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// Author: David Alexander
#pragma once
#include <list>
#include <string>
#include <utility>
#include <vector>
#include <ConsensusCore/Types.hpp>
#include <ConsensusCore/Utils.hpp>
namespace ConsensusCore {
enum Move
{
INVALID_MOVE = 0x0,
INCORPORATE = 0x1,
EXTRA = 0x2,
DELETE = 0x4,
MERGE = 0x8,
BASIC_MOVES = (INCORPORATE | EXTRA | DELETE),
ALL_MOVES = (BASIC_MOVES | MERGE)
};
/// \brief The banding optimizations to be used by a recursor
struct BandingOptions
{
float ScoreDiff;
BandingOptions(int, float scoreDiff) : ScoreDiff(scoreDiff) {}
BandingOptions(int, float scoreDiff, float, float) : ScoreDiff(scoreDiff) {}
};
/// \brief A parameter vector for analysis using the QV model
struct QvModelParams
{
std::string ChemistryName;
std::string ModelName;
float Match;
float Mismatch;
float MismatchS;
float Branch;
float BranchS;
float DeletionN;
float DeletionWithTag;
float DeletionWithTagS;
float Nce;
float NceS;
float Merge[4];
float MergeS[4];
//
// Constructor for single merge rate and merge rate slope
//
QvModelParams(const std::string& ChemistryName_, const std::string& ModelName_, float Match_,
float Mismatch_, float MismatchS_, float Branch_, float BranchS_,
float DeletionN_, float DeletionWithTag_, float DeletionWithTagS_, float Nce_,
float NceS_, float Merge_, float MergeS_)
: ChemistryName(ChemistryName_)
, ModelName(ModelName_)
, Match(Match_)
, Mismatch(Mismatch_)
, MismatchS(MismatchS_)
, Branch(Branch_)
, BranchS(BranchS_)
, DeletionN(DeletionN_)
, DeletionWithTag(DeletionWithTag_)
, DeletionWithTagS(DeletionWithTagS_)
, Nce(Nce_)
, NceS(NceS_)
{
for (int base = 0; base < 4; base++) {
this->Merge[base] = Merge_;
this->MergeS[base] = MergeS_;
}
}
//
// Constructor for per-channel merge rate and merge rate slope
//
QvModelParams(const std::string& ChemistryName_, const std::string& ModelName_, float Match_,
float Mismatch_, float MismatchS_, float Branch_, float BranchS_,
float DeletionN_, float DeletionWithTag_, float DeletionWithTagS_, float Nce_,
float NceS_, float Merge_A_, float Merge_C_, float Merge_G_, float Merge_T_,
float MergeS_A_, float MergeS_C_, float MergeS_G_, float MergeS_T_)
: ChemistryName(ChemistryName_)
, ModelName(ModelName_)
, Match(Match_)
, Mismatch(Mismatch_)
, MismatchS(MismatchS_)
, Branch(Branch_)
, BranchS(BranchS_)
, DeletionN(DeletionN_)
, DeletionWithTag(DeletionWithTag_)
, DeletionWithTagS(DeletionWithTagS_)
, Nce(Nce_)
, NceS(NceS_)
{
this->Merge[0] = Merge_A_;
this->Merge[1] = Merge_C_;
this->Merge[2] = Merge_G_;
this->Merge[3] = Merge_T_;
this->MergeS[0] = MergeS_A_;
this->MergeS[1] = MergeS_C_;
this->MergeS[2] = MergeS_G_;
this->MergeS[3] = MergeS_T_;
}
// Access to the array-stored params
float Merge_A() const { return this->Merge[0]; }
float Merge_C() const { return this->Merge[1]; }
float Merge_G() const { return this->Merge[2]; }
float Merge_T() const { return this->Merge[3]; }
float MergeS_A() const { return this->MergeS[0]; }
float MergeS_C() const { return this->MergeS[1]; }
float MergeS_G() const { return this->MergeS[2]; }
float MergeS_T() const { return this->MergeS[3]; }
};
struct QuiverConfig
{
QvModelParams QvParams;
int MovesAvailable;
BandingOptions Banding;
float FastScoreThreshold;
float AddThreshold;
QuiverConfig(const QvModelParams& qvParams, int movesAvailable,
const BandingOptions& bandingOptions, float fastScoreThreshold,
float addThreshold = 1.0f);
QuiverConfig(const QuiverConfig& qvConfig);
};
class QuiverConfigTable
{
private:
typedef std::pair<const std::string, const QuiverConfig> QuiverConfigTableEntry;
private:
std::list<QuiverConfigTableEntry> table;
bool InsertAs_(const std::string& name, const QuiverConfig& config);
public:
typedef std::list<QuiverConfigTableEntry>::const_iterator const_iterator;
QuiverConfigTable();
// Insert as the default config (when a read's chemistry is not found.
bool InsertDefault(const QuiverConfig& config);
// Insert, using the chemistry found in the config.
bool Insert(const QuiverConfig& config);
// Insert, aliasing as a different chemistry name. This is
// important, for example, when a read presents itself as
// "XL-C2" but we have no trained models for "XL-C2", so we
// want to have At("XL-C2") fetch the config for a similar
// chemistry.
bool InsertAs(const std::string& name, const QuiverConfig& config);
int Size() const;
const QuiverConfig& At(const std::string& name) const;
std::vector<std::string> Keys() const;
#ifndef SWIG
const_iterator begin() const;
const_iterator end() const;
#endif
};
}
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