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#include <fstream>
#include <iostream>
#include <string>
#include "../src/allele_functions.h"
#include "../src/call_consensus_pileup.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, 1);
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_ =
"CTGCTGGGTCATGGGCCCATCATGATGGTCTTGGCGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCA"
"TCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAG"
"AAAGAT------------------------------"
"AGGAAGGAGAAGAAGAGACGWGGCGCAGATACTAGTGTCGGAATTGTTGGMCTCCTGCTGACCACAGCTATG"
"GMAGCGGAGGTCACKAGACGTGGGAGTGCATACTATATGTACTTGGACWGAAACGATGCKGGGGAGGCCATA"
"TCTTTTCCAACCACATTGGGGTTGAATAAGTG";
std::string cN =
"CTGCTGGGTCATGGGCCCATCATGATGGTCTTGGCGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCA"
"TCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAG"
"AAAGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGAAGGAGAAGAAGAGACGWGGCGCAGATACTAGT"
"GTCGGAATTGTTGGMCTCCTGCTGACCACAGCTATGGMAGCGGAGGTCACKAGACGTGGGAGTGCATACTAT"
"ATGTACTTGGACWGAAACGATGCKGGGGAGGCCATATCTTTTCCAACCACATTGGGGTTGAATAAGTG";
std::string ck =
"CTGCTGGGTCATGGGCCCATCATGATGGTCTTGGCGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCA"
"TCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAG"
"AAAGATAGGAAGGAGAAGAAGAGACGWGGCGCAGATACTAGTGTCGGAATTGTTGGMCTCCTGCTGACCACA"
"GCTATGGMAGCGGAGGTCACKAGACGTGGGAGTGCATACTATATGTACTTGGACWGAAACGATGCKGGGGAG"
"GCCATATCTTTTCCAACCACATTGGGGTTGAATAAGTG";
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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