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#include <iostream>
#include <fstream>
#include "../src/get_masked_amplicons.h"
int main()
{
int num_tests = 1, success = 0;
get_primers_with_mismatches("../data/test.bed", "../data/test.filtered.tsv", "../data/test.masked_primer_indices", "../data/pair_information.tsv");
std::ifstream masked_indices_file("../data/test.masked_primer_indices.txt");
std::string indices;
getline(masked_indices_file, indices);
if(indices.compare("WNV_400_2_LEFT\tWNV_400_2_RIGHT\tWNV_400_2_LEFT_alt\tWNV_400_1_LEFT\tWNV_400_1_RIGHT\tWNV_400_1_LEFT_alt\tWNV_400_3_LEFT") == 0)
success += 1;
return (num_tests == success) ? 0 : -1;
}
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