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/*
* Copyright (c) Medical Research Council 2002. All rights reserved.
*
* Permission to use, copy, modify and distribute this software and its
* documentation for any purpose is hereby granted without fee, provided that
* this copyright and notice appears in all copies.
*
* This file was written as part of the Staden Package at the MRC Laboratory
* of Molecular Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
*
* MRC disclaims all warranties with regard to this software.
*
*/
#include <cassert>
#include <cmath> // For std::log10()
#include <cstring> // For std::memset()
#include <algorithm> // For std::max()
#include <dnatable.hpp>
#include <caller_base.hpp>
void BaseCaller::Init()
{
m_nPeakRatio = 0.0;
m_nConfidence = 0.0;
for( int n=0; n<3; n++ )
m_nCall[n] = '-';
for( int n=0; n<2; n++ )
{
m_nPosition[n] = -1;
m_nAmplitude[n] = 0;
}
}
void BaseCaller::MakeCall( Trace& Tr, SimpleMatrix<int>& Peak, int nPos, int nAmbiguityWindow )
{
assert(nPos>=0);
assert(nAmbiguityWindow>0);
call_t Signal[4];
// Initialisation
Init();
// m_nPosition[2] = nPos; jkb 25/06/2003. What should this be?
// Search for peaks and load them in
int peaks = LoadPeaks( Peak, nPos, nAmbiguityWindow, Signal );
// Find biggest peaks position
if( peaks > 0 )
{
int max_sig = 0;
int max_amp = -1;
for( int n=3; n>=0; n-- )
{
if( Signal[n].Position >= 0 )
{
if( Signal[n].Amplitude > max_amp )
{
max_sig = n;
max_amp = Signal[n].Amplitude;
}
}
}
nPos = Signal[max_sig].Position;
}
// Load trace amplitudes for peakless bases
for( int n=0; n<4; n++ )
{
if( Signal[n].Position < 0 )
Signal[n].Amplitude = Tr[n][nPos];
}
// Sort the entire lot by amplitude
SortAscending( Signal );
// Basecall single peak
DNATable Table;
if( peaks == 1 )
{
for( int n=3; n>=0; n-- )
{
if( Signal[n].Position >= 0 )
{
m_nCall[0] = Table.LookupBase( Signal[n].Index );
m_nCall[1] = m_nCall[0];
m_nPosition[0] = Signal[n].Position;
m_nAmplitude[0] = Signal[n].Amplitude;
}
}
}
// Basecall multiple peaks
else if( peaks >= 2 )
{
call_t highest_signal;
int highest_signal_n;
highest_signal.Index = -1;
for( int n=3; n>=0; n-- )
{
if( Signal[n].Position >= 0 )
{
if( highest_signal.Index < 0 )
{
highest_signal = Signal[n];
highest_signal_n = n;
}
else
{
m_nCall[0] = Table.LookupBase( highest_signal.Index, Signal[n].Index );
m_nCall[1] = Table.LookupBase( highest_signal.Index );
m_nCall[2] = Table.LookupBase( Signal[n].Index );
m_nPosition[0] = highest_signal.Position;
m_nAmplitude[0] = highest_signal.Amplitude;
m_nPosition[1] = Signal[n].Position;
m_nAmplitude[1] = Signal[n].Amplitude;
}
}
}
}
// Compute confidence value, just SNR(db) = 20*log(S/N)
double S = Signal[3].Amplitude;
double N = Signal[2].Amplitude;
if( N <= 0.0 )
N = 1.0;
m_nPeakRatio = S / N;
m_nConfidence = m_nPeakRatio
? 20.0 * std::log10( m_nPeakRatio )
: 0;
}
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