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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 seq_id, std::string prefix, char gap,
bool call_min_depth, int min_depth) {
std::string path = "../data/test.gap.sorted.mpileup";
std::string expctd_hdr = "";
std::ifstream mplp(path);
call_consensus_from_plup(mplp, seq_id, prefix, 20, 0, min_depth, gap,
call_min_depth, 1);
std::ifstream outFile(prefix + ".fa");
std::string l;
getline(outFile, l); // header
if (seq_id.empty()) {
char *o = new char[prefix.length() + 1];
strcpy(o, prefix.c_str());
expctd_hdr =
">Consensus_" + std::string(basename(o)) + "_threshold_0_quality_20";
} else {
expctd_hdr = ">" + seq_id;
}
return l.compare(expctd_hdr);
}
int main() {
int num_success = 0;
std::string c_ =
"CTGCTGGGTCATGGGCCCATCATGATGGTCTTGGCGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCA"
"TCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAG"
"AAAGAT------------------------------"
"AGGAAGGAGAAGAAGAGACGWGGCGCAGATACTAGTGTCGGAATTGTTGGMCTCCTGCTGACCACAGCTATG"
"GMAGCGGAGGTCACKAGACGTGGGAGTGCATACTATATGTACTTGGACWGAAACGATGCKGGGGAGGCCATA"
"TCTTTTCCAACCACATTGGGGTTGAATAAGTG";
num_success =
call_cns_check_outfile("TESTID", "../data/test.gap", '-', true, 0);
std::cout << num_success << std::endl;
num_success += call_cns_check_outfile("", "../data/test.gap", 'N', true, 0);
std::cout << num_success << std::endl;
num_success +=
call_cns_check_outfile("TESTID2", "../data/test.gap", 'N', false, 0);
std::cout << num_success << std::endl;
if (num_success == 0) return 0;
return -1;
}
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