// ***************************************************************************
// bamtools_index.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ---------------------------------------------------------------------------
// Creates a BAM index file
// ***************************************************************************

#ifndef BAMTOOLS_INDEX_H
#define BAMTOOLS_INDEX_H

#include "bamtools_tool.h"

namespace BamTools {

class IndexTool : public AbstractTool
{

public:
    IndexTool();
    ~IndexTool();

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

private:
    struct IndexSettings;
    IndexSettings* m_settings;

    struct IndexToolPrivate;
    IndexToolPrivate* m_impl;
};

}  // namespace BamTools

#endif  // BAMTOOLS_INDEX_H
