/usr/include/pbdata/PacBioDefs.h is in libpbdata-dev 0~20151014+gitbe5d1bf-2.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 | // Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
//
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted (subject to the limitations in the
// disclaimer below) provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
//
// * Neither the name of Pacific Biosciences nor the names of its
// contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
// SUCH DAMAGE.
// 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";
///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";
///PulseData/BaseCalls/ZMWMetrics/HQRegionSNR
static const std::string hqregionsnr = "HQRegionSNR";
static const std::string readscore = "ReadScore";
static const std::string productivity = "Productivity";
static const std::vector<std::string> BaxQVNames ({
deletionqv,
deletiontag,
insertionqv,
mergeqv,
substitutionqv,
substitutiontag,
prebaseframes,
widthinframes,
hqregionsnr,
readscore});
} // namespace GroupNames
namespace AttributeNames {
namespace Common {
static const std::string changelistid = "ChangeListID";
static const std::string description = "Description";
} // 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 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 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 = "ACGT"; // default, order matters!
}
} // ScanData
} // namespace AttributeValues
} // namespace PacBio
#endif
|