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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spp/src/BamWriter_p.h	Tue Nov 27 16:11:40 2012 -0500
@@ -0,0 +1,63 @@
+// ***************************************************************************
+// BamWriter_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 producing BAM files
+// ***************************************************************************
+
+#ifndef BAMWRITER_P_H
+#define BAMWRITER_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 <BamAux.h>
+#include <BGZF.h>
+#include <string>
+#include <vector>
+
+namespace BamTools {
+namespace Internal {
+
+class BamWriterPrivate {
+
+    // ctor & dtor
+    public:
+	BamWriterPrivate(void);
+	~BamWriterPrivate(void);
+
+    // "public" interface to BamWriter
+    public:
+	void Close(void);
+	bool Open(const std::string& filename,
+		  const std::string& samHeader,
+		  const BamTools::RefVector& referenceSequences,
+		  bool isWriteUncompressed);
+	void SaveAlignment(const BamAlignment& al);
+
+    // internal methods
+    public:
+	const unsigned int CalculateMinimumBin(const int begin, int end) const;
+	void CreatePackedCigar(const std::vector<BamTools::CigarOp>& cigarOperations, std::string& packedCigar);
+	void EncodeQuerySequence(const std::string& query, std::string& encodedQuery);
+
+    // data members
+    public:
+	BgzfData mBGZF;
+	bool IsBigEndian;
+};
+
+} // namespace Internal
+} // namespace BamTools
+
+#endif // BAMWRITER_P_H