// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 19 November 2010 (DB)
+// Last modified: 19 January 2011 (DB)
// ---------------------------------------------------------------------------
// Provides index operations for the standardized BAM index format (".bai")
// ***************************************************************************
// BAM index constants
const int MAX_BIN = 37450; // =(8^6-1)/7+1
const int BAM_LIDX_SHIFT = 14;
+const std::string BAI_EXTENSION = ".bai";
// --------------------------------------------------
// BamStandardIndex data structures & typedefs
// constructor
Chunk(const uint64_t& start = 0,
- const uint64_t& stop = 0)
- : Start(start)
- , Stop(stop)
+ const uint64_t& stop = 0)
+ : Start(start)
+ , Stop(stop)
{ }
};
bool HasAlignments;
// constructor
- ReferenceIndex(const BamBinMap& binMap = BamBinMap(),
- const LinearOffsetVector& offsets = LinearOffsetVector(),
- const bool hasAlignments = false)
- : Bins(binMap)
- , Offsets(offsets)
- , HasAlignments(hasAlignments)
+ ReferenceIndex(const BamBinMap& binMap = BamBinMap(),
+ const LinearOffsetVector& offsets = LinearOffsetVector(),
+ const bool hasAlignments = false)
+ : Bins(binMap)
+ , Offsets(offsets)
+ , HasAlignments(hasAlignments)
{ }
};
// ctor & dtor
public:
- BamStandardIndex(BamTools::BgzfData* bgzf, BamTools::BamReader* reader);
- ~BamStandardIndex(void);
+ BamStandardIndex(void);
+ ~BamStandardIndex(void);
// interface (implements BamIndex virtual methods)
public:
- // creates index data (in-memory) from current reader data
- bool Build(void);
- // returns supported file extension
- const std::string Extension(void) const { return std::string(".bai"); }
- // returns whether reference has alignments or no
- bool HasAlignments(const int& referenceID) const;
- // attempts to use index 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);
+ // creates index data (in-memory) from @reader data
+ bool Build(Internal::BamReaderPrivate* reader);
+ // returns supported file extension
+ const std::string Extension(void) { return BAI_EXTENSION; }
+ // returns whether reference has alignments or no
+ bool HasAlignments(const int& referenceID) const;
+ // attempts to use index to jump to @region in @reader; 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(Internal::BamReaderPrivate* reader,
+ const BamTools::BamRegion& region,
+ bool* hasAlignmentsInRegion);
+
public:
- // clear all current index offset data in memory
- void ClearAllData(void);
- // return file position after header metadata
- const off_t DataBeginOffset(void) const;
- // return true if all index data is cached
- bool HasFullDataCache(void) const;
- // clears index data from all references except the first
- void KeepOnlyFirstReferenceOffsets(void);
- // load index data for all references, return true if loaded OK
- // @saveData - save data in memory if true, just read & discard if false
- bool LoadAllReferences(bool saveData = true);
- // load first reference from file, return true if loaded OK
- // @saveData - save data in memory if true, just read & discard if false
- bool LoadFirstReference(bool saveData = true);
- // load header data from index file, return true if loaded OK
- bool LoadHeader(void);
- // position file pointer to first reference begin, return true if skipped OK
- bool SkipToFirstReference(void);
- // write index reference data
- bool WriteAllReferences(void);
- // write index header data
- bool WriteHeader(void);
+ // clear all current index offset data in memory
+ void ClearAllData(void);
+ // return file position after header metadata
+ off_t DataBeginOffset(void) const;
+ // return true if all index data is cached
+ bool HasFullDataCache(void) const;
+ // clears index data from all references except the first
+ void KeepOnlyFirstReferenceOffsets(void);
+ // load index data for all references, return true if loaded OK
+ // @saveData - save data in memory if true, just read & discard if false
+ bool LoadAllReferences(bool saveData = true);
+ // load first reference from file, return true if loaded OK
+ // @saveData - save data in memory if true, just read & discard if false
+ bool LoadFirstReference(bool saveData = true);
+ // load header data from index file, return true if loaded OK
+ bool LoadHeader(void);
+ // position file pointer to first reference begin, return true if skipped OK
+ bool SkipToFirstReference(void);
+ // write index reference data
+ bool WriteAllReferences(void);
+ // write index header data
+ bool WriteHeader(void);
// 'internal' methods
public:
- // -----------------------
- // index file operations
-
- // check index file magic number, return true if OK
- bool CheckMagicNumber(void);
- // check index file version, return true if OK
- bool CheckVersion(void);
- // load a single index bin entry from file, return true if loaded OK
- // @saveData - save data in memory if true, just read & discard if false
- bool LoadBin(ReferenceIndex& refEntry, bool saveData = true);
- bool LoadBins(ReferenceIndex& refEntry, bool saveData = true);
- // load a single index bin entry from file, return true if loaded OK
- // @saveData - save data in memory if true, just read & discard if false
- bool LoadChunk(ChunkVector& chunks, bool saveData = true);
- bool LoadChunks(ChunkVector& chunks, bool saveData = true);
- // load a single index linear offset entry from file, return true if loaded OK
- // @saveData - save data in memory if true, just read & discard if false
- bool LoadLinearOffsets(ReferenceIndex& refEntry, bool saveData = true);
- // load a single reference from file, return true if loaded OK
- // @saveData - save data in memory if true, just read & discard if false
- bool LoadReference(const int& refId, bool saveData = true);
