Major update to BamTools version 1.0

[bamtools.git] / src / api / internal / BgzfStream_p.h

diff --git a/src/api/internal/BgzfStream_p.h b/src/api/internal/BgzfStream_p.h
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+++ b/src/api/internal/BgzfStream_p.h
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+// ***************************************************************************
+// BgzfStream_p.h (c) 2011 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 24 February 2011(DB)
+// ---------------------------------------------------------------------------
+// Based on BGZF routines developed at the Broad Institute.
+// Provides the basic functionality for reading & writing BGZF files
+// Replaces the old BGZF.* files to avoid clashing with other toolkits
+// ***************************************************************************
+
+#ifndef BGZFSTREAM_P_H
+#define BGZFSTREAM_P_H
+
+//  -------------
+//  W A R N I N G
+//  -------------
+//
+// This file is not part of the BamTools API.  It exists purely as an
+// implementation detail. This header file may change from version to version
+// without notice, or even be removed.
+//
+// We mean it.
+
+#include <api/BamAux.h>
+#include <api/BamConstants.h>
+#include "zlib.h"
+#include <cstdio>
+#include <string>
+
+namespace BamTools {
+namespace Internal {
+
+class BgzfStream {
+
+    // constructor & destructor
+    public:
+        BgzfStream(void);
+        ~BgzfStream(void);
+
+    // main interface methods
+    public:
+        // closes BGZF file
+        void Close(void);
+        // opens the BGZF file (mode is either "rb" for reading, or "wb" for writing)
+        bool Open(const std::string& filename, const char* mode);
+        // reads BGZF data into a byte buffer
+        int Read(char* data, const unsigned int dataLength);
+        // seek to position in BGZF file
+        bool Seek(int64_t position);
+        // enable/disable compressed output
+        void SetWriteCompressed(bool ok);
+        // get file position in BGZF file
+        int64_t Tell(void);
+        // writes the supplied data into the BGZF buffer
+        unsigned int Write(const char* data, const unsigned int dataLen);
+
+    // internal methods
+    private:
+        // compresses the current block
+        int DeflateBlock(void);
+        // flushes the data in the BGZF block
+        void FlushBlock(void);
+        // de-compresses the current block
+        int InflateBlock(const int& blockLength);
+        // reads a BGZF block
+        bool ReadBlock(void);
+
+    // static 'utility' methods
+    public:
+        // checks BGZF block header
+        static inline bool CheckBlockHeader(char* header);
+
+    // data members
+    public:
+        unsigned int UncompressedBlockSize;
+        unsigned int CompressedBlockSize;
+        unsigned int BlockLength;
+        unsigned int BlockOffset;
+        uint64_t BlockAddress;
+        bool IsOpen;
+        bool IsWriteOnly;
+        bool IsWriteCompressed;
+        FILE* Stream;
+        char* UncompressedBlock;
+        char* CompressedBlock;
+};
+
+// -------------------------------------------------------------
+// static 'utility' method implementations
+
+// checks BGZF block header
+inline
+bool BgzfStream::CheckBlockHeader(char* header) {
+    return (header[0] == Constants::GZIP_ID1 &&
+            header[1] == (char)Constants::GZIP_ID2 &&
+            header[2] == Z_DEFLATED &&
+            (header[3] & Constants::FLG_FEXTRA) != 0 &&
+            BamTools::UnpackUnsignedShort(&header[10]) == Constants::BGZF_XLEN &&
+            header[12] == Constants::BGZF_ID1 &&
+            header[13] == Constants::BGZF_ID2 &&
+            BamTools::UnpackUnsignedShort(&header[14]) == Constants::BGZF_LEN );
+}
+
+} // namespace Internal
+} // namespace BamTools
+
+#endif // BGZFSTREAM_P_H