Reorganized source tree & build system

[bamtools.git] / src / api / BamIndex.h

diff --git a/src/api/BamIndex.h b/src/api/BamIndex.h
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+// ***************************************************************************
+// BamIndex.h (c) 2009 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 17 August 2010 (DB)
+// ---------------------------------------------------------------------------
+// Provides index functionality - both for the default (standardized) BAM 
+// index format (.bai) as well as a BamTools-specific (nonstandard) index 
+// format (.bti).
+// ***************************************************************************
+
+#ifndef BAM_INDEX_H
+#define BAM_INDEX_H
+
+#include <string>
+#include <vector>
+#include "BamAux.h"
+
+namespace BamTools {
+
+class BamReader;
+class BgzfData;
+  
+// --------------------------------------------------  
+// BamIndex base class
+class BamIndex {
+
+    public:
+        BamIndex(BamTools::BgzfData*  bgzf, 
+                 BamTools::BamReader* reader,
+                 bool isBigEndian);
+        virtual ~BamIndex(void) { }
+
+    public:
+        // creates index data (in-memory) from current reader data
+        virtual bool Build(void) =0;
+        // calculates offset(s) for a given region
+        virtual bool GetOffsets(const BamTools::BamRegion& region, const bool isRightBoundSpecified, std::vector<int64_t>& offsets) =0;
+        // loads existing data from file into memory
+        virtual bool Load(const std::string& filename)  =0;
+        // returns whether reference has alignments or no
+        virtual bool HasAlignments(const int& referenceID); 
+        // writes in-memory index data out to file 
+        // N.B. - (this is the original BAM filename, method will modify it to use applicable extension)
+        virtual bool Write(const std::string& bamFilename) =0;
+        
+    protected:
+        BamTools::BgzfData*  m_BGZF;
+        BamTools::BamReader* m_reader;
+        BamTools::RefVector  m_references;
+        bool m_isBigEndian;
+};
+
+// --------------------------------------------------
+// BamDefaultIndex class
+// 
+// implements default (per SAM/BAM spec) index file ops
+class BamDefaultIndex : public BamIndex {
+
+  
+    // ctor & dtor
+    public:
+        BamDefaultIndex(BamTools::BgzfData*  bgzf, 
+                        BamTools::BamReader* reader,
+                        bool isBigEndian);
+        ~BamDefaultIndex(void);
+        
+    // interface (implements BamIndex virtual methods)
+    public:
+        // creates index data (in-memory) from current reader data
+        bool Build(void);
+        // calculates offset(s) for a given region
+        bool GetOffsets(const BamTools::BamRegion& region, const bool isRightBoundSpecified, std::vector<int64_t>& offsets);
+         // loads existing data from file into memory
+        bool Load(const std::string& filename);
+        // writes in-memory index data out to file 
+        // N.B. - (this is the original BAM filename, method will modify it to use applicable extension)
+        bool Write(const std::string& bamFilename);
+      
+    // internal implementation
+    private:
+        struct BamDefaultIndexPrivate;
+        BamDefaultIndexPrivate* d;
+};
+
+// --------------------------------------------------
+// BamToolsIndex class
+//
+// implements BamTools-specific index file ops
+class BamToolsIndex : public BamIndex {
+
+    // ctor & dtor
+    public:
+        BamToolsIndex(BamTools::BgzfData*  bgzf, 
+                      BamTools::BamReader* reader,
+                      bool isBigEndian);
+        ~BamToolsIndex(void);
+        
+    // interface (implements BamIndex virtual methods)
+    public:
+        // creates index data (in-memory) from current reader data
+        bool Build(void);
+        // calculates offset(s) for a given region
+        bool GetOffsets(const BamTools::BamRegion& region, const bool isRightBoundSpecified, std::vector<int64_t>& offsets);
+         // loads existing data from file into memory
+        bool Load(const std::string& filename);
+        // writes in-memory index data out to file 
+        // N.B. - (this is the original BAM filename, method will modify it to use applicable extension)
+        bool Write(const std::string& bamFilename);
+    
+    // internal implementation
+    private:
+        struct BamToolsIndexPrivate;
+        BamToolsIndexPrivate* d;
+};
+
+} // namespace BamTools
+
+#endif // BAM_INDEX_H
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