X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2FBamWriter.h;h=68257ee4a8a3e3145090154cd93fb601a1ca2666;hb=9f1ce8c47aeadb6dc1320b52ee671c3341b97935;hp=910f9be6240fa40a0fe9ecefe2da52ad564cdb6c;hpb=e24bc523b0bd086dbfad7165901b2237b5d64316;p=bamtools.git

diff --git a/src/api/BamWriter.h b/src/api/BamWriter.h
index 910f9be..68257ee 100644
--- a/src/api/BamWriter.h
+++ b/src/api/BamWriter.h
@@ -1,12 +1,8 @@
 // ***************************************************************************
 // BamWriter.h (c) 2009 Michael Str�mberg, Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 19 November 2010 (DB)
-// ---------------------------------------------------------------------------
-// Uses BGZF routines were adapted from the bgzf.c code developed at the Broad
-// Institute.
+// Last modified: 10 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Provides the basic functionality for producing BAM files
 // ***************************************************************************
@@ -14,35 +10,58 @@
 #ifndef BAMWRITER_H
 #define BAMWRITER_H
 
-#include <api/api_global.h>
-#include <api/BamAlignment.h>
+#include "api/api_global.h"
+#include "api/BamAux.h"
 #include <string>
 
 namespace BamTools {
 
+class BamAlignment;
+class SamHeader;
+
+//! \cond
+namespace Internal {
+    class BamWriterPrivate;
+} // namespace Internal
+//! \endcond
+
 class API_EXPORT BamWriter {
 
-    // constructor/destructor
+    // enums
+    public:
+        enum CompressionMode { Compressed = 0
+                             , Uncompressed
+                             };
+
+    // ctor & dtor
     public:
         BamWriter(void);
         ~BamWriter(void);
 
     // public interface
     public:
-        // closes the alignment archive
+        //  closes the current BAM file
         void Close(void);
-        // opens the alignment archive
+        // returns a human-readable description of the last error that occurred
+        std::string GetErrorString(void) const;
+        // returns true if BAM file is open for writing
+        bool IsOpen(void) const;
+        // opens a BAM file for writing
         bool Open(const std::string& filename, 
-                  const std::string& samHeader, 
-                  const BamTools::RefVector& referenceSequences, 
-                  bool writeUncompressed = false);
+                  const std::string& samHeaderText,
+                  const RefVector& referenceSequences);
+        // opens a BAM file for writing
+        bool Open(const std::string& filename,
+                  const SamHeader& samHeader,
+                  const RefVector& referenceSequences);
         // saves the alignment to the alignment archive
-        void SaveAlignment(const BamTools::BamAlignment& al);
+        bool SaveAlignment(const BamAlignment& alignment);
+        // sets the output compression mode
+        void SetCompressionMode(const BamWriter::CompressionMode& compressionMode);
 
     // private implementation
     private:
-        struct BamWriterPrivate;
-        BamWriterPrivate* d;
+        Internal::BamWriterPrivate* d;
 };
 
 } // namespace BamTools