Created
November 4, 2015 15:45
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| #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; | |
| } |
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