// BamIndex.h (c) 2009 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 5 April 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides basic BAM index interface
// ***************************************************************************
#ifndef BAM_INDEX_H
#define BAM_INDEX_H
-#include <api/api_global.h>
-#include <api/BamAux.h>
+#include "api/api_global.h"
+#include "api/BamAux.h"
#include <string>
namespace BamTools {
It is exposed to the public API to allow advanced users to implement
their own custom indexing schemes.
-
- More documentation on methods & enums coming soon.
*/
class API_EXPORT BamIndex {
// enums
public:
- // specify index-caching behavior
- enum IndexCacheMode { FullIndexCaching = 0 // store entire index file contents in memory
- , LimitedIndexCaching // store only index data for current reference
- , NoIndexCaching // do not store any index data between jumps
- };
// list of supported BamIndex types
enum IndexType { BAMTOOLS = 0
// 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;
+
+ // returns the 'type' enum for derived index format
+ virtual BamIndex::IndexType Type(void) const =0;
+
+ //! \cond
+
+ // 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;
+
+ //! \endcond
};
} // namespace BamTools