-// ***************************************************************************
-// BamWriter.h (c) 2009 Michael Strömberg, Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 24 June 2009 (DB)
-// ---------------------------------------------------------------------------
-// The BGZF routines were adapted from the bgzf.c code developed at the Broad
-// Institute.
-// ---------------------------------------------------------------------------
-// Provides the basic functionality for producing BAM files
-// ***************************************************************************
-
-/*!
- \file BamWriter.h
- \brief API for writing BAM files.
-*/
-
-#pragma once
-
-// C++ includes
-#include <string>
-#include <vector>
-
-// zlib includes
-#include <zlib.h>
-
-// BamTools includes
-#include "BamAux.h"
-
-namespace BamTools {
-
- //! API for writing BAM files.
- class BamWriter {
-
- public:
-
- //! Constructor.
- BamWriter(void);
-
- //! Destructor.
- ~BamWriter(void);
-
- public:
-
- /*!
- \brief Closes the alignment archive
- \sa Open()
- */
- void Close(void);
-
- /*!
- \brief Opens the alignment archive
- \param filename output BAM file
- \param samHeader SAM-format header text
- \param referenceSequences Reference sequence data
- \sa Close()
- */
- void Open(const std::string& filename, const std::string& samHeader, const RefVector& referenceSequences);
-
- /*!
- \brief Saves an alignment to the archive
- \param al The BamAlignment to be saved
- */
- void SaveAlignment(const BamAlignment& al);
-
- // --------------------------------------------------------------------------------------
- // internal methods
- private:
- // closes the BAM file
- void BgzfClose(void);
- // compresses the current block
- int BgzfDeflateBlock(void);
- // flushes the data in the BGZF block
- void BgzfFlushBlock(void);
- // opens the BAM file for writing
- void BgzfOpen(const std::string& filename);
- // packs an unsigned integer into the specified buffer
- static inline void BgzfPackUnsignedInt(char* buffer, unsigned int value);
- // packs an unsigned short into the specified buffer
- static inline void BgzfPackUnsignedShort(char* buffer, unsigned short value);
- // writes the supplied data into the BGZF buffer
- unsigned int BgzfWrite(const char* data, const unsigned int dataLen);
- // calculates the minimum bin that contains a region [begin, end)
- static inline unsigned int CalculateMinimumBin(unsigned int begin, unsigned int end);
- // creates a packed cigar string from the supplied alignment
- static void CreatePackedCigar(const std::vector<CigarOp>& cigarOperations, std::string& packedCigar);
- // encodes the supplied query sequence into 4-bit notation
- static void EncodeQuerySequence(const std::string& query, std::string& encodedQuery);
- // our BGZF output object
- BgzfData mBGZF;
- };
-
- //! \cond
- // --------------------------------------------------------------------------------------
- // static inline methods (internal - can exclude from main documentation)
-
- // packs an unsigned integer into the specified buffer
- inline void BamWriter::BgzfPackUnsignedInt(char* buffer, unsigned int value) {
- buffer[0] = (char)value;
- buffer[1] = (char)(value >> 8);
- buffer[2] = (char)(value >> 16);
- buffer[3] = (char)(value >> 24);
- }
-
- // packs an unsigned short into the specified buffer
- inline void BamWriter::BgzfPackUnsignedShort(char* buffer, unsigned short value) {
- buffer[0] = (char)value;
- buffer[1] = (char)(value >> 8);
- }
- // --------------------------------------------------------------------------------------
- //! \endcond
-
-} // end BamTools namespace
\ No newline at end of file
+// ***************************************************************************\r
+// BamWriter.h (c) 2009 Michael Strömberg, Derek Barnett\r
+// Marth Lab, Department of Biology, Boston College\r
+// All rights reserved.\r
+// ---------------------------------------------------------------------------\r
+// Last modified: 8 December 2009 (DB)\r
+// ---------------------------------------------------------------------------\r
+// Uses BGZF routines were adapted from the bgzf.c code developed at the Broad\r
+// Institute.\r
+// ---------------------------------------------------------------------------\r
+// Provides the basic functionality for producing BAM files\r
+// ***************************************************************************\r
+\r
+#ifndef BAMWRITER_H\r
+#define BAMWRITER_H\r
+\r
+// C++ includes\r
+#include <string>\r
+\r
+// BamTools includes\r
+#include "BamAux.h"\r
+\r
+namespace BamTools {\r
+\r
+class BamWriter {\r
+\r
+ // constructor/destructor\r
+ public:\r
+ BamWriter(void);\r
+ ~BamWriter(void);\r
+\r
+ // public interface\r
+ public:\r
+ // closes the alignment archive\r
+ void Close(void);\r
+ // opens the alignment archive\r
+ void Open(const std::string& filename, const std::string& samHeader, const BamTools::RefVector& referenceSequences);\r
+ // saves the alignment to the alignment archive\r
+ void SaveAlignment(const BamTools::BamAlignment& al);\r
+\r
+ // private implementation\r
+ private:\r
+ struct BamWriterPrivate;\r
+ BamWriterPrivate* d;\r
+};\r
+\r
+} // namespace BamTools\r
+\r
+#endif // BAMWRITER_H\r
projects / bamtools.git / blobdiff