// ***************************************************************************
-// BamWriter (c) 2009 Michael Strömberg
-// Marth Lab, Deptartment of Biology, Boston College
+// 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>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <zlib.h>
-#include "BamAlignment.h"
-
-using namespace std;
-
-// our zlib constants
-#define GZIP_ID1 31
-#define GZIP_ID2 139
-#define CM_DEFLATE 8
-#define FLG_FEXTRA 4
-#define OS_UNKNOWN 255
-#define BGZF_XLEN 6
-#define BGZF_ID1 66
-#define BGZF_ID2 67
-#define BGZF_LEN 2
-#define GZIP_WINDOW_BITS -15
-#define Z_DEFAULT_MEM_LEVEL 8
-
-// our BZGF constants
-#define BLOCK_HEADER_LENGTH 18
-#define BLOCK_FOOTER_LENGTH 8
-#define MAX_BLOCK_SIZE 65536
-#define DEFAULT_BLOCK_SIZE 65536
-
-// our BAM constants
-#define BAM_CORE_SIZE 32
-#define BAM_CMATCH 0
-#define BAM_CINS 1
-#define BAM_CDEL 2
-#define BAM_CREF_SKIP 3
-#define BAM_CSOFT_CLIP 4
-#define BAM_CHARD_CLIP 5
-#define BAM_CPAD 6
-#define BAM_CIGAR_SHIFT 4
-#define BAM_CIGAR_MASK ((1 << BAM_CIGAR_SHIFT) - 1)
+// zlib includes
+#include <zlib.h>
-// our variable sizes
-#define SIZEOF_INT 4
+// BamTools includes
+#include "BamAux.h"
-// define our BZGF structure
-#ifndef BGZF_DATA
-#define BGZF_DATA
-struct BgzfData {
- unsigned int UncompressedBlockSize;
- unsigned int CompressedBlockSize;
- unsigned int BlockLength;
- unsigned int BlockOffset;
- uint64_t BlockAddress;
- bool IsOpen;
- FILE* Stream;
- char* UncompressedBlock;
- char* CompressedBlock;
+namespace BamTools {
- // constructor
- BgzfData(void)
- : UncompressedBlockSize(DEFAULT_BLOCK_SIZE)
- , CompressedBlockSize(MAX_BLOCK_SIZE)
- , BlockLength(0)
- , BlockOffset(0)
- , BlockAddress(0)
- , IsOpen(false)
- , Stream(NULL)
- , UncompressedBlock(NULL)
- , CompressedBlock(NULL)
- {
- try {
- CompressedBlock = new char[CompressedBlockSize];
- UncompressedBlock = new char[UncompressedBlockSize];
- } catch(bad_alloc&) {
- printf("ERROR: Unable to allocate memory for our BGZF object.\n");
- exit(1);
- }
- }
+ //! 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;
+ };
- // destructor
- ~BgzfData(void) {
- if(CompressedBlock) delete [] CompressedBlock;
- if(UncompressedBlock) delete [] UncompressedBlock;
+ //! \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);
}
-};
-#endif // BGZF_DATA
-class BamWriter {
-public:
- // constructor
- BamWriter(void);
- // destructor
- ~BamWriter(void);
- // closes the alignment archive
- void Close(void);
- // opens the alignment archive
- void Open(const string& filename, const string& samHeader, const RefVector& referenceSequences);
- // saves the alignment to the alignment archive
- void SaveAlignment(const BamAlignment& al);
-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 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 vector<CigarOp>& cigarOperations, string& packedCigar);
- // encodes the supplied query sequence into 4-bit notation
- static void EncodeQuerySequence(const string& query, string& encodedQuery);
- // our BGZF output object
- BgzfData mBGZF;
-};
-
-// 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);
-}
+ 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
projects / bamtools.git / blobdiff