bool CreateIndex(BamReaderPrivate* reader, const BamIndex::IndexType& type);
bool HasIndex(void) const;
bool IndexHasAlignmentsForReference(const int& refId);
- bool LocateIndex(const std::string& bamFilename, const BamIndex::IndexType& preferredType);
- bool OpenIndex(const std::string& indexFilename);
+ bool LocateIndex(BamReaderPrivate* reader, const BamIndex::IndexType& preferredType);
+ bool OpenIndex(const std::string& indexFilename, BamReaderPrivate* reader);
void SetIndex(BamIndex* index);
void SetIndexCacheMode(const BamIndex::IndexCacheMode& mode);