- // loads number of references, return true if loaded OK
- bool LoadReferenceCount(int& numReferences);
- // position file pointer to desired reference begin, return true if skipped OK
- bool SkipToReference(const int& refId);
- // write index data for bin to new index file
- bool WriteBin(const uint32_t& binId, const ChunkVector& chunks);
- // write index data for bins to new index file
- bool WriteBins(const BamBinMap& bins);
- // write index data for chunk entry to new index file
- bool WriteChunk(const Chunk& chunk);
- // write index data for chunk entry to new index file
- bool WriteChunks(const ChunkVector& chunks);
- // write index data for linear offsets entry to new index file
- bool WriteLinearOffsets(const LinearOffsetVector& offsets);
- // write index data single reference to new index file
- bool WriteReference(const ReferenceIndex& refEntry);
-
- // -----------------------
- // index data operations
-
- // calculate bins that overlap region
- int BinsFromRegion(const BamRegion& region,
- const bool isRightBoundSpecified,
- uint16_t bins[MAX_BIN]);
- // clear all index offset data for desired reference
- void ClearReferenceOffsets(const int& refId);
- // calculates offset(s) for a given region
- bool GetOffsets(const BamRegion& region,
- const bool isRightBoundSpecified,
- std::vector<int64_t>& offsets,
- bool* hasAlignmentsInRegion);
- // returns true if index cache has data for desired reference
- bool IsDataLoaded(const int& refId) const;
- // clears index data from all references except the one specified
- void KeepOnlyReferenceOffsets(const int& refId);
- // simplifies index by merging 'chunks'
- void MergeChunks(void);
- // saves BAM bin entry for index
- void SaveBinEntry(BamBinMap& binMap,
- const uint32_t& saveBin,
- const uint64_t& saveOffset,
- const uint64_t& lastOffset);
- // saves linear offset entry for index
- void SaveLinearOffset(LinearOffsetVector& offsets,
- const BamAlignment& bAlignment,
- const uint64_t& lastOffset);
- // initializes index data structure to hold @count references
- void SetReferenceCount(const int& count);
+ // -----------------------
+ // index file operations
+
+ // check index file magic number, return true if OK
+ bool CheckMagicNumber(void);
+ // check index file version, return true if OK
+ bool CheckVersion(void);
+ // load a single index bin entry from file, return true if loaded OK
+ // @saveData - save data in memory if true, just read & discard if false
+ bool LoadBin(ReferenceIndex& refEntry, bool saveData = true);
+ bool LoadBins(ReferenceIndex& refEntry, bool saveData = true);
+ // load a single index bin entry from file, return true if loaded OK
+ // @saveData - save data in memory if true, just read & discard if false
+ bool LoadChunk(ChunkVector& chunks, bool saveData = true);
+ bool LoadChunks(ChunkVector& chunks, bool saveData = true);
+ // load a single index linear offset entry from file, return true if loaded OK
+ // @saveData - save data in memory if true, just read & discard if false
+ bool LoadLinearOffsets(ReferenceIndex& refEntry, bool saveData = true);
+ // load a single reference from file, return true if loaded OK
+ // @saveData - save data in memory if true, just read & discard if false
+ bool LoadReference(const int& refId, bool saveData = true);
+ // loads number of references, return true if loaded OK
+ bool LoadReferenceCount(int& numReferences);
+ // position file pointer to desired reference begin, return true if skipped OK
+ bool SkipToReference(const int& refId);
+ // write index data for bin to new index file
+ bool WriteBin(const uint32_t& binId, const ChunkVector& chunks);
+ // write index data for bins to new index file
+ bool WriteBins(const BamBinMap& bins);
+ // write index data for chunk entry to new index file
+ bool WriteChunk(const Chunk& chunk);
+ // write index data for chunk entry to new index file
+ bool WriteChunks(const ChunkVector& chunks);
+ // write index data for linear offsets entry to new index file
+ bool WriteLinearOffsets(const LinearOffsetVector& offsets);
+ // write index data single reference to new index file
+ bool WriteReference(const ReferenceIndex& refEntry);
+
+ // -----------------------
+ // index data operations
+
+ // calculate bins that overlap region
+ int BinsFromRegion(const BamRegion& region,
+ const RefVector& references,
+ const bool isRightBoundSpecified,
+ uint16_t bins[MAX_BIN]);
+ // clear all index offset data for desired reference
+ void ClearReferenceOffsets(const int& refId);
+ // calculates offset(s) for a given region
+ bool GetOffsets(const BamRegion& region,
+ const RefVector& references,
+ const bool isRightBoundSpecified,
+ std::vector<int64_t>& offsets,
+ bool* hasAlignmentsInRegion);
+ // returns true if index cache has data for desired reference
+ bool IsDataLoaded(const int& refId) const;
+ // clears index data from all references except the one specified
+ void KeepOnlyReferenceOffsets(const int& refId);
+ // simplifies index by merging 'chunks'
+ void MergeChunks(void);
+ // saves BAM bin entry for index
+ void SaveBinEntry(BamBinMap& binMap,
+ const uint32_t& saveBin,
+ const uint64_t& saveOffset,
+ const uint64_t& lastOffset);
+ // saves linear offset entry for index
+ void SaveLinearOffset(LinearOffsetVector& offsets,
+ const BamAlignment& bAlignment,
+ const uint64_t& lastOffset);
+ // initializes index data structure to hold @count references
+ void SetReferenceCount(const int& count);
// data members
private:
- BamStandardIndexData m_indexData;
- off_t m_dataBeginOffset;
- bool m_hasFullDataCache;
- bool m_isBigEndian;
+ BamStandardIndexData m_indexData;
+ off_t m_dataBeginOffset;
+ bool m_hasFullDataCache;
+ bool m_isBigEndian;
};
} // namespace Internal
projects / bamtools.git / blobdiff