1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
|
#include<iostream>
#include<fstream>
#include<string>
#include "../src/allele_functions.h"
#include "../src/call_variants.h"
int call_var_check_outfile(std::string prefix, uint8_t min_qual, uint8_t min_depth, double min_threshold, std::string out[], int len){
std::string path = "../data/test.indel.mpileup";
std::ifstream mplp(path);
call_variants_from_plup(mplp, prefix, min_qual, min_threshold, min_depth, "../data/db/test_ref.fa", "../data/test.gff");
std::ifstream outFile(prefix+".tsv");
std::string l;
getline(outFile, l); // Ignore first line
int comp = 0, ctr = 0;
while(ctr < len){
getline(outFile, l);
std::cout << l << std::endl;
std::cout << out[ctr] << " -> CORRECT" << std::endl;
comp += l.compare(out[ctr]);
ctr++;
}
return comp;
}
int main() {
int num_success = 0;
// Quality threshold 20. Frequency threshold: 0.03. Total_DP = 3. Indel passes filters with total_depth 4. Has two lines.
std::string t_20_02_1[4] = {"test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-test3\tAAG\tK\tATG\tM", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-testedit1\tGAA\tE\tGAT\tD", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-testedit2\tAGA\tR\tTGA\t*", "test\t210\tA\t+GT\t1\t1\t41\t1\t0\t20\t0.25\t4\t0.4\tFALSE\tNA\tNA\tNA\tNA\tNA"};
// Quality threshold 3-. Frequency threshold: 0.03. Total_DP = 3. Freq = 0.666667 No Indel
std::string t_20_03[3] = {"test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-test3\tAAG\tK\tATG\tM", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-testedit1\tGAA\tE\tGAT\tD", "test\t210\tA\tT\t1\t1\t41\t2\t1\t40\t0.666667\t3\t0.2\tFALSE\tid-testedit2\tAGA\tR\tTGA\t*"};
// Quality threshold 25. Frequency threshold: 0.03. Total_DP = 2. Freq = 0.5 No Indel.
std::string t_25_03[3] = {"test\t210\tA\tT\t1\t1\t41\t1\t1\t58\t0.5\t2\t0.4\tFALSE\tid-test3\tAAG\tK\tATG\tM", "test\t210\tA\tT\t1\t1\t41\t1\t1\t58\t0.5\t2\t0.4\tFALSE\tid-testedit1\tGAA\tE\tGAT\tD", "test\t210\tA\tT\t1\t1\t41\t1\t1\t58\t0.5\t2\t0.4\tFALSE\tid-testedit2\tAGA\tR\tTGA\t*"};
// Minimum depth threshold. Should be empty
std::string t_25_03_20[] = {""};
num_success = call_var_check_outfile("../data/test.indel", 20, 0, 0.02, t_20_02_1, 4);
std::cout << num_success << std::endl;
num_success += call_var_check_outfile("../data/test.indel", 20, 0, 0.03, t_20_03, 3);
std::cout << num_success << std::endl;
num_success += call_var_check_outfile("../data/test.indel", 25, 0, 0.03, t_25_03, 3);
std::cout << num_success << std::endl;
num_success += call_var_check_outfile("../data/test.indel", 25, 20, 0.03, t_25_03_20, 0);
std::cout << num_success << std::endl;
if(num_success == 0)
return 0;
return -1;
}
|
