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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spp/src/BamReader_p.h	Tue Nov 27 16:11:40 2012 -0500
@@ -0,0 +1,137 @@
+// ***************************************************************************
+// BamReader_p.h (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 19 November 2010 (DB)
+// ---------------------------------------------------------------------------
+// Provides the basic functionality for reading BAM files
+// ***************************************************************************
+
+#ifndef BAMREADER_P_H
+#define BAMREADER_P_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 <BamAlignment.h>
+#include <BamIndex.h>
+#include <BGZF.h>
+#include <string>
+
+namespace BamTools {
+
+class BamReader;
+
+namespace Internal {
+
+class BamReaderPrivate {
+
+    // enums
+    public: enum RegionState { BEFORE_REGION = 0
+			     , WITHIN_REGION
+			     , AFTER_REGION
+			     };
+
+    // ctor & dtor
+    public:
+	BamReaderPrivate(BamReader* parent);
+	~BamReaderPrivate(void);
+
+    // 'public' interface to BamReader
+    public:
+
+	// file operations
+	void Close(void);
+	bool Open(const std::string& filename,
+		  const std::string& indexFilename,
+		  const bool lookForIndex,
+		  const bool preferStandardIndex);
+	bool Rewind(void);
+	bool SetRegion(const BamRegion& region);
+
+	// access alignment data
+	bool GetNextAlignment(BamAlignment& bAlignment);
+	bool GetNextAlignmentCore(BamAlignment& bAlignment);
+
+	// access auxiliary data
+	const std::string GetHeaderText(void) const;
+	int GetReferenceID(const std::string& refName) const;
+
+	// index operations
+	bool CreateIndex(bool useStandardIndex);
+	void SetIndexCacheMode(const BamIndex::BamIndexCacheMode mode);
+
+    // 'internal' methods
+    public:
+
+	// ---------------------------------------
+	// reading alignments and auxiliary data
+
+	// adjusts requested region if necessary (depending on where data actually begins)
+	void AdjustRegion(BamRegion& region);
+	// fills out character data for BamAlignment data
+	bool BuildCharData(BamAlignment& bAlignment);
+	// checks to see if alignment overlaps current region
+	RegionState IsOverlap(BamAlignment& bAlignment);
+	// retrieves header text from BAM file
+	void LoadHeaderData(void);
+	// retrieves BAM alignment under file pointer
+	bool LoadNextAlignment(BamAlignment& bAlignment);
+	// builds reference data structure from BAM file
+	void LoadReferenceData(void);
+	// mark references with 'HasAlignments' status
+	void MarkReferences(void);
+
+	// ---------------------------------
+	// index file handling
+
+	// clear out inernal index data structure
+	void ClearIndex(void);
+	// loads index from BAM index file
+	bool LoadIndex(const bool lookForIndex, const bool preferStandardIndex);
+
+    // data members
+    public:
+
+	// general file data
+	BgzfData  mBGZF;
+	std::string HeaderText;
+	BamIndex* Index;
+	RefVector References;
+	bool      HasIndex;
+	int64_t   AlignmentsBeginOffset;
+	std::string    Filename;
+	std::string    IndexFilename;
+
+//	Internal::BamHeader* m_header;
+
+	// index caching mode
+	BamIndex::BamIndexCacheMode IndexCacheMode;
+
+	// system data
+	bool IsBigEndian;
+
+	// user-specified region values
+	BamRegion Region;
+	bool HasAlignmentsInRegion;
+
+	// parent BamReader
+	BamReader* Parent;
+
+	// BAM character constants
+	const char* DNA_LOOKUP;
+	const char* CIGAR_LOOKUP;
+};
+
+} // namespace Internal
+} // namespace BamTools
+
+#endif // BAMREADER_P_H