Reorganized source tree & build system

[bamtools.git] / src / utils / bamtools_fasta.h

diff --git a/src/utils/bamtools_fasta.h b/src/utils/bamtools_fasta.h
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+// ***************************************************************************
+// bamtools_fasta.h (c) 2010 Derek Barnett, Erik Garrison
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 13 July 2010
+// ---------------------------------------------------------------------------
+// Provides FASTA reading/indexing functionality.
+// ***************************************************************************
+
+#ifndef BAMTOOLS_FASTA_H
+#define BAMTOOLS_FASTA_H
+
+#include <string>
+
+namespace BamTools {
+
+class Fasta {  
+  
+    // ctor & dtor
+    public:
+        Fasta(void);
+        ~Fasta(void);
+        
+    // file-handling methods
+    public:
+        bool Close(void);
+        bool Open(const std::string& filename, const std::string& indexFilename = "");
+        
+    // sequence access methods
+    public:
+        bool GetBase(const int& refID, const int& position, char& base);
+        bool GetSequence(const int& refId, const int& start, const int& stop, std::string& sequence);
+        
+    // index-handling methods
+    public:
+        bool CreateIndex(const std::string& indexFilename);
+
+    // internal implementation
+    private:
+        struct FastaPrivate;
+        FastaPrivate* d;
+};
+  
+} // BAMTOOLS_FASTA_H
+  
+#endif // BAMTOOLS_FASTA_H
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