--- /dev/null
+// ***************************************************************************
+// BamToolsIndex.h (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// ---------------------------------------------------------------------------
+// Last modified: 10 October 2011 (DB)
+// ---------------------------------------------------------------------------
+// Provides index operations for the BamTools index format (".bti")
+// ***************************************************************************
+
+#ifndef BAMTOOLS_INDEX_FORMAT_H
+#define BAMTOOLS_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 <string>
+#include <vector>
+
+namespace BamTools {
+namespace Internal {
+
+// contains data for each 'block' in a BTI index
+struct BtiBlock {
+
+ // data members
+ int32_t MaxEndPosition;
+ int64_t StartOffset;
+ int32_t StartPosition;
+
+ // ctor
+ 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)
+ { }
+};
+
+// provides (persistent) summary of BtiReferenceEntry's index data
+struct BtiReferenceSummary {
+
+ // data members
+ int NumBlocks;
+ uint64_t FirstBlockFilePosition;
+
+ // ctor
+ BtiReferenceSummary(void)
+ : NumBlocks(0)
+ , FirstBlockFilePosition(0)
+ { }
+};
+
+// convenience typedef for describing a full BTI index file summary
+typedef std::vector<BtiReferenceSummary> BtiFileSummary;
+
+class BamToolsIndex : public BamIndex {
+
+ // keep a list of any supported versions here
+ // (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 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_2_0
+ };
+
+ // ctor & dtor
+ public:
+ BamToolsIndex(Internal::BamReaderPrivate* reader);
+ ~BamToolsIndex(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 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:
+ bool m_isBigEndian;
+ 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
+} // namespace BamTools
+
+#endif // BAMTOOLS_INDEX_FORMAT_H
projects / bamtools.git / blobdiff