1 // ***************************************************************************
\r
2 // BamWriter.h (c) 2009 Michael Str�mberg, Derek Barnett
\r
3 // Marth Lab, Department of Biology, Boston College
\r
4 // All rights reserved.
\r
5 // ---------------------------------------------------------------------------
\r
6 // Last modified: 4 March 2011 (DB)
\r
7 // ---------------------------------------------------------------------------
\r
8 // Provides the basic functionality for producing BAM files
\r
9 // ***************************************************************************
\r
14 #include <api/api_global.h>
\r
15 #include <api/BamAux.h>
\r
18 namespace BamTools {
\r
23 namespace Internal {
\r
24 class BamWriterPrivate;
\r
25 } // namespace Internal
\r
27 class API_EXPORT BamWriter {
\r
29 public: enum CompressionMode { Compressed = 0
\r
40 // closes the current BAM file
\r
42 // returns true if BAM file is open for writing
\r
43 bool IsOpen(void) const;
\r
44 // opens a BAM file for writing
\r
45 bool Open(const std::string& filename,
\r
46 const std::string& samHeaderText,
\r
47 const RefVector& referenceSequences);
\r
48 // opens a BAM file for writing
\r
49 bool Open(const std::string& filename,
\r
50 const SamHeader& samHeader,
\r
51 const RefVector& referenceSequences);
\r
52 // saves the alignment to the alignment archive
\r
53 void SaveAlignment(const BamAlignment& alignment);
\r
54 // sets the output compression mode
\r
55 void SetCompressionMode(const CompressionMode& compressionMode);
\r
57 // private implementation
\r
59 Internal::BamWriterPrivate* d;
\r
62 } // namespace BamTools
\r
64 #endif // BAMWRITER_H
\r