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#ifndef __KSW2_ALIGNER_HPP__
#define __KSW2_ALIGNER_HPP__
#include <memory>
#include <vector>
#include <cstdlib>
extern "C" {
#include "ksw2pp/kalloc.h"
#include "ksw2pp/ksw2.h"
}
namespace ksw2pp {
/**
* When we use a unique_ptr to hold a kalloc allocator, this is the
* deleter we use to call the appropriate function to free / destroy the
*allocator.
**/
class KallocDeleter {
public:
void operator()(void* p) { km_destroy(p); }
};
enum class KSW2AlignmentType : uint8_t { GLOBAL = 1, EXTENSION = 2 };
// Just like Int2Type from
// https://en.wikibooks.org/wiki/More_C%2B%2B_Idioms/Int-To-Type
template <KSW2AlignmentType I> struct EnumToType {
enum { value = static_cast<uint8_t>(I) };
};
// A structure to hold the relvant parameters for the aligner
struct KSW2Config {
int8_t gapo = -1;
int8_t gape = -1;
int bandwidth = -1;
int dropoff = -1;
int flag = 0;
int alphabetSize = 5;
int end_bonus = 10;
KSW2AlignmentType atype = KSW2AlignmentType::EXTENSION;
};
class KSW2Aligner {
public:
KSW2Aligner(int8_t match = 2, int8_t mismatch = -4);
KSW2Aligner(std::vector<int8_t> mat);
int transformSequenceKSW2(const char* const queryOriginal, const int queryLength,
std::vector<unsigned char>& queryTransformed);
int transformSequencesKSW2(const char* const queryOriginal, const int queryLength,
const char* const targetOriginal, const int targetLength,
std::vector<unsigned char>& queryTransformed,
std::vector<unsigned char>& targetTransformed);
/**
* Variants of the operator that require both an explicit type tag to
* determine the type of alignment to perform, as well as a pointer to
* an `ksw_extz_t` structure that will be used to hold the output.
*/
int operator()(const char* const queryOriginal, const int queryLength,
const char* const targetOriginal, const int targetLength,
ksw_extz_t* ez, EnumToType<KSW2AlignmentType::GLOBAL>);
int operator()(const char* const queryOriginal, const int queryLength,
const char* const targetOriginal, const int targetLength,
ksw_extz_t* ez, EnumToType<KSW2AlignmentType::EXTENSION>);
int operator()(const uint8_t* const queryOriginal, const int queryLength,
const uint8_t* const targetOriginal, const int targetLength,
ksw_extz_t* ez, EnumToType<KSW2AlignmentType::GLOBAL>);
int operator()(const uint8_t* const queryOriginal, const int queryLength,
const uint8_t* const targetOriginal, const int targetLength,
ksw_extz_t* ez, EnumToType<KSW2AlignmentType::EXTENSION>);
/**
* Variants of the operator that do not require an output
* `ksw_extz_t*` variable. They will store the result in this object's
* `result_` variable, which can then be queried with the `result()` method.
*/
int operator()(const char* const queryOriginal, const int queryLength,
const char* const targetOriginal, const int targetLength,
EnumToType<KSW2AlignmentType::GLOBAL>);
int operator()(const char* const queryOriginal, const int queryLength,
const char* const targetOriginal, const int targetLength,
EnumToType<KSW2AlignmentType::EXTENSION>);
int operator()(const uint8_t* const queryOriginal, const int queryLength,
const uint8_t* const targetOriginal, const int targetLength,
EnumToType<KSW2AlignmentType::GLOBAL>);
int operator()(const uint8_t* const queryOriginal, const int queryLength,
const uint8_t* const targetOriginal, const int targetLength,
EnumToType<KSW2AlignmentType::EXTENSION>);
/**
* Variants of the operator that require neither an output
* `ksw_extz_t*` variable or an explicit type tag to select the type of
*alignment
* to perform. These variants will perform whichever type of alignment is
* currently specified in the `atype` member of this class's `config_`
* object.
**/
int operator()(const char* const queryOriginal, const int queryLength,
const char* const targetOriginal, const int targetLength);
int operator()(const uint8_t* const queryOriginal, const int queryLength,
const uint8_t* const targetOriginal, const int targetLength);
KSW2Config& config() { return config_; }
const ksw_extz_t& result() { return result_; }
void freeCIGAR(ksw_extz_t* ez) {
if (ez->cigar and kalloc_allocator_) {
kfree(kalloc_allocator_.get(), ez->cigar);
}
}
private:
std::vector<uint8_t> query_;
std::vector<uint8_t> target_;
ksw_extz_t result_;
std::unique_ptr<void, KallocDeleter> kalloc_allocator_{nullptr,
KallocDeleter()};
std::vector<int8_t> mat_;
KSW2Config config_;
bool haveSSE41{false};
bool haveSSE2{false};
};
} // namespace ksw2pp
#endif //__KSW2_ALIGNER_HPP__
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