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1
+ // ***************************************************************************
2
+ // BamWriter.cpp (c) 2009 Michael Str�mberg, Derek Barnett
3
+ // Marth Lab, Department of Biology, Boston College
4
+ // ---------------------------------------------------------------------------
5
+ // Last modified: 4 March 2011 (DB)
6
+ // ---------------------------------------------------------------------------
7
+ // Provides the basic functionality for producing BAM files
8
+ // ***************************************************************************
9
+
10
+ #include <api/BamAlignment.h>
11
+ #include <api/BamWriter.h>
12
+ #include <api/SamHeader.h>
13
+ #include <api/internal/BamWriter_p.h>
14
+ using namespace BamTools;
15
+ using namespace BamTools::Internal;
16
+
17
+ #include <iostream>
18
+ using namespace std;
19
+
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+ /*! \class BamTools::BamWriter
21
+ \brief Provides write access for generating BAM files.
22
+ */
23
+ /*! \enum BamTools::BamWriter::CompressionMode
24
+ \brief This enum describes the compression behaviors for output BAM files.
25
+ */
26
+ /*! \var BamWriter::CompressionMode BamWriter::Compressed
27
+ \brief Use normal BAM compression
28
+ */
29
+ /*! \var BamWriter::CompressionMode BamWriter::Uncompressed
30
+ \brief Disable BAM compression
31
+
32
+ Useful in situations where the BAM data is streamed (e.g. piping).
33
+ It would be wasteful to compress, and then immediately decompress
34
+ the data.
35
+ */
36
+
37
+ /*! \fn BamWriter::BamWriter(void)
38
+ \brief constructor
39
+ */
40
+ BamWriter::BamWriter(void)
41
+ : d(new BamWriterPrivate)
42
+ { }
43
+
44
+ /*! \fn BamWriter::~BamWriter(void)
45
+ \brief destructor
46
+ */
47
+ BamWriter::~BamWriter(void) {
48
+ delete d;
49
+ d = 0;
50
+ }
51
+
52
+ /*! \fn BamWriter::Close(void)
53
+ \brief Closes the current BAM file.
54
+ \sa Open()
55
+ */
56
+ void BamWriter::Close(void) {
57
+ d->Close();
58
+ }
59
+
60
+ /*! \fn bool BamWriter::IsOpen(void) const
61
+ \brief Returns \c true if BAM file is open for writing.
62
+ \sa Open()
63
+ */
64
+ bool BamWriter::IsOpen(void) const {
65
+ return d->IsOpen();
66
+ }
67
+
68
+ /*! \fn bool BamWriter::Open(const std::string& filename,
69
+ const std::string& samHeaderText,
70
+ const RefVector& referenceSequences)
71
+ \brief Opens a BAM file for writing.
72
+
73
+ Will overwrite the BAM file if it already exists.
74
+
75
+ \param filename name of output BAM file
76
+ \param samHeaderText header data, as SAM-formatted string
77
+ \param referenceSequences list of reference entries
78
+
79
+ \return \c true if opened successfully
80
+ \sa Close(), IsOpen(), BamReader::GetHeaderText(), BamReader::GetReferenceData()
81
+ */
82
+ bool BamWriter::Open(const std::string& filename,
83
+ const std::string& samHeaderText,
84
+ const RefVector& referenceSequences)
85
+ {
86
+ return d->Open(filename, samHeaderText, referenceSequences);
87
+ }
88
+
89
+ /*! \fn bool BamWriter::Open(const std::string& filename,
90
+ const SamHeader& samHeader,
91
+ const RefVector& referenceSequences)
92
+ \brief Opens a BAM file for writing.
93
+
94
+ This is an overloaded function.
95
+
96
+ Will overwrite the BAM file if it already exists.
