// ***************************************************************************\r
// BamWriter.h (c) 2009 Michael Str�mberg, Derek Barnett\r
// Marth Lab, Department of Biology, Boston College\r
-// All rights reserved.\r
// ---------------------------------------------------------------------------\r
-// Last modified: 4 March 2011 (DB)\r
+// Last modified: 10 October 2011 (DB)\r
// ---------------------------------------------------------------------------\r
// Provides the basic functionality for producing BAM files\r
// ***************************************************************************\r
#ifndef BAMWRITER_H\r
#define BAMWRITER_H\r
\r
-#include <api/api_global.h>\r
-#include <api/BamAux.h>\r
+#include "api/api_global.h"\r
+#include "api/BamAux.h"\r
#include <string>\r
\r
namespace BamTools {\r
class BamAlignment;\r
class SamHeader;\r
\r
+//! \cond\r
namespace Internal {\r
class BamWriterPrivate;\r
} // namespace Internal\r
+//! \endcond\r
\r
class API_EXPORT BamWriter {\r
\r
- public: enum CompressionMode { Compressed = 0\r
- , Uncompressed\r
- };\r
+ // enums\r
+ public:\r
+ enum CompressionMode { Compressed = 0\r
+ , Uncompressed\r
+ };\r
\r
// ctor & dtor\r
public:\r
public:\r
// closes the current BAM file\r
void Close(void);\r
+ // returns a human-readable description of the last error that occurred\r
+ std::string GetErrorString(void) const;\r
// returns true if BAM file is open for writing\r
bool IsOpen(void) const;\r
// opens a BAM file for writing\r
const SamHeader& samHeader,\r
const RefVector& referenceSequences);\r
// saves the alignment to the alignment archive\r
- void SaveAlignment(const BamAlignment& alignment);\r
+ bool SaveAlignment(const BamAlignment& alignment);\r
// sets the output compression mode\r
- void SetCompressionMode(const CompressionMode& compressionMode);\r
+ void SetCompressionMode(const BamWriter::CompressionMode& compressionMode);\r
\r
// private implementation\r
private:\r