8 const std::string alphabet =
"ATGCRYSWKMBDHVN-X#@";
9 const unsigned int MAX_CHAR = alphabet.length();
10 const int MAX_SIZE = 300;
11 const int MIN_LENGTH = 3;
12 const int MAX_MISMATCHES = 2;
16 int begin, nchildren, *end;
20 bool contains_child(
int ext);
23 std::string get_longest_common_substring(std::string s1, std::string s2);
24 std::string get_path(std::string s);
25 void extend_path(
int *e);
29 bool contains_depth(
int depth);
30 void print(std::string s);
31 bool walk_next(
int &beg,
int &suffix_length);
35 std::string get_reverse_complement(std::string rev_read);
36 std::vector<std::string> read_adapters_from_fasta(std::string p, std::string n);
37 int trim_adapter(std::string f1, std::string f2, std::string adp_path, std::string p);
Definition: suffix_tree.h:14