text: // convert a fastq file to fasta
  #include <iostream>
  #include <fstream>
  #include <string>
  #include <cstring>
  using namespace std;
  
  int main (int argc, char* argv[]) {
  
    if ( argc < 3) {
      cerr << "Usage: " << argv[0] << " <fastq file (use - to read from STDIN)> <fasta file>\n";
      return 1;
    }
  
  
    ifstream fastq;
    streambuf* orig_cin = 0;
    if (strcmp(argv[1], "-") != 0) {
      cout << "reading from " << argv[1] << '\n';
      fastq.open(argv[1]);
      if (!fastq) return 1;
      orig_cin = cin.rdbuf(fastq.rdbuf());
      cin.tie(0); // tied to cout by default
    }
  
    string line;
    ofstream fasta(argv[2]);
    if (!fasta) return 2;
    int c=0;
    
    while (getline(cin, line))
    {
      //cout << c << " : " << line << '\n';
      if ( c==0 ) {
        line.replace(0, 1, ">");
        fasta << line << '\n';
      }
      if ( c==1 ) {
        fasta << line << '\n';
      }
      c++;
      if ( c == 4) { c=0 ;}
    }
  
    if ( c != 0 ) {
  	  cerr << "ERROR: There appears to be the wrong number of lines in your file!" << endl;
  	return 1;
    }
  
    return 0;
  }
  