fastqIO.cc

#include <Sequence/fastq.hpp>
#include <fstream>
#include <boost/test/unit_test.hpp>
#include <unistd.h>
#include <iterator>
#include <iostream>
#include <stdexcept>

BOOST_AUTO_TEST_SUITE(FASTQIOTest)

BOOST_AUTO_TEST_CASE( input_test )
{
  std::ifstream in("data/data.fastq");
  if (!in)
    {
      std::cerr << "Error, couldn't find input file!\n";
      exit(1);
    }
  Sequence::fastq f;

  unsigned count = 0;
  BOOST_REQUIRE_NO_THROW 
    (
     while(!in.eof())
       {
         in >> f >> std::ws;
         ++count;
       }
     );
  BOOST_CHECK_EQUAL(count,50);
}

BOOST_AUTO_TEST_CASE( input_test2 )
{
  std::ifstream in("data/data.fastq");
  if (!in)
    {
      std::cerr << "Error, couldn't find input file!\n";
      exit(1);
    }
  Sequence::fastq f;

  unsigned count = 0;
  BOOST_REQUIRE_NO_THROW 
    (
     unsigned count = 0;
     std::istream_iterator<Sequence::fastq> i(in);
     for( ; i != std::istream_iterator<Sequence::fastq>() ; ++i )
       {
         ++count;  
       }
     BOOST_CHECK_EQUAL(count,50);
     in.close();
     ); 
}

BOOST_AUTO_TEST_CASE( output_test )
{
  BOOST_REQUIRE_NO_THROW 
    (
     std::ifstream in("data/data.fastq");
     if (!in)
       {
         std::cerr << "Error, couldn't find input file!\n";
         exit(1);
       }

     Sequence::fastq f;
     
     std::vector<Sequence::fastq> vf;
     std::ofstream out("fastqIOtest.txt");
     unsigned count = 0;
     while(!in.eof())
       {
         in >> f >> std::ws;
         f.repname(false);
         vf.push_back(f);
         out << f << '\n';
         ++count;
       }
     BOOST_CHECK_EQUAL(count,50);
     out.close();
     in.close();
     in.open("fastqIOtest.txt");
     count = 0;
     while(!in.eof())
       {
         in >> f >> std::ws;
         BOOST_CHECK_EQUAL(f,vf[count]);
         ++count;
       }
     unlink("fastqIOtest.txt");
     in.close(); 
     );
}
BOOST_AUTO_TEST_SUITE_END()