// Marth Lab, Department of Biology, Boston College\r
// All rights reserved.\r
// ---------------------------------------------------------------------------\r
-// Last modified: 11 January 2010 (DB)\r
+// Last modified: 16 August 2010 (DB)\r
// ---------------------------------------------------------------------------\r
// BGZF routines were adapted from the bgzf.c code developed at the Broad\r
// Institute.\r
// zlib includes\r
#include "zlib.h"\r
\r
+// Platform-specific large-file support\r
+#ifndef BAMTOOLS_LFS\r
+#define BAMTOOLS_LFS\r
+ #ifdef WIN32\r
+ #define ftell64(a) _ftelli64(a)\r
+ #define fseek64(a,b,c) _fseeki64(a,b,c)\r
+ #else\r
+ #define ftell64(a) ftello(a)\r
+ #define fseek64(a,b,c) fseeko(a,b,c) \r
+ #endif\r
+#endif // BAMTOOLS_LFS\r
+\r
// Platform-specific type definitions\r
#ifndef BAMTOOLS_TYPES\r
#define BAMTOOLS_TYPES\r
- #ifdef _MSC_VER\r
- typedef char int8_t;\r
- typedef unsigned char uint8_t;\r
- typedef short int16_t;\r
- typedef unsigned short uint16_t;\r
- typedef int int32_t;\r
- typedef unsigned int uint32_t;\r
- typedef long long int64_t;\r
- typedef unsigned long long uint64_t;\r
- #else\r
- #include <stdint.h>\r
- #endif\r
+ #ifdef _MSC_VER\r
+ typedef char int8_t;\r
+ typedef unsigned char uint8_t;\r
+ typedef short int16_t;\r
+ typedef unsigned short uint16_t;\r
+ typedef int int32_t;\r
+ typedef unsigned int uint32_t;\r
+ typedef long long int64_t;\r
+ typedef unsigned long long uint64_t;\r
+ #else \r
+ #include <stdint.h>\r
+ #endif\r
#endif // BAMTOOLS_TYPES\r
\r
namespace BamTools {\r
struct BgzfData {\r
\r
// data members\r
- unsigned int UncompressedBlockSize;\r
- unsigned int CompressedBlockSize;\r
- unsigned int BlockLength;\r
- unsigned int BlockOffset;\r
- uint64_t BlockAddress;\r
- bool IsOpen;\r
- bool IsWriteOnly;\r
- FILE* Stream;\r
- char* UncompressedBlock;\r
- char* CompressedBlock;\r
+ public:\r
+ unsigned int UncompressedBlockSize;\r
+ unsigned int CompressedBlockSize;\r
+ unsigned int BlockLength;\r
+ unsigned int BlockOffset;\r
+ uint64_t BlockAddress;\r
+ bool IsOpen;\r
+ bool IsWriteOnly;\r
+ bool IsWriteUncompressed;\r
+ FILE* Stream;\r
+ char* UncompressedBlock;\r
+ char* CompressedBlock;\r
\r
// constructor & destructor\r
- BgzfData(void);\r
- ~BgzfData(void);\r
-\r
- // closes BGZF file\r
- void Close(void);\r
- // compresses the current block\r
- int DeflateBlock(void);\r
- // flushes the data in the BGZF block\r
- void FlushBlock(void);\r
- // de-compresses the current block\r
- int InflateBlock(const int& blockLength);\r
- // opens the BGZF file for reading (mode is either "rb" for reading, or "wb" for writing\r
- void Open(const std::string& filename, const char* mode);\r
- // reads BGZF data into a byte buffer\r
- int Read(char* data, const unsigned int dataLength);\r
- // reads BGZF block\r
- int ReadBlock(void);\r
- // seek to position in BAM file\r
- bool Seek(int64_t position);\r
- // get file position in BAM file\r
- int64_t Tell(void);\r
- // writes the supplied data into the BGZF buffer\r
- unsigned int Write(const char* data, const unsigned int dataLen);\r
-\r
- // checks BGZF block header\r
- static inline bool CheckBlockHeader(char* header);\r
- // packs an unsigned integer into the specified buffer\r
- static inline void PackUnsignedInt(char* buffer, unsigned int value);\r
- // packs an unsigned short into the specified buffer\r
- static inline void PackUnsignedShort(char* buffer, unsigned short value);\r
- \r
- // unpacks a buffer into a signed int\r
