BamTools Namespace Reference

Contains all BamTools classes & methods. More...

Namespaces
namespace	Algorithms
	Provides convenient classes & methods for working with BAM data.
namespace	Constants
	Provides basic constants for handling BAM files.
Classes
class	BamAlignment
	The main BAM alignment data structure. More...
struct	CigarOp
	Represents a CIGAR alignment operation. More...
struct	RefData
	Represents a reference sequence entry. More...
struct	BamRegion
	Represents a sequential genomic region. More...
struct	RaiiBuffer
class	BamIndex
	Provides methods for generating & loading BAM index files. More...
class	BamMultiReader
	Convenience class for reading multiple BAM files. More...
class	BamReader
	Provides read access to BAM files. More...
class	BamWriter
	Provides write access for generating BAM files. More...
class	IBamIODevice
struct	SamHeader
	Represents the SAM-formatted text header that is part of the BAM file header. More...
struct	SamProgram
	Represents a SAM program record. More...
class	SamProgramChain
	Sorted container "chain" of SamProgram records. More...
struct	SamReadGroup
	Represents a SAM read group entry. More...
class	SamReadGroupDictionary
	Container of SamReadGroup entries. More...
struct	SamSequence
	Represents a SAM sequence entry. More...
class	SamSequenceDictionary
	Container of SamSequence entries. More...
Typedefs
typedef std::vector< BamAlignment >	BamAlignmentVector
typedef std::vector< RefData >	RefVector
	convenience typedef for vector of RefData entries
typedef std::vector< SamProgram >	SamProgramContainer
typedef SamProgramContainer::iterator	SamProgramIterator
typedef SamProgramContainer::const_iterator	SamProgramConstIterator
typedef std::vector< SamReadGroup >	SamReadGroupContainer
typedef SamReadGroupContainer::iterator	SamReadGroupIterator
typedef SamReadGroupContainer::const_iterator	SamReadGroupConstIterator
typedef std::vector< SamSequence >	SamSequenceContainer
typedef SamSequenceContainer::iterator	SamSequenceIterator
typedef SamSequenceContainer::const_iterator	SamSequenceConstIterator
Functions
template<>
bool	BamAlignment::AddTag< std::string > (const std::string &tag, const std::string &type, const std::string &value)
template<>
bool	BamAlignment::GetTag< std::string > (const std::string &tag, std::string &destination) const
API_EXPORT bool	FileExists (const std::string &filename)
	returns true if the file exists
API_EXPORT void	SwapEndian_16 (int16_t &x)
	swaps endianness of signed 16-bit integer, in place
API_EXPORT void	SwapEndian_16 (uint16_t &x)
	swaps endianness of unsigned 16-bit integer, in place
API_EXPORT void	SwapEndian_32 (int32_t &x)
	swaps endianness of signed 32-bit integer, in place
API_EXPORT void	SwapEndian_32 (uint32_t &x)
	swaps endianness of unsigned 32-bit integer, in place
API_EXPORT void	SwapEndian_64 (int64_t &x)
	swaps endianness of signed 64-bit integer, in place
API_EXPORT void	SwapEndian_64 (uint64_t &x)
	swaps endianness of unsigned 64-bit integer, in place
API_EXPORT void	SwapEndian_16p (char *data)
	swaps endianness of the next 2 bytes in a buffer, in place
API_EXPORT void	SwapEndian_32p (char *data)
	swaps endianness of the next 4 bytes in a buffer, in place
API_EXPORT void	SwapEndian_64p (char *data)
	swaps endianness of the next 8 bytes in a buffer, in place
API_EXPORT bool	SystemIsBigEndian (void)
	checks host architecture's byte order
API_EXPORT void	PackUnsignedInt (char *buffer, unsigned int value)
	stores unsigned integer value in a byte buffer
API_EXPORT void	PackUnsignedShort (char *buffer, unsigned short value)
	stores unsigned short integer value in a byte buffer
API_EXPORT double	UnpackDouble (const char *buffer)
	reads a double value from byte buffer
API_EXPORT double	UnpackDouble (char *buffer)
	reads a double value from byte buffer
API_EXPORT float	UnpackFloat (const char *buffer)
	reads a float value from byte buffer
API_EXPORT float	UnpackFloat (char *buffer)
	reads a float value from byte buffer
API_EXPORT signed int	UnpackSignedInt (const char *buffer)
	reads a signed integer value from byte buffer
API_EXPORT signed int	UnpackSignedInt (char *buffer)
	reads a signed integer value from byte buffer
API_EXPORT signed short	UnpackSignedShort (const char *buffer)
	reads a signed short integer value from byte buffer
API_EXPORT signed short	UnpackSignedShort (char *buffer)
	reads a signed short integer value from byte buffer
API_EXPORT unsigned int	UnpackUnsignedInt (const char *buffer)
	reads an unsigned integer value from byte buffer
API_EXPORT unsigned int	UnpackUnsignedInt (char *buffer)
	reads an unsigned integer value from byte buffer
API_EXPORT unsigned short	UnpackUnsignedShort (const char *buffer)
	reads an unsigned short integer value from byte buffer
API_EXPORT unsigned short	UnpackUnsignedShort (char *buffer)
	reads an unsigned short integer value from byte buffer
API_EXPORT bool	operator== (const SamProgram &lhs, const SamProgram &rhs)
	tests equality by comparing program IDs
API_EXPORT bool	operator== (const SamReadGroup &lhs, const SamReadGroup &rhs)
	tests equality by comparing read group IDs
API_EXPORT bool	operator== (const SamSequence &lhs, const SamSequence &rhs)
	tests equality by comparing sequence names, lengths, & checksums (if available)

