X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=BamWriter.h;h=b0cb6ceba3457cc58f3f3670522148a394a39a96;hb=acdea352102b176dc519f6cbdd7980d1041079c2;hp=18f8e0a08e2ab7e9f2c5cb70fff2263e3ba50c87;hpb=e38ea1095fe8f77bb1fa75a1e8c13c4b904280ae;p=bamtools.git

diff --git a/BamWriter.h b/BamWriter.h
index 18f8e0a..b0cb6ce 100644
--- a/BamWriter.h
+++ b/BamWriter.h
@@ -1,151 +1,52 @@
-// ***************************************************************************
-// BamWriter (c) 2009 Michael Strömberg
-// Marth Lab, Deptartment of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// The BGZF routines were adapted from the bgzf.c code developed at the Broad
-// Institute.
-// ---------------------------------------------------------------------------
-// Provides the basic functionality for producing BAM files
-// ***************************************************************************
-
-#pragma once
-
-#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)
-
-// our variable sizes
-#define SIZEOF_INT 4
-
-// 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;
-
-	// 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);
-		}
-	}
-
-	// destructor
-	~BgzfData(void) {
-		if(CompressedBlock)   delete [] CompressedBlock;
-		if(UncompressedBlock) delete [] UncompressedBlock;
-	}
-};
-#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);
-}
+// ***************************************************************************
+// BamWriter.h (c) 2009 Michael Str�mberg, Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 17 August 2010 (DB)
+// ---------------------------------------------------------------------------
+// Uses BGZF routines were adapted from the bgzf.c code developed at the Broad
+// Institute.
+// ---------------------------------------------------------------------------
+// Provides the basic functionality for producing BAM files
+// ***************************************************************************
+
+#ifndef BAMWRITER_H
+#define BAMWRITER_H
+
+// C++ includes
+#include <string>
+
+// BamTools includes
+#include "BamAux.h"
+
+namespace BamTools {
+
+class BamWriter {
+
+    // constructor/destructor
+    public:
+        BamWriter(void);
+        ~BamWriter(void);
+
+    // public interface
+    public:
+        // closes the alignment archive
+        void Close(void);
+        // opens the alignment archive
+        bool Open(const std::string& filename, 
+                  const std::string& samHeader, 
+                  const BamTools::RefVector& referenceSequences, 
+                  bool writeUncompressed = false);
+        // saves the alignment to the alignment archive
+        void SaveAlignment(const BamTools::BamAlignment& al);
+
+    // private implementation
+    private:
+        struct BamWriterPrivate;
+        BamWriterPrivate* d;
+};
+
+} // namespace BamTools
+
+#endif // BAMWRITER_H