// ***************************************************************************
// BamReader_p.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ***************************************************************************
// BamReader_p.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Provides the basic functionality for reading BAM files
// ***************************************************************************
// ---------------------------------------------------------------------------
// Provides the basic functionality for reading BAM files
// ***************************************************************************
-#include <api/BamAlignment.h>
-#include <api/BamIndex.h>
-#include <api/BamReader.h>
-#include <api/SamHeader.h>
-#include <api/internal/BamHeader_p.h>
-#include <api/internal/BamRandomAccessController_p.h>
-#include <api/internal/BgzfStream_p.h>
+#include "api/BamAlignment.h"
+#include "api/BamIndex.h"
+#include "api/BamReader.h"
+#include "api/SamHeader.h"
+#include "api/internal/BamHeader_p.h"
+#include "api/internal/BamRandomAccessController_p.h"
+#include "api/internal/BgzfStream_p.h"
- // BamReaderPrivate interface
- public:
- BgzfStream* Stream(void);
+ // error handling
+ std::string GetErrorString(void) const;
+ void SetErrorString(const std::string& where, const std::string& what);
// retrieves BAM alignment under file pointer
// (does no overlap checking or character data parsing)
bool LoadNextAlignment(BamAlignment& alignment);
// builds reference data structure from BAM file
bool LoadReferenceData(void);
// retrieves BAM alignment under file pointer
// (does no overlap checking or character data parsing)
bool LoadNextAlignment(BamAlignment& alignment);
// builds reference data structure from BAM file
bool LoadReferenceData(void);