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...

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...

struct	BamRegion
	Represents a sequential genomic region. More...

class	BamWriter
	Provides write access for generating BAM files. More...

struct	CigarOp
	Represents a CIGAR alignment operation. More...

struct	CustomHeaderTag

class	IBamIODevice

struct	RaiiBuffer

struct	RefData
	Represents a reference sequence entry. More...

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 More...

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

bool	FileExists (const std::string &filename)
	returns true if the file exists More...

void	SwapEndian_16 (uint16_t &x)
	swaps endianness of unsigned 16-bit integer, in place More...

void	SwapEndian_16 (int16_t &x)
	swaps endianness of signed 16-bit integer, in place More...

void	SwapEndian_32 (uint32_t &x)
	swaps endianness of unsigned 32-bit integer, in place More...

void	SwapEndian_32 (int32_t &x)
	swaps endianness of signed 32-bit integer, in place More...

void	SwapEndian_64 (uint64_t &x)
	swaps endianness of unsigned 64-bit integer, in place More...

void	SwapEndian_64 (int64_t &x)
	swaps endianness of signed 64-bit integer, in place More...

void	SwapEndian_16p (char *data)
	swaps endianness of the next 2 bytes in a buffer, in place More...

void	SwapEndian_32p (char *data)
	swaps endianness of the next 4 bytes in a buffer, in place More...

void	SwapEndian_64p (char *data)
	swaps endianness of the next 8 bytes in a buffer, in place More...

bool	SystemIsBigEndian ()
	checks host architecture's byte order More...

void	PackUnsignedInt (char *buffer, unsigned int value)
	stores unsigned integer value in a byte buffer More...

void	PackUnsignedShort (char *buffer, unsigned short value)
	stores unsigned short integer value in a byte buffer More...

double	UnpackDouble (const char *buffer)
	reads a double value from byte buffer More...

float	UnpackFloat (const char *buffer)
	reads a float value from byte buffer More...

signed int	UnpackSignedInt (const char *buffer)
	reads a signed integer value from byte buffer More...

signed short	UnpackSignedShort (const char *buffer)
	reads a signed short integer value from byte buffer More...

unsigned int	UnpackUnsignedInt (const char *buffer)
	reads an unsigned integer value from byte buffer More...

unsigned short	UnpackUnsignedShort (const char *buffer)
	reads an unsigned short integer value from byte buffer More...

bool	operator== (const SamProgram &lhs, const SamProgram &rhs)
	tests equality by comparing program IDs More...

bool	operator== (const SamReadGroup &lhs, const SamReadGroup &rhs)
	tests equality by comparing read group IDs More...

bool	operator== (const SamSequence &lhs, const SamSequence &rhs)
	tests equality by comparing sequence names, lengths, & checksums (if available) More...

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

◆ BamAlignmentVector

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

◆ RefVector

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

convenience typedef for vector of RefData entries

◆ SamProgramConstIterator

typedef SamProgramContainer::const_iterator BamTools::SamProgramConstIterator

◆ SamProgramContainer

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

◆ SamProgramIterator

typedef SamProgramContainer::iterator BamTools::SamProgramIterator

◆ SamReadGroupConstIterator

typedef SamReadGroupContainer::const_iterator BamTools::SamReadGroupConstIterator

◆ SamReadGroupContainer

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

◆ SamReadGroupIterator

typedef SamReadGroupContainer::iterator BamTools::SamReadGroupIterator

◆ SamSequenceConstIterator

typedef SamSequenceContainer::const_iterator BamTools::SamSequenceConstIterator

◆ SamSequenceContainer

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

◆ SamSequenceIterator

typedef SamSequenceContainer::iterator BamTools::SamSequenceIterator

Function Documentation

◆ BamAlignment::AddTag< std::string >()

template<>

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

inline

◆ BamAlignment::GetTag< std::string >()

template<>

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

inline

◆ FileExists()

