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//
#include <cstdlib>
#include <ios>
#include <iostream>
#include <fstream>
#include <sstream>
#include <string>
#include <stddef.h>
#include <SRF_util.hh>
#include <SRF_File.hh>
#include <SRF_ReadSet.hh>
#include <SRF_Container.hh>
using namespace std;
template <class T>
std::string SRF_to_string(T t, std::ios_base & (*f)(std::ios_base&))
{
std::ostringstream oss;
oss << f << t;
return oss.str();
}
int main(int argc, char **argv)
{
SRF_File::openType mode = SRF_File::openTypeWrite;
SRF_File file( "myFirstSSRFFile", mode );
ifstream infile;
SRF_Container container;
if ( argc != 2 )
{
std::cout << "Usage: writer <input file>\n";
exit(1);
}
infile.open (argv[1], ifstream::in);
container.setup( "Test",
"0.0" );
container.write( file.getFile() );
SRF_ReadSet newReadSet;
newReadSet.setup( "Test", "" );
int readIdCounter = 0;
int a,b,c,d;
string str;
std::vector<SRF_BasePrb> prbs;
std::vector<ztr_t> ztrBlobs;
std::vector<std::string> readIds;
while( infile.good() )
{
infile >> a >> skipws >> b >> skipws >> c >> skipws >> d >> skipws >> str;
Read* read = SRF_create_read( str.c_str(), prbs );
ztr_t* ztr = NULL;
ztr = SRF_output_ztr( read );
string readId;
readId = SRF_to_string<int>(readIdCounter, std::dec);
ztrBlobs.push_back( *ztr );
readIds.push_back( readId );
readIdCounter++;
read_deallocate(read);
}
newReadSet.write( file.getFile(), ztrBlobs, readIds );
/* FIXME: memory leak on ztr here still */
infile.close();
return 0;
}
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