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// Author: David Alexander
#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 <ConsensusCore/Features.hpp>
#include <ConsensusCore/Quiver/QuiverConfig.hpp>
#include <ConsensusCore/Quiver/detail/SseMath.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 {
//
// Utility functions
//
static inline int encodeTplBase(char base)
{
switch (base) {
case 'A':
return 0;
case 'C':
return 1;
case 'G':
return 2;
case 'T':
return 3;
case 'M':
return 4; // For testing
case 'N':
return 5; // For testing
default:
ShouldNotReachHere();
}
}
//
// Evaluator classes
//
/// \brief An Evaluator that can compute move scores using a QvSequenceFeatures
class QvEvaluator
{
public:
typedef QvSequenceFeatures FeaturesType;
typedef QvModelParams ParamsType;
public:
QvEvaluator(const Read& read, const std::string& tpl, const QvModelParams& params,
bool pinStart = true, bool pinEnd = true)
: read_(read), params_(params), tpl_(tpl), pinStart_(pinStart), pinEnd_(pinEnd)
{
}
~QvEvaluator() {}
std::string ReadName() const { return read_.Name; }
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()[i] == tpl_[j]);
}
float Inc(int i, int j) const
{
assert(0 <= j && j < TemplateLength() && 0 <= i && i < ReadLength());
return (IsMatch(i, j)) ? params_.Match
: params_.Mismatch + params_.MismatchS * Features().SubsQv[i];
}
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 tplBase = tpl_[j];
return (i < ReadLength() && tplBase == Features().DelTag[i])
? params_.DeletionWithTag + params_.DeletionWithTagS * Features().DelQv[i]
: params_.DeletionN;
}
}
float Extra(int i, int j) const
{
assert(0 <= j && j <= TemplateLength() && 0 <= i && i < ReadLength());
return (j < TemplateLength() && IsMatch(i, j))
? params_.Branch + params_.BranchS * Features().InsQv[i]
: params_.Nce + params_.NceS * Features().InsQv[i];
}
float Merge(int i, int j) const
{
assert(0 <= j && j < TemplateLength() - 1 && 0 <= i && i < ReadLength());
if (!(Features()[i] == tpl_[j] && Features()[i] == tpl_[j + 1])) {
return -FLT_MAX;
} else {
int tplBase = encodeTplBase(tpl_[j]);
return params_.Merge[tplBase] + params_.MergeS[tplBase] * Features().MergeQv[i];
}
}
//
// SSE
//
__m128 Inc4(int i, int j) const
{
assert(0 <= i && i <= ReadLength() - 4);
assert(0 <= j && j < TemplateLength());
float tplBase = tpl_[j];
__m128 match = _mm_set_ps1(params_.Match);
__m128 mismatch = AFFINE4(params_.Mismatch, params_.MismatchS, &Features().SubsQv[i]);
// Mask to see it the base is equal to the template
__m128 mask =
_mm_cmpeq_ps(_mm_loadu_ps(&Features().SequenceAsFloat[i]), _mm_set_ps1(tplBase));
return MUX4(mask, match, mismatch);
}
__m128 Del4(int i, int j) const
{
assert(0 <= i && i <= ReadLength());
assert(0 <= j && j < TemplateLength());
if (i != 0 && i + 3 != ReadLength()) {
float tplBase = tpl_[j];
__m128 delWTag =
AFFINE4(params_.DeletionWithTag, params_.DeletionWithTagS, &Features().DelQv[i]);
__m128 delNoTag = _mm_set_ps1(params_.DeletionN);
__m128 mask = _mm_cmpeq_ps(_mm_loadu_ps(&Features().DelTag[i]), _mm_set_ps1(tplBase));
return MUX4(mask, delWTag, delNoTag);
} else {
// Have to do PinStart/PinEnd logic, and weird
// logic for last row. Punt.
__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
{
assert(0 <= i && i <= ReadLength() - 4);
assert(0 <= j && j <= TemplateLength());
if (i != 0 && i + 3 != ReadLength()) {
float tplBase = tpl_[j];
__m128 branch = AFFINE4(params_.Branch, params_.BranchS, &Features().InsQv[i]);
__m128 nce = AFFINE4(params_.Nce, params_.NceS, &Features().InsQv[i]);
__m128 mask =
_mm_cmpeq_ps(_mm_loadu_ps(&Features().SequenceAsFloat[i]), _mm_set_ps1(tplBase));
return MUX4(mask, branch, nce);
} else {
__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
{
assert(0 <= i && i <= ReadLength() - 4);
assert(0 <= j && j < TemplateLength() - 1);
float tplBase = tpl_[j];
float tplBaseNext = tpl_[j + 1];
int tplBase_ = encodeTplBase(tpl_[j]);
__m128 merge =
AFFINE4(params_.Merge[tplBase_], params_.MergeS[tplBase_], &Features().MergeQv[i]);
__m128 noMerge = _mm_set_ps1(-FLT_MAX);
if (tplBase == tplBaseNext) {
__m128 mask =
_mm_cmpeq_ps(_mm_loadu_ps(&Features().SequenceAsFloat[i]), _mm_set_ps1(tplBase));
return MUX4(mask, merge, noMerge);
} else {
return noMerge;
}
}
protected:
inline const QvSequenceFeatures& Features() const { return read_.Features; }
protected:
Read read_;
QvModelParams params_;
std::string tpl_;
bool pinStart_;
bool pinEnd_;
};
}
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