BamAux.h File Reference

#include "api/api_global.h"
#include <cstring>
#include <fstream>
#include <iostream>
#include <string>
#include <vector>

Go to the source code of this file.

Classes
struct	BamTools::CigarOp
	Represents a CIGAR alignment operation. More...
struct	BamTools::RefData
	Represents a reference sequence entry. More...
struct	BamTools::BamRegion
	Represents a sequential genomic region. More...
Namespaces
namespace	BamTools
	Contains all BamTools classes & methods.
Typedefs
typedef std::vector< RefData >	BamTools::RefVector
	convenience typedef for vector of RefData entries
Functions
API_EXPORT bool	BamTools::FileExists (const std::string &filename)
	returns true if the file exists
API_EXPORT void	BamTools::SwapEndian_16 (int16_t &x)
	swaps endianness of signed 16-bit integer, in place
API_EXPORT void	BamTools::SwapEndian_16 (uint16_t &x)
	swaps endianness of unsigned 16-bit integer, in place
API_EXPORT void	BamTools::SwapEndian_32 (int32_t &x)
	swaps endianness of signed 32-bit integer, in place
API_EXPORT void	BamTools::SwapEndian_32 (uint32_t &x)
	swaps endianness of unsigned 32-bit integer, in place
API_EXPORT void	BamTools::SwapEndian_64 (int64_t &x)
	swaps endianness of signed 64-bit integer, in place
API_EXPORT void	BamTools::SwapEndian_64 (uint64_t &x)
	swaps endianness of unsigned 64-bit integer, in place
API_EXPORT void	BamTools::SwapEndian_16p (char *data)
	swaps endianness of the next 2 bytes in a buffer, in place
API_EXPORT void	BamTools::SwapEndian_32p (char *data)
	swaps endianness of the next 4 bytes in a buffer, in place
API_EXPORT void	BamTools::SwapEndian_64p (char *data)
	swaps endianness of the next 8 bytes in a buffer, in place
API_EXPORT bool	BamTools::SystemIsBigEndian (void)
	checks host architecture's byte order
API_EXPORT void	BamTools::PackUnsignedInt (char *buffer, unsigned int value)
	stores unsigned integer value in a byte buffer
API_EXPORT void	BamTools::PackUnsignedShort (char *buffer, unsigned short value)
	stores unsigned short integer value in a byte buffer
API_EXPORT double	BamTools::UnpackDouble (const char *buffer)
	reads a double value from byte buffer
API_EXPORT double	BamTools::UnpackDouble (char *buffer)
	reads a double value from byte buffer
API_EXPORT float	BamTools::UnpackFloat (const char *buffer)
	reads a float value from byte buffer
API_EXPORT float	BamTools::UnpackFloat (char *buffer)
	reads a float value from byte buffer
API_EXPORT signed int	BamTools::UnpackSignedInt (const char *buffer)
	reads a signed integer value from byte buffer
API_EXPORT signed int	BamTools::UnpackSignedInt (char *buffer)
	reads a signed integer value from byte buffer
API_EXPORT signed short	BamTools::UnpackSignedShort (const char *buffer)
	reads a signed short integer value from byte buffer
API_EXPORT signed short	BamTools::UnpackSignedShort (char *buffer)
	reads a signed short integer value from byte buffer
API_EXPORT unsigned int	BamTools::UnpackUnsignedInt (const char *buffer)
	reads an unsigned integer value from byte buffer
API_EXPORT unsigned int	BamTools::UnpackUnsignedInt (char *buffer)
	reads an unsigned integer value from byte buffer
API_EXPORT unsigned short	BamTools::UnpackUnsignedShort (const char *buffer)
	reads an unsigned short integer value from byte buffer
API_EXPORT unsigned short	BamTools::UnpackUnsignedShort (char *buffer)
	reads an unsigned short integer value from byte buffer

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Detailed Description

Provides data structures & utility methods that are used throughout the API.