// ***************************************************************************\r
// BamReader.h (c) 2009 Derek Barnett, Michael Str�mberg\r
// Marth Lab, Department of Biology, Boston College\r
// ***************************************************************************\r
// BamReader.h (c) 2009 Derek Barnett, Michael Str�mberg\r
// Marth Lab, Department of Biology, Boston College\r
// ---------------------------------------------------------------------------\r
// Provides read access to BAM files.\r
// ***************************************************************************\r
// ---------------------------------------------------------------------------\r
// Provides read access to BAM files.\r
// ***************************************************************************\r
-#include <api/api_global.h>\r
-#include <api/BamAlignment.h>\r
-#include <api/BamIndex.h>\r
-#include <api/SamHeader.h>\r
+#include "api/api_global.h"\r
+#include "api/BamAlignment.h"\r
+#include "api/BamIndex.h"\r
+#include "api/SamHeader.h"\r
// returns filename of current BAM file\r
const std::string GetFilename(void) const;\r
// returns true if a BAM file is open for reading\r
// returns filename of current BAM file\r
const std::string GetFilename(void) const;\r
// returns true if a BAM file is open for reading\r
SamHeader GetHeader(void) const;\r
// returns SAM header data, as SAM-formatted text\r
std::string GetHeaderText(void) const;\r
SamHeader GetHeader(void) const;\r
// returns SAM header data, as SAM-formatted text\r
std::string GetHeaderText(void) const;\r
bool OpenIndex(const std::string& indexFilename);\r
// sets a custom BamIndex on this reader\r
void SetIndex(BamIndex* index);\r
bool OpenIndex(const std::string& indexFilename);\r
// sets a custom BamIndex on this reader\r
void SetIndex(BamIndex* index);\r
- // deprecated methods\r
- public:\r
- // returns true if index data is available\r
- bool IsIndexLoaded(void) const;\r
+ // ----------------------\r
+ // error handling\r
+ // ----------------------\r
+\r
+ // returns a human-readable description of the last error that occurred\r
+ std::string GetErrorString(void) const;\r