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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 <zlib.h>
int main(int argc, char* argv[])
{
if ( argc != 3 )
{
cout << "Usage: fastaWriter <fasta 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<SRF_BasePrb> prbs;
std::vector<std::string> readIds;
// open fasta
std::ifstream fastaInput;
fastaInput.open(argv[1], std::ios::in );
int where = 0;
string readId;
while( fastaInput.good() )
{
fastaInput >> str;
if ( str[0] == '@' )
{
str.erase( 0, 1 );
readId = str;
where = 0;
}
else if ( str[0] == '+' )
{
where = 1;
}
else if ( where == 0 )
{
seq = str;
}
else if ( where == 1 )
{
SRF_BasePrb singlePrb;
int ii = 0;
while (ii < seq.length() )
{
singlePrb.a_prb = 0;
singlePrb.c_prb = 0;
singlePrb.g_prb = 0;
singlePrb.t_prb = 0;
int prb = int( str[ii + 1 ] ) - 33 ;
// int prb = int( str[ii + 1 ] );
switch( seq[ii] )
{
case 'A':
singlePrb.a_prb = prb;
break;
case 'C':
singlePrb.c_prb = prb;
break;
case 'G':
singlePrb.g_prb = prb;
break;
case 'T':
singlePrb.t_prb = prb;
break;
}
prbs.push_back( singlePrb );
ii++;
}
Read* read = SRF_create_read( seq.c_str(), prbs );
ztr_t* ztr = NULL;
ztr = SRF_output_ztr( read );
cout << readId << endl;
ztrBlobs.push_back( *ztr );
readIds.push_back( readId );
}
}
newReadSet.write( file.getFile(), ztrBlobs, readIds );
return 0;
}
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