// BamMultiReader.h (c) 2010 Erik Garrison, Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 15 March 2011 (DB)
+// Last modified: 1 October 2011 (DB)
// ---------------------------------------------------------------------------
// Convenience class for reading multiple BAM files.
// ***************************************************************************
class API_EXPORT BamMultiReader {
- public:
- enum SortOrder { SortedByPosition = 0
- , SortedByReadName
- , Unsorted
- };
-
// constructor / destructor
public:
BamMultiReader(void);
// retrieves next available alignment
bool GetNextAlignment(BamAlignment& alignment);
- // retrieves next available alignmnet (without populating the alignment's string data fields)
+ // retrieves next available alignment (without populating the alignment's string data fields)
bool GetNextAlignmentCore(BamAlignment& alignment);
- // sets the expected sorting order for reading across multiple BAM files
- void SetSortOrder(const SortOrder& order);
-
// ----------------------
// access auxiliary data
// ----------------------
// changes the caching behavior of the index data
void SetIndexCacheMode(const BamIndex::IndexCacheMode& mode);
- // deprecated methods
- public:
- // returns \c true if all BAM files have index data available.
- bool IsIndexLoaded(void) const;
- // convenience method for printing filenames to stdout
- void PrintFilenames(void) const;
-
// private implementation
private:
Internal::BamMultiReaderPrivate* d;