97
+
98
+ \param filename name of output BAM file
99
+ \param samHeader header data, wrapped in SamHeader object
100
+ \param referenceSequences list of reference entries
101
+
102
+ \return \c true if opened successfully
103
+ \sa Close(), IsOpen(), BamReader::GetHeader(), BamReader::GetReferenceData()
104
+ */
105
+ bool BamWriter::Open(const std::string& filename,
106
+ const SamHeader& samHeader,
107
+ const RefVector& referenceSequences)
108
+ {
109
+ return d->Open(filename, samHeader.ToString(), referenceSequences);
110
+ }
111
+
112
+ /*! \fn void BamWriter::SaveAlignment(const BamAlignment& alignment)
113
+ \brief Saves an alignment to the BAM file.
114
+
115
+ \param alignment BamAlignment record to save
116
+ \sa BamReader::GetNextAlignment(), BamReader::GetNextAlignmentCore()
117
+ */
118
+ void BamWriter::SaveAlignment(const BamAlignment& alignment) {
119
+ d->SaveAlignment(alignment);
120
+ }
121
+
122
+ /*! \fn void BamWriter::SetCompressionMode(const CompressionMode& compressionMode)
123
+ \brief Sets the output compression mode.
124
+
125
+ Default mode is BamWriter::Compressed.
126
+
127
+ N.B. - Changing the compression mode is disabled on open files (i.e. the request will be ignored).
128
+ Be sure to call this function before opening the BAM file.
129
+
130
+ \code
131
+ BamWriter writer;
132
+ writer.SetCompressionMode(BamWriter::Uncompressed);
133
+ writer.Open( ... );
134
+ // ...
135
+ \endcode
136
+
137
+ \param compressionMode desired output compression behavior
138
+ \sa IsOpen(), Open()
139
+ */
140
+ void BamWriter::SetCompressionMode(const CompressionMode& compressionMode) {
141
+ d->SetWriteCompressed( compressionMode == BamWriter::Compressed );
142
+ }
@@ -0,0 +1,63 @@
1
+ // ***************************************************************************
2
+ // BamWriter.h (c) 2009 Michael Str�mberg, Derek Barnett
3
+ // Marth Lab, Department of Biology, Boston College
4
+ // ---------------------------------------------------------------------------
5
+ // Last modified: 4 March 2011 (DB)
6
+ // ---------------------------------------------------------------------------
7
+ // Provides the basic functionality for producing BAM files
8
+ // ***************************************************************************
9
+
10
+ #ifndef BAMWRITER_H
11
+ #define BAMWRITER_H
12
+
13
+ #include <api/api_global.h>
14
+ #include <api/BamAux.h>
15
+ #include <string>
16
+
17
+ namespace BamTools {
18
+
19
+ class BamAlignment;
20
+ class SamHeader;
21
+
22
+ namespace Internal {
23
+ class BamWriterPrivate;
24
+ } // namespace Internal
25
+
26
+ class API_EXPORT BamWriter {
27
+
28
+ public: enum CompressionMode { Compressed = 0
29
+ , Uncompressed
30
+ };
31
+
32
+ // ctor & dtor
33
+ public:
34
+ BamWriter(void);
35
+ ~BamWriter(void);
36
+
37
+ // public interface
38
+ public:
39
+ // closes the current BAM file
40
+ void Close(void);
41
+ // returns true if BAM file is open for writing
42
+ bool IsOpen(void) const;
43
+ // opens a BAM file for writing
44
+ bool Open(const std::string& filename,
45
+ const std::string& samHeaderText,
46
+ const RefVector& referenceSequences);
47
+ // opens a BAM file for writing
48
+ bool Open(const std::string& filename,
49
+ const SamHeader& samHeader,
50
+ const RefVector& referenceSequences);
51
+ // saves the alignment to the alignment archive
52
+ void SaveAlignment(const BamAlignment& alignment);
53
+ // sets the output compression mode
54
+ void SetCompressionMode(const CompressionMode& compressionMode);
55
+
56
+ // private implementation
57
+ private:
58
+ Internal::BamWriterPrivate* d;
59
+ };
60
+
61
+ } // namespace BamTools
62
+
63
+ #endif // BAMWRITER_H
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