

Enumeration of instrument types

Note
This macro requires the macro INTEROP_TUPLE1 to be defined before use
See also
illumina::interop::constants::instrument_type
#define INTEROP_ENUM_METRIC_BASE_TYPES
Value:
\
INTEROP_TUPLE1(BaseTileType),\\
INTEROP_TUPLE1(BaseCycleType),\\
INTEROP_TUPLE1(BaseReadType),\\
INTEROP_TUPLE1(BaseLaneType),\\
INTEROP_TUPLE1(BaseRunType), \
INTEROP_TUPLE1(BaseMetricCount),\
INTEROP_TUPLE1(UnknownBaseType)

Enumeration of metric types

Note
This macro requires the macro INTEROP_TUPLE1 to be defined before use
See also
illumina::interop::constants::metric_base_type
#define INTEROP_ENUM_METRIC_DATA_TYPES
Value:
INTEROP_TUPLE1(ValueType),\
INTEROP_TUPLE1(StructType),\
INTEROP_TUPLE1(ChannelArray),\
INTEROP_TUPLE1(BaseArray),\
INTEROP_TUPLE1(MetricDataCount),\
INTEROP_TUPLE1(UnknownMetricData)
#define INTEROP_TUPLE1(X)
Definition: enums.h:260

Enumeration of each metric data type

Note
This macro requires the macro INTEROP_TUPLE1 to be defined before use
See also
illumina::interop::constants::metric_data
#define INTEROP_ENUM_METRIC_FEATURE_TYPE
Value:
INTEROP_TUPLE_ASSIGN(CycleFeature, 0x02), \
INTEROP_TUPLE_ASSIGN(ReadFeature, 0x04), \
INTEROP_TUPLE_ASSIGN(BaseFeature, 0x08), \
INTEROP_TUPLE_ASSIGN(ChannelFeature, 0x10), \
INTEROP_TUPLE_ASSIGN(LaneFeature, 0x20), \
INTEROP_TUPLE_ASSIGN(DiskFeature, 0x400), \
INTEROP_TUPLE1(UnknownMetricFeature)
#define INTEROP_TUPLE_ASSIGN(X, V)
Definition: enums.h:264

Enumeration of specific features that can belong to a metric

Note
This macro requires the macro INTEROP_TUPLE_ASSIGN to be defined before use
This macro requires the macro INTEROP_TUPLE1 to be defined before use
See also
illumina::interop::constants::metric_feature_type
#define INTEROP_ENUM_METRIC_GROUPS
Value:
INTEROP_TUPLE2(Error, CycleFeature|DiskFeature), \
INTEROP_TUPLE2(Index, ReadFeature|DiskFeature), \
INTEROP_TUPLE2(Q, CycleFeature|DiskFeature), \
INTEROP_TUPLE2(Tile, TileFeature|DiskFeature), \
INTEROP_TUPLE2(QByLane, LaneFeature), \
INTEROP_TUPLE2(QCollapsed, CycleFeature), \
INTEROP_TUPLE2(DynamicPhasing, CycleFeature), \
INTEROP_TUPLE2(ExtendedTile, TileFeature|DiskFeature), \
INTEROP_TUPLE2(SummaryRun, DiskFeature), \
INTEROP_TUPLE1(MetricCount),\
INTEROP_TUPLE1(UnknownMetricGroup)
Definition: enums.h:291
Definition: enums.h:291
#define INTEROP_TUPLE2(X, V)
Definition: enums.h:262

