// ***************************************************************************
// bamtools_count.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ---------------------------------------------------------------------------
// Prints alignment count for BAM file(s)
// ***************************************************************************

#ifndef BAMTOOLS_COUNT_H
#define BAMTOOLS_COUNT_H

#include "bamtools_tool.h"

namespace BamTools {

class CountTool : public AbstractTool
{

public:
    CountTool();
    ~CountTool();

public:
    int Help();
    int Run(int argc, char* argv[]);

private:
    struct CountSettings;
    CountSettings* m_settings;

    struct CountToolPrivate;
    CountToolPrivate* m_impl;
};

}  // namespace BamTools

#endif  // BAMTOOLS_COUNT_H