- static inline signed int UnpackSignedInt(char* buffer);\r
- // unpacks a buffer into an unsigned int\r
- static inline unsigned int UnpackUnsignedInt(char* buffer);\r
- // unpacks a buffer into a signed short\r
- static inline signed short UnpackSignedShort(char* buffer);\r
- // unpacks a buffer into an unsigned short\r
- static inline unsigned short UnpackUnsignedShort(char* buffer);\r
- // unpacks a buffer into a double\r
- static inline double UnpackDouble(char* buffer);\r
- // unpacks a buffer into a float\r
- static inline float UnpackFloat(char* buffer); \r
+ public:\r
+ BgzfData(void);\r
+ ~BgzfData(void);\r
+\r
+ // main interface methods\r
+ public: \r
+ // closes BGZF file\r
+ void Close(void);\r
+ // opens the BGZF file (mode is either "rb" for reading, or "wb" for writing)\r
+ bool Open(const std::string& filename, const char* mode, bool isWriteUncompressed = false);\r
+ // reads BGZF data into a byte buffer\r
+ int Read(char* data, const unsigned int dataLength);\r
+ // seek to position in BGZF file\r
+ bool Seek(int64_t position);\r
+ // get file position in BGZF file\r
+ int64_t Tell(void);\r
+ // writes the supplied data into the BGZF buffer\r
+ unsigned int Write(const char* data, const unsigned int dataLen);\r
+\r
+ // internal methods\r
+ private:\r
+ // compresses the current block\r
+ int DeflateBlock(void);\r
+ // flushes the data in the BGZF block\r
+ void FlushBlock(void);\r
+ // de-compresses the current block\r
+ int InflateBlock(const int& blockLength);\r
+ // reads a BGZF block\r
+ bool ReadBlock(void);\r
\r
- // unpacks a buffer into a signed int\r
- static inline signed int UnpackSignedInt(const char* buffer);\r
- // unpacks a buffer into an unsigned int\r
- static inline unsigned int UnpackUnsignedInt(const char* buffer);\r
- // unpacks a buffer into a signed short\r
- static inline signed short UnpackSignedShort(const char* buffer);\r
- // unpacks a buffer into an unsigned short\r
- static inline unsigned short UnpackUnsignedShort(const char* buffer);\r
- // unpacks a buffer into a double\r
- static inline double UnpackDouble(const char* buffer);\r
- // unpacks a buffer into a float\r
- static inline float UnpackFloat(const char* buffer); \r
+ // static 'utility' methods\r
+ public:\r
+ // checks BGZF block header\r
+ static inline bool CheckBlockHeader(char* header);\r
+ // packs an unsigned integer into the specified buffer\r
+ static inline void PackUnsignedInt(char* buffer, unsigned int value);\r
+ // packs an unsigned short into the specified buffer\r
+ static inline void PackUnsignedShort(char* buffer, unsigned short value);\r
+ // unpacks a buffer into a double\r
+ static inline double UnpackDouble(char* buffer);\r
+ static inline double UnpackDouble(const char* buffer);\r
+ // unpacks a buffer into a float\r
+ static inline float UnpackFloat(char* buffer);\r
+ static inline float UnpackFloat(const char* buffer);\r
+ // unpacks a buffer into a signed int\r
+ static inline signed int UnpackSignedInt(char* buffer);\r
+ static inline signed int UnpackSignedInt(const char* buffer);\r
+ // unpacks a buffer into a signed short\r
+ static inline signed short UnpackSignedShort(char* buffer);\r
+ static inline signed short UnpackSignedShort(const char* buffer);\r
+ // unpacks a buffer into an unsigned int\r
+ static inline unsigned int UnpackUnsignedInt(char* buffer);\r
+ static inline unsigned int UnpackUnsignedInt(const char* buffer);\r
+ // unpacks a buffer into an unsigned short\r
+ static inline unsigned short UnpackUnsignedShort(char* buffer);\r
