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// Author: Patrick Marks
#pragma once
#define SIMDE_ENABLE_NATIVE_ALIASES
#include <simde/x86/sse3.h>
#include <algorithm>
#include <cassert>
#include <cfloat>
#include <climits>
#include <cmath>
#include <iostream>
#include <string>
#include <utility>
#include <vector>
#include <ConsensusCore/Edna/EdnaConfig.hpp>
#include <ConsensusCore/Features.hpp>
#include <ConsensusCore/LFloat.hpp>
#include <ConsensusCore/Read.hpp>
#include <ConsensusCore/Types.hpp>
#include <ConsensusCore/Utils.hpp>
#ifndef SWIG
using std::min;
using std::max;
#endif // SWIG
#define NEG_INF -FLT_MAX
namespace ConsensusCore {
/// \brief An Evaluator for the Edna Edna model
class EdnaEvaluator
{
public:
typedef ChannelSequenceFeatures FeaturesType;
typedef EdnaModelParams ParamsType;
public:
EdnaEvaluator(const ChannelSequenceFeatures& features, const std::string& tpl,
const std::vector<int> channelTpl, const EdnaModelParams& params)
: features_(features)
, params_(params)
, tpl_(tpl)
, channelTpl_(&(channelTpl[0]), tpl_.length())
, pinStart_(true)
, pinEnd_(true)
{
}
~EdnaEvaluator() {}
std::string ReadName() const { return "(anonymous)"; }
std::string Basecalls() const { return features_.Sequence(); }
std::string Template() const { return tpl_; }
void Template(std::string tpl) { tpl_ = tpl; }
int ReadLength() const { return features_.Length(); }
int TemplateLength() const { return tpl_.length(); }
bool PinEnd() const { return pinEnd_; }
bool PinStart() const { return pinStart_; }
bool IsMatch(int i, int j) const
{
assert(0 <= i && i < ReadLength());
assert(0 <= j && j < TemplateLength());
return (features_.Channel[i] == channelTpl_[j]);
}
bool mergeable(int j) const
{
if (j < TemplateLength() - 1 && channelTpl_[j] == channelTpl_[j + 1]) return true;
return false;
}
int templateBase(int j) const
{
if (j >= TemplateLength()) return 1;
return channelTpl_[j];
}
float pStay(int j) const { return params_.pStay_[templateBase(j) - 1]; }
float pMerge(int j) const
{
if (mergeable(j)) return params_.pMerge_[templateBase(j) - 1];
return 0.0;
}
float moveDist(int obs, int j) const
{
int tplBase = templateBase(j) - 1;
return params_.moveDists_[tplBase * 5 + obs];
}
float stayDist(int obs, int j) const
{
int tplBase = templateBase(j) - 1;
return params_.stayDists_[tplBase * 5 + obs];
}
float Inc(int i, int j) const
{
assert(0 <= j && j < TemplateLength() && 0 <= i && i < ReadLength());
float ps = pStay(j);
float pm = (1.0f - ps) * pMerge(j);
float trans = 1.0f - ps - pm;
float em = moveDist(features_.Channel[i], j);
return log(trans * em);
}
float Del(int i, int j) const
{
assert(0 <= j && j < TemplateLength() && 0 <= i && i <= ReadLength());
if ((!PinStart() && i == 0) || (!PinEnd() && i == ReadLength())) {
return 0.0f;
} else {
float ps = pStay(j);
float pm = (1.0f - ps) * pMerge(j);
float trans = 1.0f - ps - pm;
float em = moveDist(0, j);
return log(trans * em);
}
}
float Extra(int i, int j) const
{
assert(0 <= j && j <= TemplateLength() && 0 <= i && i < ReadLength());
float trans = pStay(j);
float em = stayDist(features_.Channel[i], j);
return log(trans * em);
}
float Merge(int i, int j) const
{
assert(0 <= j && j < TemplateLength() - 1 && 0 <= i && i < ReadLength());
if (!(features_.Channel[i] == channelTpl_[j] &&
features_.Channel[i] == channelTpl_[j + 1])) {
return -FLT_MAX;
} else {
float ps = pStay(j);
float pm = (1.0f - ps) * pMerge(j);
return log(pm);
}
}
float ScoreMove(int j1, int j2, int obs)
{
if (j1 == j2) {
float trans = pStay(j1);
float em = stayDist(obs, j1);
return log(trans * em);
} else if (j1 + 1 == j2) {
float ps = pStay(j1);
float pm = (1.0f - ps) * pMerge(j1);
float trans = 1.0f - ps - pm;
float em = moveDist(obs, j1);
return log(trans * em);
} else if (j1 + 2 == j2) {
float ps = pStay(j1);
float pm = (1.0f - ps) * pMerge(j1);
if (obs == templateBase(j1))
return log(pm);
else
return NEG_INF;
}
return NEG_INF;
}
float Burst(int, int, int) const
{
NotYetImplemented();
return NEG_INF;
}
//
// SSE
//
__m128 Inc4(int i, int j) const
{
__m128 res = _mm_setr_ps(Inc(i + 0, j), Inc(i + 1, j), Inc(i + 2, j), Inc(i + 3, j));
return res;
}
__m128 Del4(int i, int j) const
{
__m128 res = _mm_setr_ps(Del(i + 0, j), Del(i + 1, j), Del(i + 2, j), Del(i + 3, j));
return res;
}
__m128 Extra4(int i, int j) const
{
__m128 res =
_mm_setr_ps(Extra(i + 0, j), Extra(i + 1, j), Extra(i + 2, j), Extra(i + 3, j));
return res;
}
__m128 Merge4(int i, int j) const
{
__m128 res =
_mm_setr_ps(Merge(i + 0, j), Merge(i + 1, j), Merge(i + 2, j), Merge(i + 3, j));
return res;
}
__m128 Burst4(int, int, int) const
{
NotYetImplemented();
return Zero4<lfloat>();
}
protected:
ChannelSequenceFeatures features_;
EdnaModelParams params_;
std::string tpl_;
Feature<int> channelTpl_;
bool pinStart_;
bool pinEnd_;
};
}
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