Parse 'samtools depth' and obtain lines with sufficient coverage. Assumes two samples in the output. Same as, awk '$3 >= cutoff && $4 >= cutoff'

get_count_with_sufficient_coverage.cc

#include <stdint.h>
#include <cstdlib>
#include <iostream>
#include <fstream>
#include <sstream>

using namespace std;
void usage() {
    cerr << "Usage: ./get_count_with_sufficient_coverage samtools_depth_file cutoff[INT]";
    cerr << "Assumes 2 samples.";
    cerr << endl;
    return;
}

int count_number_satisfying_lines(string depth_file, int cutoff) {
    ifstream fin;
    fin.open(depth_file.c_str());
    string line;
    string chr;
    uint32_t pos, s1_readcount, s2_readcount;
    int lines_satisfying = 0;
    while(getline(fin, line)) {
        stringstream ss(line);
        ss >> chr >> pos >> s1_readcount >> s2_readcount;
        if(s1_readcount >= cutoff &&  s2_readcount >= cutoff) {
            lines_satisfying++;
        }
    }
    return lines_satisfying;
}

int main(int argc, char* argv[]) {
    if (argc < 3) {
        usage();
        return 1;
    }
    string samtools_depth_file = string(argv[1]);
    int cutoff = atoi(argv[2]);
    cerr << "\nCutoff " << cutoff;
    cerr << "\nSamtools file: " << samtools_depth_file;
    cerr << "\nNumber of lines satisfying cutoff: ";
    cout << count_number_satisfying_lines(samtools_depth_file, cutoff);
    cout << endl;
    return 0;
}