diff spp/src/BamToolsIndex_p.h @ 6:ce08b0efa3fd draft

Uploaded

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+++ b/spp/src/BamToolsIndex_p.h	Tue Nov 27 16:11:40 2012 -0500
@@ -0,0 +1,192 @@
+// ***************************************************************************
+// BamToolsIndex.h (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 19 November 2010 (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 <BamAux.h>
+#include <BamIndex.h>
+#include <map>
+#include <string>
+#include <vector>
+
+namespace BamTools {
+
+namespace Internal {
+
+// individual index offset entry
+struct BamToolsIndexEntry {
+
+    // data members
+    int32_t MaxEndPosition;
+    int64_t StartOffset;
+    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)
+    { }
+};
+
+// reference index entry
+struct BamToolsReferenceEntry {
+
+    // data members
+    bool HasAlignments;
+    std::vector<BamToolsIndexEntry> Offsets;
+
+    // ctor
+    BamToolsReferenceEntry(void)
+	: HasAlignments(false)
+    { }
+};
+
+// the actual index data structure
+typedef std::map<int, BamToolsReferenceEntry> BamToolsIndexData;
+
+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 (hypothetical) BTI_1_2 would 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
+		 };
+
+
+    // ctor & dtor
+    public:
+	BamToolsIndex(BamTools::BgzfData* bgzf, BamTools::BamReader* 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);
+    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
+    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);
+	// 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);
+
+    // 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;
+};
+
+} // namespace Internal
+} // namespace BamTools
+
+#endif // BAMTOOLS_INDEX_FORMAT_H