// 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"
// internal methods, but available as a BamReaderPrivate 'interface'
//
// these methods should only be used by BamTools::Internal classes
// (currently only used by the BamIndex subclasses)
public:
// retrieves header text from BAM file
// internal methods, but available as a BamReaderPrivate 'interface'
//
// these methods should only be used by BamTools::Internal classes
// (currently only used by the BamIndex subclasses)
public:
// retrieves header text from BAM file
// retrieves BAM alignment under file pointer
// (does no overlap checking or character data parsing)
bool LoadNextAlignment(BamAlignment& alignment);
// retrieves BAM alignment under file pointer
// (does no overlap checking or character data parsing)
bool LoadNextAlignment(BamAlignment& alignment);