// ***************************************************************************
// BamStandardIndex.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 November 2011 (DB)
// ---------------------------------------------------------------------------
// Provides index operations for the standardized BAM index format (".bai")
// ***************************************************************************

#ifndef BAM_STANDARD_INDEX_FORMAT_H
#define BAM_STANDARD_INDEX_FORMAT_H

#include "api/api_global.h"

//  -------------
//  W A R N I N G
//  -------------
//
// This file is not part of the BamTools API.  It exists purely as an
// implementation detail.  This header file may change from version to
// version without notice, or even be removed.
//
// We mean it.

#include <map>
#include <set>
#include <string>
#include <vector>
#include "api/BamAux.h"
#include "api/BamIndex.h"
#include "api/IBamIODevice.h"

namespace BamTools {
namespace Internal {

// -----------------------------------------------------------------------------
// BamStandardIndex data structures

// defines start and end of a contiguous run of alignments
struct API_NO_EXPORT BaiAlignmentChunk
{

    // data members
    uint64_t Start;
    uint64_t Stop;

    // constructor
    BaiAlignmentChunk(const uint64_t& start = 0, const uint64_t& stop = 0)
        : Start(start)
        , Stop(stop)
    {}
};

// comparison operator (for sorting)
inline bool operator<(const BaiAlignmentChunk& lhs, const BaiAlignmentChunk& rhs)
{
    return lhs.Start < rhs.Start;
}

// convenience typedef for a list of all alignment 'chunks' in a BAI bin
typedef std::vector<BaiAlignmentChunk> BaiAlignmentChunkVector;

// convenience typedef for a map of all BAI bins in a reference (ID => chunks)
typedef std::map<uint32_t, BaiAlignmentChunkVector> BaiBinMap;

// convenience typedef for a list of all 'linear offsets' in a reference
typedef std::vector<uint64_t> BaiLinearOffsetVector;

// contains all fields necessary for building, loading, & writing
// full BAI index data for a single reference
struct API_NO_EXPORT BaiReferenceEntry
{

    // data members
    int32_t ID;
    BaiBinMap Bins;
    BaiLinearOffsetVector LinearOffsets;

    // ctor
    BaiReferenceEntry(const int32_t& id = -1)
        : ID(id)
    {}
};

// provides (persistent) summary of BaiReferenceEntry's index data
struct API_NO_EXPORT BaiReferenceSummary
{

    // data members
    int NumBins;
    int NumLinearOffsets;
    uint64_t FirstBinFilePosition;
    uint64_t FirstLinearOffsetFilePosition;

    // ctor
    BaiReferenceSummary()
        : NumBins(0)
        , NumLinearOffsets(0)
        , FirstBinFilePosition(0)
        , FirstLinearOffsetFilePosition(0)
    {}
};

// convenience typedef for describing a full BAI index file summary
typedef std::vector<BaiReferenceSummary> BaiFileSummary;

// end BamStandardIndex data structures
// -----------------------------------------------------------------------------

class API_NO_EXPORT BamStandardIndex : public BamIndex
{

    // ctor & dtor
public:
    BamStandardIndex(Internal::BamReaderPrivate* reader);
    ~BamStandardIndex();

    // BamIndex implementation
public:
    // builds index from associated BAM file & writes out to index file
    bool Create();
    // returns whether reference has alignments or no
    bool HasAlignments(const int& referenceID) const;
    // 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
    bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion);
    // loads existing data from file into memory
    bool Load(const std::string& filename);
    BamIndex::IndexType Type() const
    {
        return BamIndex::STANDARD;
    }

public:
    // returns format's file extension
    static const std::string Extension();

    // internal methods
private:
    // index file ops
    void CheckMagicNumber();
    void CloseFile();
    bool IsDeviceOpen() const;
    void OpenFile(const std::string& filename, IBamIODevice::OpenMode mode);
    void Seek(const int64_t& position, const int origin);
    int64_t Tell() const;

