1 // ***************************************************************************
2 // BamWriter_p.h (c) 2010 Derek Barnett
3 // Marth Lab, Department of Biology, Boston College
4 // All rights reserved.
5 // ---------------------------------------------------------------------------
6 // Last modified: 19 November 2010 (DB)
7 // ---------------------------------------------------------------------------
8 // Provides the basic functionality for producing BAM files
9 // ***************************************************************************
18 // This file is not part of the BamTools API. It exists purely as an
19 // implementation detail. This header file may change from version to
20 // version without notice, or even be removed.
24 #include <api/BamAux.h>
32 class BamWriterPrivate {
36 BamWriterPrivate(void);
37 ~BamWriterPrivate(void);
39 // "public" interface to BamWriter
42 bool Open(const std::string& filename,
43 const std::string& samHeader,
44 const BamTools::RefVector& referenceSequences,
45 bool isWriteUncompressed);
46 void SaveAlignment(const BamAlignment& al);
50 const unsigned int CalculateMinimumBin(const int begin, int end) const;
51 void CreatePackedCigar(const std::vector<BamTools::CigarOp>& cigarOperations, std::string& packedCigar);
52 void EncodeQuerySequence(const std::string& query, std::string& encodedQuery);
60 } // namespace Internal
61 } // namespace BamTools
63 #endif // BAMWRITER_P_H