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TestRevComp.cpp

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#include "gn/gnSourceFactory.h"
#include "gn/gnFASSource.h"
#include "gn/gnDNXSource.h"
#include "gn/gnSEQSource.h"
#include "gn/gnSequence.h"
#include <iostream>
#include <fstream>

#include "gn/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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