- bool CreateIndex(bool useStandardIndex);
- void SetIndexCacheMode(const BamIndex::BamIndexCacheMode mode);
-
- // 'internal' methods
+ bool CreateIndex(const BamIndex::IndexType& type);
+ bool HasIndex(void) const;
+ bool LocateIndex(const BamIndex::IndexType& preferredType);
+ bool OpenIndex(const std::string& indexFilename);
+ void SetIndex(BamIndex* index);
+ void SetIndexCacheMode(const BamIndex::IndexCacheMode& mode);
+
+ // error handling
+ std::string GetErrorString(void) const;
+ void SetErrorString(const std::string& where, const std::string& what);
+
+ // 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)