Enumeration of each metric group

Note
This macro requires the macro INTEROP_TUPLE2 to be defined before use
This macro requires the macro INTEROP_TUPLE1 to be defined before use
See also
illumina::interop::constants::metric_group
#define INTEROP_ENUM_METRIC_TYPES
Value:
INTEROP_TUPLE7(Intensity, "Intensity", Extraction, CycleFeature|ChannelFeature, extraction_metric, max_intensity, channel)\
INTEROP_TUPLE7(FWHM, "FWHM", Extraction, CycleFeature|ChannelFeature, extraction_metric, focus_score, channel)\
INTEROP_TUPLE7(BasePercent, "% Base", CorrectedInt, CycleFeature|BaseFeature, corrected_intensity_metric, percent_base, base)\
INTEROP_TUPLE7(PercentNoCall, "% NoCall", CorrectedInt, CycleFeature, corrected_intensity_metric, percent_nocall, Void)\
INTEROP_TUPLE7(Q20Percent, "% >=Q20", Q, CycleFeature, q_collapsed_metric, percent_over_q20, Void)\
INTEROP_TUPLE7(Q30Percent, "% >=Q30", Q, CycleFeature, q_collapsed_metric, percent_over_q30, Void)\
INTEROP_TUPLE7(AccumPercentQ20, "% >=Q20 (Accumulated)", Q, CycleFeature, q_collapsed_metric, cumulative_percent_over_q20, Void)\
INTEROP_TUPLE7(AccumPercentQ30, "% >=Q30 (Accumulated)", Q, CycleFeature, q_collapsed_metric, cumulative_percent_over_q30, Void)\
INTEROP_TUPLE7(QScore, "Median QScore", Q, CycleFeature, q_collapsed_metric, median_qscore_flt, Void)\
INTEROP_TUPLE7(Clusters, "Density", Tile, TileFeature, tile_metric, cluster_density_k, Void)\
INTEROP_TUPLE7(ClustersPF, "Density PF", Tile, TileFeature, tile_metric, cluster_density_pf_k, Void)\
INTEROP_TUPLE7(ClusterCount, "Cluster Count", Tile, TileFeature, tile_metric, cluster_count_m, Void)\
INTEROP_TUPLE7(ClusterCountPF, "Clusters PF", Tile, TileFeature, tile_metric, cluster_count_pf_m, Void)\
INTEROP_TUPLE7(ErrorRate, "Error Rate", Error, CycleFeature, error_metric, error_rate, Void)\
INTEROP_TUPLE7(PercentPhasing, "Legacy Phasing Rate", Tile, ReadFeature, tile_metric, percent_phasing_at, read)\
INTEROP_TUPLE7(PercentPrephasing, "Legacy Prephasing Rate", Tile, ReadFeature, tile_metric, percent_prephasing_at, read)\
INTEROP_TUPLE7(PercentAligned, "% Aligned", Tile, ReadFeature, tile_metric, percent_aligned_at, read)\
INTEROP_TUPLE7(Phasing, "Phasing Weight", EmpiricalPhasing, CycleFeature, phasing_metric, phasing_weight, Void)\
INTEROP_TUPLE7(PrePhasing, "Prephasing Weight", EmpiricalPhasing, CycleFeature, phasing_metric, prephasing_weight, Void)\
INTEROP_TUPLE7(CorrectedIntensity, "Corrected Int", CorrectedInt, CycleFeature|BaseFeature, corrected_intensity_metric, corrected_int_all_float, base)\
INTEROP_TUPLE7(CalledIntensity, "Called Int", CorrectedInt, CycleFeature|BaseFeature, corrected_intensity_metric, corrected_int_called, base)\
INTEROP_TUPLE7(SignalToNoise, "Signal to Noise", CorrectedInt, CycleFeature, corrected_intensity_metric, signal_to_noise, Void)\
INTEROP_TUPLE7(OccupiedCountK, "Occupied Count (K)", ExtendedTile, TileFeature, extended_tile_metric, cluster_count_occupied_k, Void)\
INTEROP_TUPLE7(PercentOccupied, "% Occupied", ExtendedTile, TileFeature, extended_tile_metric, percent_occupied, Void)\
INTEROP_TUPLE7(PercentPF, "% PF", Tile, TileFeature, tile_metric, percent_pf, Void)\
INTEROP_TUPLE4(MetricTypeCount, "!!!!BAD!!!!", UnknownMetricGroup, UnknownMetricFeature)\
INTEROP_TUPLE1(UnknownMetricType)
Definition: enums.h:291
def read(run, valid_to_load=None, requires=None, search_paths=None, extra)
Definition: core.py:752
Definition: enums.h:286
Definition: enums.h:291
#define INTEROP_TUPLE7(X, Unused1, Unused2, Unused3, Unused4, Unused5, Unused6)
Definition: enums.h:254

