iVar: src/allele_functions.h Source File

iVar

allele_functions.h
1 #include<string>
2 #include<vector>
3
4 #ifndef allele_functions
5 #define allele_functions
6
7 struct allele{
8 std::string nuc;
9 uint32_t depth;
10 uint32_t reverse;
11 uint8_t mean_qual;
12 uint32_t beg;
13 uint32_t end;
14 float tmp_mean_qual;
15 bool operator < (const allele& a) const{
16 return (nuc.compare(a.nuc) > 0) ? true : false;
17 }
18 bool operator == (const allele& a) const{
19 return (nuc.compare(a.nuc) == 0) ? true : false;
20 }
21 };
22
23 int check_allele_exists(std::string n, std::vector<allele> ad);
24 std::vector<allele> update_allele_depth(char ref,std::string bases, std::string qualities, uint8_t min_qual);
25 void print_allele_depths(std::vector<allele> ad);
26 int find_ref_in_allele(std::vector<allele> ad, char ref);
27 char gt2iupac(char a, char b);
28
29 #endif
allele
Definition: allele_functions.h:7