- bool CreateIndex(bool useStandardIndex);
- void SetIndexCacheMode(const BamIndex::BamIndexCacheMode mode);
+ 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);
+
+ // BamReaderPrivate interface
+ public:
+ BgzfStream* Stream(void);