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SVMipv4.h
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SVMipv4.h
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#include <string>
#include <vector>
#include <map>
using namespace std;
class SVMipv4
{
public:
static map<string, double> junction_scores;
int ext_probe_start;
int ext_probe_stop;
int lig_probe_start;
int lig_probe_stop;
string strand;
string chr;
char translocation_failed;
char snp_failed;
char mapping_failed;
char masking_failed;
int extension_arm_length;
int ligation_arm_length;
int scan_size;
string ext_probe_sequence;
string ext_masked_sequence;
string lig_probe_sequence;
string lig_masked_sequence;
string scan_target_sequence;
int ext_probe_copy;
int lig_probe_copy;
double arm_fraction_masked;
int scan_start_position;
int scan_stop_position;
int snp_count;
vector<int> snp_positions;
string mip_seq;
string ligation_junction;
double score;
bool has_snp_mip;
string snp_ext_sequence;
string snp_lig_sequence;
string snp_mip_sequence;
SVMipv4 (string chromosome, int scan_start, int scan_stop, int ext_length, int lig_length);
virtual ~SVMipv4(){};
virtual void set_ext_probe_seq(string seq) =0;
virtual void set_lig_probe_seq(string seq) =0;
virtual int get_mip_start() =0;
double count_ext_mer(string sub);
double count_lig_mer(string sub);
double count_insert_mer(string sub);
void get_parameters(vector<double> & parameters, double long_range_content[]);
double get_score ();
static void set_junction_scores();
};