// BamIndex.h (c) 2009 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 5 April 2011 (DB)
+// Last modified: 6 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides basic BAM index interface
// ***************************************************************************
// index interface
public:
// builds index from associated BAM file & writes out to index file
- virtual bool Create(void) =0; // creates index file from BAM file
+ virtual bool Create(void) =0;
+
+ // returns a human-readable description of the last error encountered
+ std::string GetErrorString(void) { return m_errorString; }
+
// returns whether reference has alignments or no
virtual bool HasAlignments(const int& referenceID) const =0;
+
// attempts to use index data to jump to @region, returns success/fail
// a "successful" jump indicates no error, but not whether this region has data
// * thus, the method sets a flag to indicate whether there are alignments
// available after the jump position
virtual bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion) =0;
+
// loads existing data from file into memory
virtual bool Load(const std::string& filename) =0;
+
// change the index caching behavior
virtual void SetCacheMode(const BamIndex::IndexCacheMode& mode) =0;
+ // internal methods
+ protected:
+ void SetErrorString(const std::string& where, const std::string& what) const {
+ m_errorString = where + ": " + what;
+ }
+
// data members
protected:
- Internal::BamReaderPrivate* m_reader; // copy, not ownedprivate:
+ Internal::BamReaderPrivate* m_reader; // copy, not owned
+ mutable std::string m_errorString;
};
} // namespace BamTools