    // BAI index building methods
    void ClearReferenceEntry(BaiReferenceEntry& refEntry);
    void SaveAlignmentChunkToBin(BaiBinMap& binMap, const uint32_t& currentBin,
                                 const uint64_t& currentOffset, const uint64_t& lastOffset);
    void SaveLinearOffsetEntry(BaiLinearOffsetVector& offsets, const int& alignmentStartPosition,
                               const int& alignmentStopPosition, const uint64_t& lastOffset);

    // random-access methods
    void AdjustRegion(const BamRegion& region, uint32_t& begin, uint32_t& end);
    void CalculateCandidateBins(const uint32_t& begin, const uint32_t& end,
                                std::set<uint16_t>& candidateBins);
    void CalculateCandidateOffsets(const BaiReferenceSummary& refSummary, const uint64_t& minOffset,
                                   std::set<uint16_t>& candidateBins,
                                   std::vector<int64_t>& offsets);
    uint64_t CalculateMinOffset(const BaiReferenceSummary& refSummary, const uint32_t& begin);
    void GetOffset(const BamRegion& region, int64_t& offset, bool* hasAlignmentsInRegion);
    uint64_t LookupLinearOffset(const BaiReferenceSummary& refSummary, const int& index);

    // BAI summary (create/load) methods
    void ReserveForSummary(const int& numReferences);
    void SaveBinsSummary(const int& refId, const int& numBins);
    void SaveLinearOffsetsSummary(const int& refId, const int& numLinearOffsets);
    void SkipBins(const int& numBins);
    void SkipLinearOffsets(const int& numLinearOffsets);
    void SummarizeBins(BaiReferenceSummary& refSummary);
    void SummarizeIndexFile();
    void SummarizeLinearOffsets(BaiReferenceSummary& refSummary);
    void SummarizeReference(BaiReferenceSummary& refSummary);

    // BAI full index input methods
    void ReadBinID(uint32_t& binId);
    void ReadBinIntoBuffer(uint32_t& binId, int32_t& numAlignmentChunks);
    void ReadIntoBuffer(const unsigned int& bytesRequested);
    void ReadLinearOffset(uint64_t& linearOffset);
    void ReadNumAlignmentChunks(int& numAlignmentChunks);
    void ReadNumBins(int& numBins);
    void ReadNumLinearOffsets(int& numLinearOffsets);
    void ReadNumReferences(int& numReferences);

    // BAI full index output methods
    void MergeAlignmentChunks(BaiAlignmentChunkVector& chunks);
    void SortLinearOffsets(BaiLinearOffsetVector& linearOffsets);
    void WriteAlignmentChunk(const BaiAlignmentChunk& chunk);
    void WriteAlignmentChunks(BaiAlignmentChunkVector& chunks);
    void WriteBin(const uint32_t& binId, BaiAlignmentChunkVector& chunks);
    void WriteBins(const int& refId, BaiBinMap& bins);
    void WriteHeader();
    void WriteLinearOffsets(const int& refId, BaiLinearOffsetVector& linearOffsets);
    void WriteReferenceEntry(BaiReferenceEntry& refEntry);

    // data members
private:
    bool m_isBigEndian;
    BaiFileSummary m_indexFileSummary;

    // our input buffer
    unsigned int m_bufferLength;
    struct RaiiWrapper
    {
        IBamIODevice* Device;
        char* Buffer;
        RaiiWrapper();
        ~RaiiWrapper();
    };
    RaiiWrapper m_resources;

    // static methods
private:
    // checks if the buffer is large enough to accomodate the requested size
    static void CheckBufferSize(char*& buffer, unsigned int& bufferLength,
                                const unsigned int& requestedBytes);
    // checks if the buffer is large enough to accomodate the requested size
    static void CheckBufferSize(unsigned char*& buffer, unsigned int& bufferLength,
                                const unsigned int& requestedBytes);
    // static constants
private:
    static const int MAX_BIN;
    static const int BAM_LIDX_SHIFT;
    static const std::string BAI_EXTENSION;
    static const char* const BAI_MAGIC;
    static const int SIZEOF_ALIGNMENTCHUNK;
    static const int SIZEOF_BINCORE;
    static const int SIZEOF_LINEAROFFSET;
};

}  // namespace Internal
}  // namespace BamTools

#endif  // BAM_STANDARD_INDEX_FORMAT_H
