// BamRandomAccessController_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// BamRandomAccessController_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// ---------------------------------------------------------------------------
// Manages random access operations in a BAM file
// ***************************************************************************
// ---------------------------------------------------------------------------
// Manages random access operations in a BAM file
// ***************************************************************************
void ClearIndex(void);
bool CreateIndex(BamReaderPrivate* reader, const BamIndex::IndexType& type);
bool HasIndex(void) const;
void ClearIndex(void);
bool CreateIndex(BamReaderPrivate* reader, const BamIndex::IndexType& type);
bool HasIndex(void) const;
void ClearRegion(void);
bool HasRegion(void) const;
RegionState AlignmentState(const BamAlignment& alignment) const;
bool RegionHasAlignments(void) const;
void ClearRegion(void);
bool HasRegion(void) const;
RegionState AlignmentState(const BamAlignment& alignment) const;
bool RegionHasAlignments(void) const;
- bool SetRegion(BamReaderPrivate* reader,
- const BamRegion& region,
- const int& referenceCount);
+ bool SetRegion(const BamRegion& region, const int& referenceCount);
// adjusts requested region if necessary (depending on where data actually begins)
void AdjustRegion(const int& referenceCount);
// adjusts requested region if necessary (depending on where data actually begins)
void AdjustRegion(const int& referenceCount);