// ***************************************************************************
// BamToolsIndex.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 19 November 2010 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides index operations for the BamTools index format (".bti")
// ***************************************************************************
//
// We mean it.
-#include <api/BamAux.h>
-#include <api/BamIndex.h>
+#include "api/BamAux.h"
+#include "api/BamIndex.h"
#include <map>
#include <string>
#include <vector>
namespace BamTools {
-
namespace Internal {
-// individual index offset entry
-struct BamToolsIndexEntry {
+// contains data for each 'block' in a BTI index
+struct BtiBlock {
// data members
int32_t MaxEndPosition;
int32_t StartPosition;
// ctor
- BamToolsIndexEntry(const int32_t& maxEndPosition = 0,
- const int64_t& startOffset = 0,
- const int32_t& startPosition = 0)
- : MaxEndPosition(maxEndPosition)
- , StartOffset(startOffset)
- , StartPosition(startPosition)
+ BtiBlock(const int32_t& maxEndPosition = 0,
+ const int64_t& startOffset = 0,
+ const int32_t& startPosition = 0)
+ : MaxEndPosition(maxEndPosition)
+ , StartOffset(startOffset)
+ , StartPosition(startPosition)
+ { }
+};
+
+// convenience typedef for describing a a list of BTI blocks on a reference
+typedef std::vector<BtiBlock> BtiBlockVector;
+
+// contains all fields necessary for building, loading, & writing
+// full BTI index data for a single reference
+struct BtiReferenceEntry {
+
+ // data members
+ int32_t ID;
+ BtiBlockVector Blocks;
+
+ // ctor
+ BtiReferenceEntry(const int& id = -1)
+ : ID(id)
{ }
};
-// reference index entry
-struct BamToolsReferenceEntry {
+// provides (persistent) summary of BtiReferenceEntry's index data
+struct BtiReferenceSummary {
// data members
- bool HasAlignments;
- std::vector<BamToolsIndexEntry> Offsets;
+ int NumBlocks;
+ uint64_t FirstBlockFilePosition;
// ctor
- BamToolsReferenceEntry(void)
- : HasAlignments(false)
+ BtiReferenceSummary(void)
+ : NumBlocks(0)
+ , FirstBlockFilePosition(0)
{ }
};
-// the actual index data structure
-typedef std::map<int, BamToolsReferenceEntry> BamToolsIndexData;
+// convenience typedef for describing a full BTI index file summary
+typedef std::vector<BtiReferenceSummary> BtiFileSummary;
class BamToolsIndex : public BamIndex {
// (might be useful later to handle any 'legacy' versions if the format changes)
// listed for example like: BTI_1_0 = 1, BTI_1_1 = 2, BTI_1_2 = 3, BTI_2_0 = 4, and so on
//
- // so a change introduced in (hypothetical) BTI_1_2 would be handled from then on by:
+ // so a change introduced in BTI_1_2 may be handled from then on by:
//
// if ( indexVersion >= BTI_1_2 )
// do something new
// else
// do the old thing
enum Version { BTI_1_0 = 1
- , BTI_1_1
- , BTI_1_2
- };
-
+ , BTI_1_1
+ , BTI_1_2
+ , BTI_2_0
+ };
// ctor & dtor
public:
- BamToolsIndex(BamTools::BgzfData* bgzf, BamTools::BamReader* reader);
- ~BamToolsIndex(void);
+ BamToolsIndex(Internal::BamReaderPrivate* reader);
+ ~BamToolsIndex(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(".bti"); }
- // 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);
+ // BamIndex implementation
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);
-
- // 'internal' methods
+ // 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);
+ // change the index caching behavior
+ void SetCacheMode(const BamIndex::IndexCacheMode& mode);
public:
+ // returns format's file extension
+ static const std::string Extension(void);
- // -----------------------
- // 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);
- // return true if FILE* is open
- bool IsOpen(void) const;
- // load a single index entry from file, return true if loaded OK
- // @saveData - save data in memory if true, just read & discard if false
- bool LoadIndexEntry(const int& refId, 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 current reference index data to new index file
- bool WriteReferenceEntry(const BamToolsReferenceEntry& refEntry);
- // write current index offset entry to new index file
- bool WriteIndexEntry(const BamToolsIndexEntry& entry);
-
- // -----------------------
- // index data operations
-
- // clear all index offset data for desired reference
- void ClearReferenceOffsets(const int& refId);
- // calculate BAM file offset for desired region
- // return true if no error (*NOT* equivalent to "has alignments or valid offset")
- // check @hasAlignmentsInRegion to determine this status
- // @region - target region
- // @offset - resulting seek target
- // @hasAlignmentsInRegion - sometimes a file just lacks data in region, this flag indicates that status
- bool GetOffset(const BamRegion& region, int64_t& offset, 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);
- // saves an index offset entry in memory
- void SaveOffsetEntry(const int& refId, const BamToolsIndexEntry& entry);
- // pre-allocates size for offset vector
- void SetOffsetCount(const int& refId, const int& offsetCount);
- // initializes index data structure to hold @count references
- void SetReferenceCount(const int& count);
+ // internal methods
+ private:
+
+ // index file ops
+ void CheckMagicNumber(void);
+ void CheckVersion(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;
+
+ // index-creation methods
+ void ClearReferenceEntry(BtiReferenceEntry& refEntry);
+ void WriteBlock(const BtiBlock& block);
+ void WriteBlocks(const BtiBlockVector& blocks);
+ void WriteHeader(void);
+ void WriteReferenceEntry(const BtiReferenceEntry& refEntry);
+
+ // random-access methods
+ void GetOffset(const BamRegion& region, int64_t& offset, bool* hasAlignmentsInRegion);
+ void ReadBlock(BtiBlock& block);
+ void ReadBlocks(const BtiReferenceSummary& refSummary, BtiBlockVector& blocks);
+ void ReadReferenceEntry(BtiReferenceEntry& refEntry);
+
+ // BTI summary data methods
+ void InitializeFileSummary(const int& numReferences);
+ void LoadFileSummary(void);
+ void LoadHeader(void);
+ void LoadNumBlocks(int& numBlocks);
+ void LoadNumReferences(int& numReferences);
+ void LoadReferenceSummary(BtiReferenceSummary& refSummary);
+ void SkipBlocks(const int& numBlocks);
// data members
private:
- int32_t m_blockSize;
- BamToolsIndexData m_indexData;
- off_t m_dataBeginOffset;
- bool m_hasFullDataCache;
- bool m_isBigEndian;
- int32_t m_inputVersion; // Version is serialized as int
- Version m_outputVersion;
+ bool m_isBigEndian;
+ BamIndex::IndexCacheMode m_cacheMode;
+ BtiFileSummary m_indexFileSummary;
+ uint32_t m_blockSize;
+ int32_t m_inputVersion; // Version is serialized as int
+ Version m_outputVersion;
+
+ struct RaiiWrapper {
+ FILE* IndexStream;
+ RaiiWrapper(void);
+ ~RaiiWrapper(void);
+ };
+ RaiiWrapper Resources;
+
+ // static constants
+ private:
+ static const uint32_t DEFAULT_BLOCK_LENGTH;
+ static const std::string BTI_EXTENSION;
+ static const char* const BTI_MAGIC;
+ static const int SIZEOF_BLOCK;
};
} // namespace Internal
projects / bamtools.git / blobdiff