+++ /dev/null
-// ***************************************************************************
-// BamStandardIndex.h (c) 2010 Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// ---------------------------------------------------------------------------
-// Last modified: 10 October 2011 (DB)
-// ---------------------------------------------------------------------------
-// Provides index operations for the standardized BAM index format (".bai")
-// ***************************************************************************
-
-#ifndef BAM_STANDARD_INDEX_FORMAT_H
-#define BAM_STANDARD_INDEX_FORMAT_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 "api/BamAux.h"
-#include "api/BamIndex.h"
-#include <map>
-#include <set>
-#include <string>
-#include <vector>
-
-namespace BamTools {
-namespace Internal {
-
-// -----------------------------------------------------------------------------
-// BamStandardIndex data structures
-
-// defines start and end of a contiguous run of alignments
-struct 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 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 BaiReferenceSummary {
-
- // data members
- int NumBins;
- int NumLinearOffsets;
- uint64_t FirstBinFilePosition;
- uint64_t FirstLinearOffsetFilePosition;
-
- // ctor
- BaiReferenceSummary(void)
- : 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 BamStandardIndex : public BamIndex {
-
- // ctor & dtor
- public:
- BamStandardIndex(Internal::BamReaderPrivate* reader);
- ~BamStandardIndex(void);
-
- // BamIndex implementation
- public:
- // builds index from associated BAM file & writes out to index file
- bool Create(void);
- // 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);
- public:
- // returns format's file extension
- static const std::string Extension(void);
-
- // internal methods
- private:
-
- // index file ops
- void CheckMagicNumber(void);
- void CloseFile(void);
- bool IsFileOpen(void) const;
- void OpenFile(const std::string& filename, const char* mode);
- void Seek(const int64_t& position, const int& origin);
- int64_t Tell(void) 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);
- 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);
- 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 {
- FILE* IndexStream;
- char* Buffer;
- RaiiWrapper(void);
- ~RaiiWrapper(void);
- };
- RaiiWrapper 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
projects / bamtools.git / blobdiff