// ***************************************************************************
// bamtools_pileup_engine.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 October 2011
// ---------------------------------------------------------------------------
// Provides pileup at position functionality for various tools.
// ***************************************************************************

#ifndef BAMTOOLS_PILEUP_ENGINE_H
#define BAMTOOLS_PILEUP_ENGINE_H

#include "utils/utils_global.h"

#include <api/BamAlignment.h>
#include <vector>

namespace BamTools {

// contains auxiliary data about a single BamAlignment
// at current position considered
struct UTILS_EXPORT PileupAlignment {
  
    // data members
    BamAlignment Alignment;
    int32_t PositionInAlignment;
    bool IsCurrentDeletion;
    bool IsNextDeletion;
    bool IsNextInsertion;
    int DeletionLength;
    int InsertionLength;
    bool IsSegmentBegin;
    bool IsSegmentEnd;
    
    // ctor
    PileupAlignment(const BamAlignment& al)
        : Alignment(al)
        , PositionInAlignment(-1)
        , IsCurrentDeletion(false)
        , IsNextDeletion(false)
        , IsNextInsertion(false)
        , DeletionLength(0)
        , InsertionLength(0)
        , IsSegmentBegin(false)
        , IsSegmentEnd(false)
    { }
};
  
// contains all data at a position
struct UTILS_EXPORT PileupPosition {
  
    // data members
    int RefId;
    int Position;
    std::vector<PileupAlignment> PileupAlignments;

    // ctor
    PileupPosition(const int& refId = 0,
                   const int& position = 0, 
                   const std::vector<PileupAlignment>& alignments = std::vector<PileupAlignment>())
        : RefId(refId)
        , Position(position)
        , PileupAlignments(alignments)
    { }
};
  
class UTILS_EXPORT PileupVisitor {
  
    public:
        PileupVisitor(void) { }
        virtual ~PileupVisitor(void) { }
  
    public:
        virtual void Visit(const PileupPosition& pileupData) =0;
};

class UTILS_EXPORT PileupEngine {
  
    public:
        PileupEngine(void);
        ~PileupEngine(void);
        
    public:
        bool AddAlignment(const BamAlignment& al);
        void AddVisitor(PileupVisitor* visitor);
        void Flush(void);
        
    private:
        struct PileupEnginePrivate;
        PileupEnginePrivate* d;
};

} // namespace BamTools

#endif // BAMTOOLS_PILEUP_ENGINE_H