21 const int unit_score = 2;
    23 const int substitution[5][5] = {
    24   {unit_score,-unit_score,-unit_score,-unit_score, 0},
    25   {-unit_score,unit_score,-unit_score,-unit_score, 0},
    26   {-unit_score,-unit_score,unit_score,-unit_score, 0},
    27   {-unit_score,-unit_score,-unit_score,unit_score, 0},
    31 const int gap_open = unit_score - 1;
    32 const int gap_extension = -1;
    33 const int max_read_size = 500;
    34 const int max_adapter_size = 60;
    35 const int MAX_GAP = 2;
    37 int get_sub_score(
char a, 
char b);
    38 int get_gap_penalty(
int k, 
char a);
    39 void print_matrix(
int h[][max_adapter_size], 
int r, 
int c, std::string read, std::string adap);
    40 int*  get_score_cell(
int h[][max_adapter_size], 
int i, 
int j, std::string read, std::string adap);
    41 void print_alignment(
char a[2][max_read_size], 
int n);
    42 int* align_seqs(std::string read, std::string adap);
    43 int find_adapters_contaminants(std::istream &cin, std::string adp_cntms_file);
    44 int main(
int argc, 
char* argv[]);
 int main(int argc, char *argv[])
Definition: ivar.cpp:144