+ static inline unsigned short UnpackUnsignedShort(const char* buffer);\r
};\r
\r
// -------------------------------------------------------------\r
+// static 'utility' method implementations\r
\r
+// checks BGZF block header\r
inline\r
bool BgzfData::CheckBlockHeader(char* header) {\r
return (header[0] == GZIP_ID1 &&\r
buffer[1] = (char)(value >> 8);\r
}\r
\r
-// 'unpacks' a buffer into a signed int\r
+// 'unpacks' a buffer into a double (includes both non-const & const char* flavors)\r
inline\r
-signed int BgzfData::UnpackSignedInt(char* buffer) {\r
- union { signed int value; unsigned char valueBuffer[sizeof(signed int)]; } un;\r
+double BgzfData::UnpackDouble(char* buffer) {\r
+ union { double value; unsigned char valueBuffer[sizeof(double)]; } un;\r
un.value = 0;\r
un.valueBuffer[0] = buffer[0];\r
un.valueBuffer[1] = buffer[1];\r
un.valueBuffer[2] = buffer[2];\r
un.valueBuffer[3] = buffer[3];\r
+ un.valueBuffer[4] = buffer[4];\r
+ un.valueBuffer[5] = buffer[5];\r
+ un.valueBuffer[6] = buffer[6];\r
+ un.valueBuffer[7] = buffer[7];\r
return un.value;\r
}\r
\r
-// 'unpacks' a buffer into an unsigned int\r
inline\r
-unsigned int BgzfData::UnpackUnsignedInt(char* buffer) {\r
- union { unsigned int value; unsigned char valueBuffer[sizeof(unsigned int)]; } un;\r
+double BgzfData::UnpackDouble(const char* buffer) {\r
+ union { double value; unsigned char valueBuffer[sizeof(double)]; } un;\r
un.value = 0;\r
un.valueBuffer[0] = buffer[0];\r
un.valueBuffer[1] = buffer[1];\r
un.valueBuffer[2] = buffer[2];\r
un.valueBuffer[3] = buffer[3];\r
+ un.valueBuffer[4] = buffer[4];\r
+ un.valueBuffer[5] = buffer[5];\r
+ un.valueBuffer[6] = buffer[6];\r
+ un.valueBuffer[7] = buffer[7];\r
return un.value;\r
}\r
\r
-// 'unpacks' a buffer into a signed short\r
-inline\r
-signed short BgzfData::UnpackSignedShort(char* buffer) {\r
- union { signed short value; unsigned char valueBuffer[sizeof(signed short)]; } un;\r
- un.value = 0;\r
- un.valueBuffer[0] = buffer[0];\r
- un.valueBuffer[1] = buffer[1];\r
- return un.value;\r
-}\r
-\r
-// 'unpacks' a buffer into an unsigned short\r
+// 'unpacks' a buffer into a float (includes both non-const & const char* flavors)\r
inline\r
-unsigned short BgzfData::UnpackUnsignedShort(char* buffer) {\r
- union { unsigned short value; unsigned char valueBuffer[sizeof(unsigned short)]; } un;\r
+float BgzfData::UnpackFloat(char* buffer) {\r
+ union { float value; unsigned char valueBuffer[sizeof(float)]; } un;\r
un.value = 0;\r
un.valueBuffer[0] = buffer[0];\r
un.valueBuffer[1] = buffer[1];\r
+ un.valueBuffer[2] = buffer[2];\r
+ un.valueBuffer[3] = buffer[3];\r
return un.value;\r
}\r
\r
-// 'unpacks' a buffer into a double\r
inline\r
-double BgzfData::UnpackDouble(char* buffer) {\r
- union { double value; unsigned char valueBuffer[sizeof(double)]; } un;\r
+float BgzfData::UnpackFloat(const char* buffer) {\r
+ union { float value; unsigned char valueBuffer[sizeof(float)]; } un;\r
un.value = 0;\r
un.valueBuffer[0] = buffer[0];\r
un.valueBuffer[1] = buffer[1];\r
un.valueBuffer[2] = buffer[2];\r
un.valueBuffer[3] = buffer[3];\r
- un.valueBuffer[4] = buffer[4];\r
- un.valueBuffer[5] = buffer[5];\r
- un.valueBuffer[6] = buffer[6];\r
- un.valueBuffer[7] = buffer[7];\r
return un.value;\r
}\r
\r
-// 'unpacks' a buffer into a float\r
+// 'unpacks' a buffer into a signed int (includes both non-const & const char* flavors)\r
inline\r
-float BgzfData::UnpackFloat(char* buffer) {\r
- union { float value; unsigned char valueBuffer[sizeof(float)]; } un;\r
