Unitig.hpp

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#ifndef BIFROST_UNITIG_HPP
#define BIFROST_UNITIG_HPP
 
#include "Common.hpp"
#include "Kmer.hpp"
#include "CompressedSequence.hpp"
#include "CompressedCoverage.hpp"
 
template<typename T = void>
class Unitig {
 
    public:
 
        Unitig() {}
        Unitig(const CompressedSequence& s, const CompressedCoverage& c) : seq(s), cov(c) {}
        Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
        Unitig(const char* s, bool full = false) : seq(s), cov(seq.size() - Kmer::k + 1, full) {}
 
        BFG_INLINE size_t numKmers() const {
 
            return seq.size( ) - Kmer::k + 1;
        }
 
        BFG_INLINE size_t length() const {
 
            return seq.size();
        }
 
        BFG_INLINE const CompressedSequence& getSeq() const {
 
            return seq;
        }
 
        BFG_INLINE CompressedSequence& getSeq() {
 
            return seq;
        }
 
        BFG_INLINE const CompressedCoverage& getCov() const {
 
            return cov;
        }
 
        BFG_INLINE CompressedCoverage& getCov() {
 
            return cov;
        }
 
        BFG_INLINE const T* getData() const {
 
            return &data;
        }
 
        BFG_INLINE T* getData() {
 
            return &data;
        }
 
    private:
 
        CompressedSequence seq;
        CompressedCoverage cov;
 
        T data;
};
 
template<>
class Unitig<void> {
 
    public:
 
        Unitig() {}
        Unitig(const CompressedSequence& s, const CompressedCoverage& c) : seq(s), cov(c) {}
        Unitig(CompressedSequence&& s, CompressedCoverage&& c) : seq(move(s)), cov(move(c)) {}
        Unitig(const char* s, bool full = false) : seq(s), cov(seq.size() - Kmer::k + 1, full) {}
 
        BFG_INLINE size_t numKmers() const {
 
            return seq.size( ) - Kmer::k + 1;
        }
 
        BFG_INLINE size_t length() const {
 
            return seq.size();
        }
 
        BFG_INLINE const CompressedSequence& getSeq() const {
 
            return seq;
        }
 
        BFG_INLINE CompressedSequence& getSeq() {
 
            return seq;
        }
 
        BFG_INLINE const CompressedCoverage& getCov() const {
 
            return cov;
        }
 
        BFG_INLINE CompressedCoverage& getCov() {
 
            return cov;
        }
 
        BFG_INLINE const void* getData() const {
 
            return nullptr;
        }
 
        BFG_INLINE void* getData() {
 
            return nullptr;
        }
 
    private:
 
        CompressedSequence seq;
        CompressedCoverage cov;
};
 
#endif // BFG_CONTIG_HPP