X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2Finternal%2FBamWriter_p.h;h=cf109416b6f80c57866bd1d4fe518d31cd9e9826;hb=9f1ce8c47aeadb6dc1320b52ee671c3341b97935;hp=4fe626a892b5bbdfb4ffbebdf3dd9ce9f4bff275;hpb=369e2de20a6d939d07ffc09462167a3b688bbdde;p=bamtools.git

diff --git a/src/api/internal/BamWriter_p.h b/src/api/internal/BamWriter_p.h
index 4fe626a..cf10941 100644
--- a/src/api/internal/BamWriter_p.h
+++ b/src/api/internal/BamWriter_p.h
@@ -1,9 +1,8 @@
 // ***************************************************************************
 // BamWriter_p.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 19 November 2010 (DB)
+// Last modified: 10 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Provides the basic functionality for producing BAM files
 // ***************************************************************************
@@ -21,40 +20,51 @@
 //
 // We mean it.
 
-#include <api/BamAux.h>
-#include <api/BGZF.h>
+#include "api/BamAux.h"
+#include "api/internal/BgzfStream_p.h"
 #include <string>
 #include <vector>
 
 namespace BamTools {
+
+class BamAlignment;
+
 namespace Internal {
 
 class BamWriterPrivate {
 
     // ctor & dtor
     public:
-	BamWriterPrivate(void);
-	~BamWriterPrivate(void);
+        BamWriterPrivate(void);
+        ~BamWriterPrivate(void);
 
-    // "public" interface to BamWriter
+    // interface methods
     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
+        void Close(void);
+        std::string GetErrorString(void) const;
+        bool IsOpen(void) const;
+        bool Open(const std::string& filename,
+                  const std::string& samHeaderText,
+                  const BamTools::RefVector& referenceSequences);
+        bool SaveAlignment(const BamAlignment& al);
+        void SetWriteCompressed(bool ok);
+
+    // '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);
+        uint32_t 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);
+        void WriteAlignment(const BamAlignment& al);
+        void WriteCoreAlignment(const BamAlignment& al);
+        void WriteMagicNumber(void);
+        void WriteReferences(const BamTools::RefVector& referenceSequences);
+        void WriteSamHeaderText(const std::string& samHeaderText);
 
     // data members
-    public:
-	BgzfData mBGZF;
-	bool IsBigEndian;
+    private:
+        BgzfStream m_stream;
+        bool m_isBigEndian;
+        std::string m_errorString;
 };
 
 } // namespace Internal