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#pragma once
#include <map>
#include "analysis/sequenceUtil.h"
class DeBruijnKmer {
public:
DeBruijnKmer(kmer_int_type_t k);
DeBruijnKmer(const DeBruijnKmer& dk);
unsigned int getID() const;
kmer_int_type_t get_kmer_int_val() const;
vector<kmer_int_type_t> get_prev_kmers(unsigned int kmer_length);
vector<kmer_int_type_t> get_next_kmers(unsigned int kmer_length);
void add_prev_kmer(kmer_int_type_t k, unsigned int kmer_length);
void add_next_kmer(kmer_int_type_t k, unsigned int kmer_length);
//private:
static unsigned int id_counter;
unsigned int id;
kmer_int_type_t _kmer ;
char _prev; // bit array GATC indicating prev kmers
char _next; // ditto for next kmers
static const char _G_mask; // = 8;
static const char _A_mask; // = 4;
static const char _T_mask; // = 2;
static const char _C_mask; // = 1;
};
typedef map<kmer_int_type_t,DeBruijnKmer> DeBruijnKmerMap;
class DeBruijnGraph {
public:
DeBruijnGraph(unsigned int kmer_length);
void add_sequence(const string& sequence);
DeBruijnKmer& get_kmer_node(kmer_int_type_t t);
string toString();
string toChrysalisFormat(int component_id, bool sStrand);
vector<kmer_int_type_t> get_root_kmers();
bool kmerExists(kmer_int_type_t kval);
vector<string> get_candidate_weldmers(kmer_int_type_t kmer_val, int weldmer_length);
unsigned int get_kmer_length();
private:
unsigned int _kmer_length;
map<kmer_int_type_t,DeBruijnKmer> _kmer_map;
vector<DeBruijnKmer> deconvolute_DS_mirror_graph();
void recursively_construct_kmer_extensions(kmer_int_type_t seed_kmer_val,
vector<char>& kmer_extension_chars,
vector<string>& extension_kmer_strings,
char direction, // L | R fg left or right from the seed.
map<kmer_int_type_t,bool>& kmer_seen,
int flank_extension_length);
string get_kmer_from_char_vector(vector<char> char_vec, char direction);
};
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