+signed int BgzfData::UnpackSignedInt(char* buffer) {\r
+ union { signed int value; unsigned char valueBuffer[sizeof(signed int)]; } un;\r
un.value = 0;\r
un.valueBuffer[0] = buffer[0];\r
un.valueBuffer[1] = buffer[1];\r
return un.value;\r
}\r
\r
-// ---------\r
-\r
-// 'unpacks' a buffer into a signed int\r
inline\r
signed int BgzfData::UnpackSignedInt(const char* buffer) {\r
union { signed int value; unsigned char valueBuffer[sizeof(signed int)]; } un;\r
return un.value;\r
}\r
\r
-// 'unpacks' a buffer into an unsigned int\r
+// 'unpacks' a buffer into a signed short (includes both non-const & const char* flavors)\r
inline\r
-unsigned int BgzfData::UnpackUnsignedInt(const char* buffer) {\r
- union { unsigned int value; unsigned char valueBuffer[sizeof(unsigned int)]; } un;\r
+signed short BgzfData::UnpackSignedShort(char* buffer) {\r
+ union { signed short value; unsigned char valueBuffer[sizeof(signed short)]; } un;\r
un.value = 0;\r
un.valueBuffer[0] = buffer[0];\r
un.valueBuffer[1] = buffer[1];\r
- un.valueBuffer[2] = buffer[2];\r
- un.valueBuffer[3] = buffer[3];\r
return un.value;\r
}\r
\r
-// 'unpacks' a buffer into a signed short\r
inline\r
signed short BgzfData::UnpackSignedShort(const char* buffer) {\r
union { signed short value; unsigned char valueBuffer[sizeof(signed short)]; } un;\r
return un.value;\r
}\r
\r
-// 'unpacks' a buffer into an unsigned short\r
+// 'unpacks' a buffer into an unsigned int (includes both non-const & const char* flavors)\r
inline\r
-unsigned short BgzfData::UnpackUnsignedShort(const char* buffer) {\r
- union { unsigned short value; unsigned char valueBuffer[sizeof(unsigned short)]; } un;\r
+unsigned int BgzfData::UnpackUnsignedInt(char* buffer) {\r
+ union { unsigned int value; unsigned char valueBuffer[sizeof(unsigned int)]; } un;\r
un.value = 0;\r
un.valueBuffer[0] = buffer[0];\r
un.valueBuffer[1] = buffer[1];\r
+ un.valueBuffer[2] = buffer[2];\r
+ un.valueBuffer[3] = buffer[3];\r
return un.value;\r
}\r
\r
-// 'unpacks' a buffer into a double\r
inline\r
-double BgzfData::UnpackDouble(const char* buffer) {\r
- union { double value; unsigned char valueBuffer[sizeof(double)]; } un;\r
+unsigned int BgzfData::UnpackUnsignedInt(const char* buffer) {\r
+ union { unsigned int value; unsigned char valueBuffer[sizeof(unsigned int)]; } un;\r
un.value = 0;\r
un.valueBuffer[0] = buffer[0];\r
un.valueBuffer[1] = buffer[1];\r
un.valueBuffer[2] = buffer[2];\r
un.valueBuffer[3] = buffer[3];\r
- un.valueBuffer[4] = buffer[4];\r
- un.valueBuffer[5] = buffer[5];\r
- un.valueBuffer[6] = buffer[6];\r
- un.valueBuffer[7] = buffer[7];\r
return un.value;\r
}\r
\r
-// 'unpacks' a buffer into a float\r
+// 'unpacks' a buffer into an unsigned short (includes both non-const & const char* flavors)\r
inline\r
-float BgzfData::UnpackFloat(const char* buffer) {\r
- union { float value; unsigned char valueBuffer[sizeof(float)]; } un;\r
+unsigned short BgzfData::UnpackUnsignedShort(char* buffer) {\r
+ union { unsigned short value; unsigned char valueBuffer[sizeof(unsigned short)]; } un;\r
+ un.value = 0;\r
+ un.valueBuffer[0] = buffer[0];\r
+ un.valueBuffer[1] = buffer[1];\r
+ return un.value;\r
+}\r
+\r
+inline\r
+unsigned short BgzfData::UnpackUnsignedShort(const char* buffer) {\r
+ union { unsigned short value; unsigned char valueBuffer[sizeof(unsigned short)]; } un;\r
un.value = 0;\r
un.valueBuffer[0] = buffer[0];\r
un.valueBuffer[1] = buffer[1];\r
- un.valueBuffer[2] = buffer[2];\r
- un.valueBuffer[3] = buffer[3];\r
return un.value;\r
}\r
\r
projects / bamtools.git / blobdiff