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//
#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;
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <io_lib/Read.h>
#include <io_lib/misc.h>
#include <io_lib/hash_table.h>
#include <io_lib/ztr.h>
#include <io_lib/sff.h>
#include <zlib.h>
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();
}
main(int argc, char* argv[])
{
if ( argc != 3 )
{
cout << "Usage: sffWriter <SFF file> <output file>\n";
exit(1);
}
SRF_File::openType mode = SRF_File::openTypeWrite;
SRF_File file( argv[2], mode );
SRF_Container container;
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, seq;
std::vector<ztr_t> ztrBlobs;
std::vector<std::string> readIds;
// open fasta
// std::ifstream fastaInput;
// fastaInput.open(argv[1], std::ios::in );
Read* read = NULL;
mFILE* mf = mfopen(argv[1], "r");
while ( ( read = mfread_sff( mf ) ) != NULL )
{
string readId;
readId = SRF_to_string<int>(readIdCounter, std::dec);
ztr_t* ztr = NULL;
ztr = SRF_output_ztr( read );
ztrBlobs.push_back( *ztr );
readIds.push_back( readId );
readIdCounter++;
}
newReadSet.write( file.getFile(), ztrBlobs, readIds );
}
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