/usr/include/pbseq/pbdata/PacBioDefs.h is in libpbdata-dev 0~20161219-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 | // Author: Yuan Li
#ifndef _PBDATA_PACBIO_DEFS_H_
#define _PBDATA_PACBIO_DEFS_H_
#include <string>
#include <vector>
namespace PacBio {
namespace GroupNames {
///PulseData
static const std::string pulsedata = "PulseData";
///PulseData/BaseCalls
static const std::string basecalls = "BaseCalls";
///PulseData/Regions
static const std::string regions = "Regions";
///PulseData/BaseCalls/BaseCall
static const std::string basecall = "Basecall";
static const std::string qualityvalue = "QualityValue";
static const std::string deletionqv = "DeletionQV";
static const std::string deletiontag = "DeletionTag";
static const std::string insertionqv = "InsertionQV";
static const std::string mergeqv = "MergeQV";
static const std::string substitutionqv = "SubstitutionQV";
static const std::string substitutiontag = "SubstitutionTag";
static const std::string prebaseframes = "PreBaseFrames";
static const std::string widthinframes = "WidthInFrames";
static const std::string pulseindex = "PulseIndex";
///PulseData/BaseCalls/ZMW
static const std::string zmw = "ZMW";
static const std::string zmwmetrics = "ZMWMetrics";
///PulseData/BaseCalls/ZMW/HoleNumber
static const std::string holenumber = "HoleNumber";
static const std::string holestatus = "HoleStatus";
static const std::string holexy = "HoleXY";
static const std::string numevent = "NumEvent";
static const std::string baselinesigma = "BaselineSigma";
static const std::string baselinelevel = "BaselineLevel";
static const std::string signallevel = "SignalLevel";
static const std::string signalsigma = "SignalSigma";
///PulseData/BaseCalls/ZMWMetrics/HQRegionSNR
static const std::string hqregionsnr = "HQRegionSNR";
static const std::string readscore = "ReadScore";
static const std::string productivity = "Productivity";
///PulseData/PulseCalls/*
static const std::string pulsecalls = "PulseCalls";
static const std::string channel = "Channel";
static const std::string ispulse = "IsPulse";
static const std::string labelqv = "LabelQV";
static const std::string meansignal = "MeanSignal";
static const std::string midsignal = "MidSignal";
static const std::string maxsignal = "MaxSignal";
static const std::string startframe = "StartFrame";
static const std::string altlabel = "AltLabel";
static const std::string altlabelqv = "AltLabelQV";
static const std::string chi2 = "Chi2";
static const std::string midstddev = "MidStdDev";
} // namespace Group
namespace AttributeNames {
namespace Common {
static const std::string changelistid = "ChangeListID";
static const std::string description = "Description";
static const std::string content = "Content";
static const std::string contentstored = "ContentStored";
static const std::string datacreated = "DataCreated";
static const std::string schemarevision = "SchemaRevision";
} // Common
namespace ZMW {
namespace HoleStatus {
static const std::string lookuptable = "LookupTable";
}
}
namespace Regions {
static const std::string columnnames = "ColumnNames";
static const std::string regiontypes = "RegionTypes";
static const std::string regiondescriptions = "RegionDescriptions";
static const std::string regionsources = "RegionSources";
} // Regions
namespace ScanData {
namespace DyeSet {
static const std::string basemap = "BaseMap";
}
} // ScanData
} // namespace AttributeNames
namespace AttributeValues {
namespace Common {
static const std::string schemarevision = "1.1";
}
namespace ZMW {
namespace HoleNumber {
static const std::string description = "Hole number on chip array";
} //namespace HoleNumber
namespace HoleStatus {
static const std::string description = "Type of data coming from ZMW";
static const std::vector<std::string> lookuptable =
{"SEQUENCING", "ANTIHOLE", "FIDUCIAL", "SUSPECT",
"ANTIMIRROR", "FDZMW", "FBZMW", "ANTIBEAMLET", "OUTSIDEFOV"};
static const unsigned char sequencingzmw = 0; // not '0'
static const unsigned char outsidefov = 8; // not '8'
} // namespace HoleStatus
namespace HoleXY {
static const std::string description = "Coordinates of ZMW on Chip";
} // namespace HoleXY
namespace BaseLineSigma {
static const std::string description = "Estimated baseline sigma (std dev) over trace";
} // namespace BaseLineSigma
} // namespace ZMW
namespace Regions {
static const std::vector<std::string> columnnames =
{"HoleNumber", "Region type index", "Region start in bases",
"Region end in bases", "Region score"};
static const std::vector<std::string> regiontypes =
{"Adapter", "Insert", "HQRegion"};
static const std::vector<std::string> regiondescriptions =
{"Adapter Hit", "Insert Region",
"High Quality bases region. Score is 1000 * predicted accuracy, where predicted accuary is 0 to 1.0"};
static const std::vector<std::string> regionsources =
{"AdapterFinding", "AdapterFinding", "PulseToBase Region classifer"};
}
namespace ZMWMetrics {
namespace HQRegionSNR {
static const std::string description = "HQRegion average signal to noise ratio";
}
namespace ReadScore {
static const std::string description = "Read raw accuracy prediction";
}
namespace Productivity {
static const std::string description = "ZMW productivity classification";
}
} // ZMWMetrics
namespace ScanData {
namespace DyeSet {
static const std::string basemap = "TGCA"; // default, order matters!
}
} // ScanData
} // namespace AttributeValues
} // namespace PacBio
#endif
|