/usr/include/pbdata/loadpulses/MetricField.hpp 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 | #ifndef _LOADPULSES_METRICFIELD_HPP_
#define _LOADPULSES_METRICFIELD_HPP_
#include <iostream>
#include <string>
#include <vector>
#include <stdlib.h>
#include "Types.h"
enum FieldType {BasField, PlsField};
class Field {
public:
std::string name;
FieldType type;
Field(std::string n, FieldType t);
bool operator == (const Field &another) const;
};
class FieldsRequirement {
public:
std::string metric;
std::vector<Field> fieldsUseBasFile;
std::vector<Field> fieldsUsePlsFile;
// Return fields that are required for computing this metric.
// Eighteen metrics are supported in total.
// [1/18] metric requires only an attribute (not a field):
// WhenStarted
//
// [9/18] metrics require exactly one BaseCall field
// QualityValue InsertionQV MergeQV DeletionQV
// DeletionTag SubstitutionTag SubstitutionQV PreBaseFrames
// PulseIndex
//
// [4/18] metrics require more than one field and can be computed using
// only one method:
// BaseCall PulseCall
// ----------------------------------------------------
// ClassifierQV PulseIndex NumEvent
// ClassifierQV
// ----------------------------------------------------
// pkmid PulseIndex NumEvent
// MidSignal
// ----------------------------------------------------
// Light PulseIndex NumEvent
// WidthInFrames
// MeanSignal
// ----------------------------------------------------
// StartTimeOffset PulseIndex NumEvent
// StartFrame
// ----------------------------------------------------
// [4/18] metrics can be computed from both BaseCalls and PulseCalls.
// But sometimes the value computed from BaseCalls can be wrong,
// because the value of BaseCalls/PreBaseFrames may exceed 2^16-1.
// Method BaseCall PulseCall
// ----------------------------------------------------
// PulseWidth (1) WidthInFrames
// =======================================
// (2) PulseIndex NumEvent
// WidthInFrames
// ----------------------------------------------------
// WidthInFrames : The same as PulseWidth
// ----------------------------------------------------
// StartFrame (1) PreBaseFrames
// WidthInFrames
// =======================================
// (2) PulseIndex NumEvent
// StartFrame
// ----------------------------------------------------
// IPD (1) PreBaseFrames
// =======================================
// (2) PulseIndex NumEvent
// StartFrame
// WidthInFrames
// ----------------------------------------------------
// Note: PulseWidth and WidthInFrames have the same meaning and are
// computed in the same way.
//
// Note: StartFrame can be loaded for both bas.h5 and pls.h5 files
// for bas.h5, StartFrame is computed from PreBaseFrames and WidthInFrames
// Let x = PreBaseFrames for bases 0 ... n-1, where x[0] is 0 and
// x[i] is the inter-pulse distance between start of pulse
// for base i and end of pulse for base i-1
// Let y = WidthInFrames for bases 0 ... n-1, where y[i] is the
// number of pulses within base i
// Then,
// StartFrame[0] = x[0]
// StartFrame[i] = sum(x[0] ... x[i]) + sum(y[0] ... y[i-1])
// for i in [1 ... n-1]
// for pls.h5, StartFrame can be directly read from dataset
// /PulseData/PulseCalls/StartFrame
//
// Note: StartTimeOffset is the StartFrame for the very first base of a read, it
// can only be computed from PulseCalls
//
// Note: IPD has the same meaning as PreBaseFrames:
// = the inter-pulse distance between this base and end of last base,
// = the number of Frames between the ending pulse of the last base and
// the starting pulse of this base.
// However, PreBaseFrames can only be read directly from BaseCalls, while
// IPD can also be computed from PulseCalls
// If use BaseCalls,
// IPD[i] = PreBaseFrames[i] for i in [0 ... n-1]
// If use PulseCalls,
// IPD[0] = 0
// IPD[i] = StartFrame[i] - StartFrame[i-1] - WidthInFrames[i-1]
// for i in [1 ... n-1]
//
//void GetRequiredFieldsForMetric(const string & metric, FieldType & field){
FieldsRequirement(const std::string & m);
};
#endif
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