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#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libGenome/gnSourceFactory.h"
#include "libGenome/gnFASSource.h"
#include "libGenome/gnDNXSource.h"
#include "libGenome/gnSEQSource.h"
#include "libGenome/gnSequence.h"
#include <iostream>
#include <fstream>
#include "libGenome/gnFilter.h"
int main( int32 argc, char* argv[])
{
argc; argv;
string filename;
cout << "Enter a filename to read bases from.\n";
cin >> filename;
cout << "Opening " + filename + "\n";
gnSequence gnseq, smallseq;
if(gnseq.LoadSource(filename))
cout << "Sequence has " << gnseq.length() << " base pairs.\n";
smallseq = gnseq.subseq(3836480, 10);
cout << smallseq;
string dump;
cin >> dump;
cout << "Give a file name to output reverse complement data: ";
string outfilename;
cin >> outfilename;
cout << "Bases are:\n";
// cout << gpseq;
cout << "\nComplement Bases are:\n";
gnBaseSpec* gpbs = gnseq.GetSpec();
gpbs->SetReverseComplement(true);
// cout << gpseq << "\n";
gnFASSource::Write(gnseq, outfilename);
// gnGBKSource::Write(gpbs, "testfile.seq");
// gnDNXSource::Write(gpbs, "testfile.dnx");
cout << "All done. RevComp is in " << outfilename << "\n";
char bubba[50];
cin >> bubba;
}
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