Enumeration of each metric type

Note
This macro requires the macro INTEROP_TUPLE1, INTEROP_TUPLE4, INTEROP_TUPLE7 to be defined before use
See also
illumina::interop::constants::metric_type
#define INTEROP_ENUM_PLOT_COLORS
Value:
\
INTEROP_TUPLE1(Red), /*#FF0000*/\\
INTEROP_TUPLE1(Green), /*#00FF00*/\\
INTEROP_TUPLE1(Blue), /*#0000FF*/\\
INTEROP_TUPLE1(Black), /*#000000*/\
INTEROP_TUPLE1(PlotColorCount), \
INTEROP_TUPLE1(UnknownColor)
Definition: enums.h:321
Definition: enums.h:321

Enumeration of channel colors (assuming expected order)

Note
This macro requires the macro INTEROP_TUPLE1 to be defined before use
See also
illumina::interop::constants::plot_colors
#define INTEROP_ENUM_PLOT_TYPES
Value:
\
INTEROP_TUPLE1(FlowcellPlot),\\
INTEROP_TUPLE1(ByCyclePlot),\\
INTEROP_TUPLE1(ByLanePlot),\\
INTEROP_TUPLE1(QHistogramPlot),\\
INTEROP_TUPLE1(QHeatmapPlot),\\
INTEROP_TUPLE1(SampleQCPlot),\\
INTEROP_TUPLE1(UnknownPlotType)

Enumeration of plot types

Note
This macro requires the macro INTEROP_TUPLE1 to be defined before use
See also
illumina::interop::constants::plot_types
#define INTEROP_ENUM_SURFACE_TYPES
Value:
INTEROP_TUPLE1(Top), \
INTEROP_TUPLE1(Bottom), \
INTEROP_TUPLE1(UnknownSurface)
#define INTEROP_TUPLE1(X)
Definition: enums.h:260
Definition: enums.h:306

Enumeration of surface types

Note
This macro requires the macro INTEROP_TUPLE1 to be defined before use
See also
illumina::interop::constants::surface_type
#define INTEROP_ENUM_TILE_NAMING_METHODS
Value:
\
INTEROP_TUPLE1(FourDigit), \\
INTEROP_TUPLE1(FiveDigit), \\
INTEROP_TUPLE1(Absolute), \\
INTEROP_TUPLE1(TileNamingMethodCount), \
INTEROP_TUPLE1(UnknownTileNamingMethod)

Enumeration of tile naming methods

Note
This macro requires the macro INTEROP_TUPLE1 to be defined before use
See also
illumina::interop::constants::tile_naming_method
#define INTEROP_TUPLE1 (   X)    X

This temp macro converts an enum to an enum

#define INTEROP_TUPLE2 (   X,
 
)    X

This temp macro converts an enum/value pair to an enum

#define INTEROP_TUPLE3 (   X,
  Y,
 
)    X

This temp macro converts a enum/description pair into the an enum (first element of the pair)

#define INTEROP_TUPLE4 (   X,
  Y,
  Z,
 
)    X,

This temp macro converts a enum/description pair into the an enum (first element of the pair)

#define INTEROP_TUPLE7 (   X,
  Unused1,
  Unused2,
  Unused3,
  Unused4,
  Unused5,
  Unused6 
)    X,

This temp macro converts a enum/description pair into the an enum (first element of the pair)

#define INTEROP_TUPLE_ASSIGN (   X,
 
)    X=V

This temp macro converts an enum/value pair to an enum

#define INTEROP_UNKNOWN   0x800

Sentinel for an unknown enum type