ngs_server 0.1

data/ext/bamtools/src/api/BamWriter.cpp

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+// ***************************************************************************
+// BamWriter.cpp (c) 2009 Michael Str�mberg, Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// ---------------------------------------------------------------------------
+// Last modified: 4 March 2011 (DB)
+// ---------------------------------------------------------------------------
+// Provides the basic functionality for producing BAM files
+// ***************************************************************************
+
+#include <api/BamAlignment.h>
+#include <api/BamWriter.h>
+#include <api/SamHeader.h>
+#include <api/internal/BamWriter_p.h>
+using namespace BamTools;
+using namespace BamTools::Internal;
+
+#include <iostream>
+using namespace std;
+
+/*! \class BamTools::BamWriter
+    \brief Provides write access for generating BAM files.
+*/
+/*! \enum BamTools::BamWriter::CompressionMode
+    \brief This enum describes the compression behaviors for output BAM files.
+*/
+/*! \var BamWriter::CompressionMode BamWriter::Compressed
+    \brief Use normal BAM compression
+*/
+/*! \var BamWriter::CompressionMode BamWriter::Uncompressed
+    \brief Disable BAM compression
+
+    Useful in situations where the BAM data is streamed (e.g. piping).
+    It would be wasteful to compress, and then immediately decompress
+    the data.
+*/
+
+/*! \fn BamWriter::BamWriter(void)
+    \brief constructor
+*/
+BamWriter::BamWriter(void)
+    : d(new BamWriterPrivate)
+{ }
+
+/*! \fn BamWriter::~BamWriter(void)
+    \brief destructor
+*/
+BamWriter::~BamWriter(void) {
+    delete d;
+    d = 0;
+}
+
+/*! \fn BamWriter::Close(void)
+    \brief Closes the current BAM file.
+    \sa Open()
+*/
+void BamWriter::Close(void) {
+    d->Close();
+}
+
+/*! \fn bool BamWriter::IsOpen(void) const
+    \brief Returns \c true if BAM file is open for writing.
+    \sa Open()
+*/
+bool BamWriter::IsOpen(void) const {
+    return d->IsOpen();
+}
+
+/*! \fn bool BamWriter::Open(const std::string& filename,
+                             const std::string& samHeaderText,
+                             const RefVector& referenceSequences)
+    \brief Opens a BAM file for writing.
+
+    Will overwrite the BAM file if it already exists.
+
+    \param filename           name of output BAM file
+    \param samHeaderText      header data, as SAM-formatted string
+    \param referenceSequences list of reference entries
+
+    \return \c true if opened successfully
+    \sa Close(), IsOpen(), BamReader::GetHeaderText(), BamReader::GetReferenceData()
+*/
+bool BamWriter::Open(const std::string& filename,
+                     const std::string& samHeaderText,
+                     const RefVector& referenceSequences)
+{
+    return d->Open(filename, samHeaderText, referenceSequences);
+}
+
+/*! \fn bool BamWriter::Open(const std::string& filename,
+                             const SamHeader& samHeader,
+                             const RefVector& referenceSequences)
+    \brief Opens a BAM file for writing.
+
+    This is an overloaded function.
+
+    Will overwrite the BAM file if it already exists.
+
+    \param filename           name of output BAM file
+    \param samHeader          header data, wrapped in SamHeader object
+    \param referenceSequences list of reference entries
+
+    \return \c true if opened successfully
+    \sa Close(), IsOpen(), BamReader::GetHeader(), BamReader::GetReferenceData()
+*/
+bool BamWriter::Open(const std::string& filename,
+                     const SamHeader& samHeader,
+                     const RefVector& referenceSequences)
+{
+    return d->Open(filename, samHeader.ToString(), referenceSequences);
+}
+
+/*! \fn void BamWriter::SaveAlignment(const BamAlignment& alignment)
+    \brief Saves an alignment to the BAM file.
+
+    \param alignment BamAlignment record to save
+    \sa BamReader::GetNextAlignment(), BamReader::GetNextAlignmentCore()
+*/
+void BamWriter::SaveAlignment(const BamAlignment& alignment) {
+    d->SaveAlignment(alignment);
+}
+
+/*! \fn void BamWriter::SetCompressionMode(const CompressionMode& compressionMode)
+    \brief Sets the output compression mode.
+
+    Default mode is BamWriter::Compressed.
+
+    N.B. - Changing the compression mode is disabled on open files (i.e. the request will be ignored).
+    Be sure to call this function before opening the BAM file.
+
+    \code
+        BamWriter writer;
+        writer.SetCompressionMode(BamWriter::Uncompressed);
+        writer.Open( ... );
+        // ...
+    \endcode
+
+    \param compressionMode desired output compression behavior
+    \sa IsOpen(), Open()
+*/
+void BamWriter::SetCompressionMode(const CompressionMode& compressionMode) {
+    d->SetWriteCompressed( compressionMode == BamWriter::Compressed );
+}

data/ext/bamtools/src/api/BamWriter.h

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+// ***************************************************************************
+// BamWriter.h (c) 2009 Michael Str�mberg, Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// ---------------------------------------------------------------------------
+// Last modified: 4 March 2011 (DB)
+// ---------------------------------------------------------------------------
+// Provides the basic functionality for producing BAM files
+// ***************************************************************************
+
+#ifndef BAMWRITER_H
+#define BAMWRITER_H
+
+#include <api/api_global.h>
+#include <api/BamAux.h>
+#include <string>
+
+namespace BamTools {
+
+class BamAlignment;
+class SamHeader;
+
+namespace Internal {
+    class BamWriterPrivate;
+} // namespace Internal
+
+class API_EXPORT BamWriter {
+
+    public: enum CompressionMode { Compressed = 0
+                                 , Uncompressed
+                                 };
+
+    // ctor & dtor
+    public:
+        BamWriter(void);
+        ~BamWriter(void);
+
+    // public interface
+    public:
+        //  closes the current BAM file
+        void Close(void);
+        // returns true if BAM file is open for writing
+        bool IsOpen(void) const;
+        // opens a BAM file for writing
+        bool Open(const std::string& filename, 
+                  const std::string& samHeaderText,
+                  const RefVector& referenceSequences);
+        // opens a BAM file for writing
+        bool Open(const std::string& filename,
+                  const SamHeader& samHeader,
+                  const RefVector& referenceSequences);
+        // saves the alignment to the alignment archive
+        void SaveAlignment(const BamAlignment& alignment);
+        // sets the output compression mode
+        void SetCompressionMode(const CompressionMode& compressionMode);
+
+    // private implementation
+    private:
+        Internal::BamWriterPrivate* d;
+};
+
+} // namespace BamTools
+
+#endif // BAMWRITER_H

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