Detailed Description

Contains all BamTools classes & methods.

The BamTools API contained in this namespace contains classes and methods for reading, writing, and manipulating BAM alignment files.

Typedef Documentation

typedef std::vector<BamAlignment> BamTools::BamAlignmentVector

typedef std::vector<RefData> BamTools::RefVector

convenience typedef for vector of RefData entries

typedef SamProgramContainer::const_iterator BamTools::SamProgramConstIterator

typedef std::vector<SamProgram> BamTools::SamProgramContainer

typedef SamProgramContainer::iterator BamTools::SamProgramIterator

typedef SamReadGroupContainer::const_iterator BamTools::SamReadGroupConstIterator

typedef std::vector<SamReadGroup> BamTools::SamReadGroupContainer

typedef SamReadGroupContainer::iterator BamTools::SamReadGroupIterator

typedef SamSequenceContainer::const_iterator BamTools::SamSequenceConstIterator

typedef std::vector<SamSequence> BamTools::SamSequenceContainer

typedef SamSequenceContainer::iterator BamTools::SamSequenceIterator

Function Documentation

template<>

bool BamTools::BamAlignment::AddTag< std::string >	(	const std::string &	tag,
		const std::string &	type,
		const std::string &	value
	)			`[inline]`

template<>

bool BamTools::BamAlignment::GetTag< std::string >	(	const std::string &	tag,
		std::string &	destination
	)			const `[inline]`

bool BamTools::FileExists ( const std::string & filename ) [inline]

returns true if the file exists

bool BamTools::operator==	(	const SamSequence &	lhs,
		const SamSequence &	rhs
	)			`[inline]`

tests equality by comparing sequence names, lengths, & checksums (if available)

bool BamTools::operator==	(	const SamReadGroup &	lhs,
		const SamReadGroup &	rhs
	)			`[inline]`

tests equality by comparing read group IDs

bool BamTools::operator==	(	const SamProgram &	lhs,
		const SamProgram &	rhs
	)			`[inline]`

tests equality by comparing program IDs

void BamTools::PackUnsignedInt	(	char *	buffer,
		unsigned int	value
	)			`[inline]`

stores unsigned integer value in a byte buffer

Parameters:

`[out]`	buffer	destination buffer
`[in]`	value	value to 'pack' in buffer

void BamTools::PackUnsignedShort	(	char *	buffer,
		unsigned short	value
	)			`[inline]`

stores unsigned short integer value in a byte buffer

Parameters:

`[out]`	buffer	destination buffer
`[in]`	value	value to 'pack' in buffer

void BamTools::SwapEndian_16 ( uint16_t & x ) [inline]

swaps endianness of unsigned 16-bit integer, in place

void BamTools::SwapEndian_16 ( int16_t & x ) [inline]

swaps endianness of signed 16-bit integer, in place

void BamTools::SwapEndian_16p ( char * data ) [inline]

swaps endianness of the next 2 bytes in a buffer, in place

void BamTools::SwapEndian_32 ( uint32_t & x ) [inline]

swaps endianness of unsigned 32-bit integer, in place

void BamTools::SwapEndian_32 ( int32_t & x ) [inline]

swaps endianness of signed 32-bit integer, in place

void BamTools::SwapEndian_32p ( char * data ) [inline]

swaps endianness of the next 4 bytes in a buffer, in place

void BamTools::SwapEndian_64 ( uint64_t & x ) [inline]

swaps endianness of unsigned 64-bit integer, in place

void BamTools::SwapEndian_64 ( int64_t & x ) [inline]

swaps endianness of signed 64-bit integer, in place

void BamTools::SwapEndian_64p ( char * data ) [inline]

swaps endianness of the next 8 bytes in a buffer, in place

bool BamTools::SystemIsBigEndian ( void ) [inline]

checks host architecture's byte order

Returns:: true if system uses big-endian ordering

double BamTools::UnpackDouble ( char * buffer ) [inline]

reads a double value from byte buffer

This is an overloaded function.

Parameters: