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#ifndef _LOADPULSES_METRICFIELD_HPP_
#define _LOADPULSES_METRICFIELD_HPP_
#include <cstdlib>
#include <iostream>
#include <string>
#include <vector>
#include <pbdata/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 std::string & metric, FieldType & field){
FieldsRequirement(const std::string &m);
};
#endif
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