BamIndex.h

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// ***************************************************************************
// BamIndex.h (c) 2009 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides basic BAM index interface
// ***************************************************************************

#ifndef BAM_INDEX_H
#define BAM_INDEX_H

#include "api/api_global.h"
#include "api/BamAux.h"
#include <string>

namespace BamTools {

namespace Internal {
    class BamReaderPrivate;
} // namespace Internal

class API_EXPORT BamIndex {

    // enums
    public:

        // list of supported BamIndex types
        enum IndexType { BAMTOOLS = 0
                       , STANDARD
                       };
  
    // ctor & dtor
    public:
        BamIndex(Internal::BamReaderPrivate* reader) : m_reader(reader) { }
        virtual ~BamIndex(void) { }
        
    // index interface
    public:
        // builds index from associated BAM file & writes out to index file
        virtual bool Create(void) =0;

        // returns a human-readable description of the last error encountered
        std::string GetErrorString(void) { return m_errorString; }

        // returns whether reference has alignments or no
        virtual bool HasAlignments(const int& referenceID) const =0;

        // attempts to use index data to jump to @region, returns success/fail
        // a "successful" jump indicates no error, but not whether this region has data
        //   * thus, the method sets a flag to indicate whether there are alignments
        //     available after the jump position
        virtual bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion) =0;

        // loads existing data from file into memory
        virtual bool Load(const std::string& filename) =0;

        // returns the 'type' enum for derived index format
        virtual BamIndex::IndexType Type(void) const =0;


    // internal methods
    protected:
        void SetErrorString(const std::string& where, const std::string& what) const {
            m_errorString = where + ": " + what;
        }

    // data members
    protected:
        Internal::BamReaderPrivate* m_reader; // copy, not owned
        mutable std::string m_errorString;

};

} // namespace BamTools

#endif // BAM_INDEX_H