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#include<iostream>
#include<fstream>
#include<string>
#include "../src/call_consensus_pileup.h"
#include "../src/allele_functions.h"
int call_cns_check_outfile(std::string input_id, std::string prefix, std::string cns, char gap, bool call_min_depth, int min_depth){
std::string path = "../data/test.gap.sorted.mpileup";
std::ifstream mplp(path);
call_consensus_from_plup(mplp, input_id, prefix, 20, 0, min_depth, gap, call_min_depth);
std::ifstream outFile(prefix+".fa");
std::string l;
getline(outFile, l); // Ignore first line
getline(outFile, l);
return l.compare(cns);
}
int main() {
int num_success = 0;
std::string c_ = "CTGCTGGGTCATGGGCCCATCATGATGGTCTTGGCGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCATCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAGAAAGAT------------------------------AGGAAGGAGAAGAAGAGACGWGGCGCAGATACTAGTGTCGGAATTGTTGGMCTCCTGCTGACCACAGCTATGGMAGCGGAGGTCACKAGACGTGGGAGTGCATACTATATGTACTTGGACWGAAACGATGCKGGGGAGGCCATATCTTTTCCAACCACATTGGGGTTGAATAAGTG";
std::string cN = "CTGCTGGGTCATGGGCCCATCATGATGGTCTTGGCGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCATCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAGAAAGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGAAGGAGAAGAAGAGACGWGGCGCAGATACTAGTGTCGGAATTGTTGGMCTCCTGCTGACCACAGCTATGGMAGCGGAGGTCACKAGACGTGGGAGTGCATACTATATGTACTTGGACWGAAACGATGCKGGGGAGGCCATATCTTTTCCAACCACATTGGGGTTGAATAAGTG";
std::string ck = "CTGCTGGGTCATGGGCCCATCATGATGGTCTTGGCGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCATCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAGAAAGATAGGAAGGAGAAGAAGAGACGWGGCGCAGATACTAGTGTCGGAATTGTTGGMCTCCTGCTGACCACAGCTATGGMAGCGGAGGTCACKAGACGTGGGAGTGCATACTATATGTACTTGGACWGAAACGATGCKGGGGAGGCCATATCTTTTCCAACCACATTGGGGTTGAATAAGTG";
num_success = call_cns_check_outfile("", "../data/test.gap", c_, '-', true, 0);
std::cout << num_success << std::endl;
num_success += call_cns_check_outfile("TESTID", "../data/test.gap", cN, 'N', true, 0);
std::cout << num_success << std::endl;
num_success += call_cns_check_outfile("TESTID", "../data/test.gap", ck, 'N', false, 0);
std::cout << num_success << std::endl;
if(num_success == 0)
return 0;
return -1;
}
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