bool BamTools::FileExists ( const std::string & filename )

inline

returns true if the file exists

◆ operator==() [1/3]

bool BamTools::operator==	(	const SamProgram &	lhs,
		const SamProgram &	rhs
	)

inline

tests equality by comparing program IDs

◆ operator==() [2/3]

bool BamTools::operator==	(	const SamReadGroup &	lhs,
		const SamReadGroup &	rhs
	)

inline

tests equality by comparing read group IDs

◆ operator==() [3/3]

bool BamTools::operator==	(	const SamSequence &	lhs,
		const SamSequence &	rhs
	)

inline

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

◆ PackUnsignedInt()

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

◆ PackUnsignedShort()

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

◆ SwapEndian_16() [1/2]

void BamTools::SwapEndian_16 ( int16_t & x )

inline

swaps endianness of signed 16-bit integer, in place

◆ SwapEndian_16() [2/2]

void BamTools::SwapEndian_16 ( uint16_t & x )

inline

swaps endianness of unsigned 16-bit integer, in place

◆ SwapEndian_16p()

void BamTools::SwapEndian_16p ( char * data )

inline

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

◆ SwapEndian_32() [1/2]

void BamTools::SwapEndian_32 ( int32_t & x )

inline

swaps endianness of signed 32-bit integer, in place

◆ SwapEndian_32() [2/2]

void BamTools::SwapEndian_32 ( uint32_t & x )

inline

swaps endianness of unsigned 32-bit integer, in place

◆ SwapEndian_32p()

void BamTools::SwapEndian_32p ( char * data )

inline

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

◆ SwapEndian_64() [1/2]

void BamTools::SwapEndian_64 ( int64_t & x )

inline

swaps endianness of signed 64-bit integer, in place

◆ SwapEndian_64() [2/2]

void BamTools::SwapEndian_64 ( uint64_t & x )

inline

swaps endianness of unsigned 64-bit integer, in place

◆ SwapEndian_64p()

void BamTools::SwapEndian_64p ( char * data )

inline

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

◆ SystemIsBigEndian()

bool BamTools::SystemIsBigEndian ( )

inline

checks host architecture's byte order

Returns: true if system uses big-endian ordering

◆ UnpackDouble()

double BamTools::UnpackDouble ( const char * buffer )

inline

reads a double value from byte buffer

Parameters

[in] buffer source byte buffer

Returns: the (double) value read from the buffer

◆ UnpackFloat()

double BamTools::UnpackFloat ( const char * buffer )

inline

reads a float value from byte buffer

Parameters

[in] buffer source byte buffer

Returns: the (float) value read from the buffer

◆ UnpackSignedInt()

signed int BamTools::UnpackSignedInt ( const char * buffer )

inline

reads a signed integer value from byte buffer

Parameters

[in] buffer source byte buffer

Returns: the (signed int) value read from the buffer

◆ UnpackSignedShort()

signed short BamTools::UnpackSignedShort ( const char * buffer )

inline

reads a signed short integer value from byte buffer

Parameters

[in] buffer source byte buffer

Returns: the (signed short) value read from the buffer

◆ UnpackUnsignedInt()

unsigned int BamTools::UnpackUnsignedInt ( const char * buffer )

inline

reads an unsigned integer value from byte buffer

Parameters

[in] buffer source byte buffer

Returns: the (unsigned int) value read from the buffer

◆ UnpackUnsignedShort()

unsigned short BamTools::UnpackUnsignedShort ( const char * buffer )

inline

reads an unsigned short integer value from byte buffer

Parameters

[in] buffer source byte buffer

Returns: the (unsigned short) value read from the buffer

Namespaces

Classes

Typedefs

Functions

Detailed Description

Typedef Documentation

◆ BamAlignmentVector

◆ RefVector

◆ SamProgramConstIterator

◆ SamProgramContainer

◆ SamProgramIterator

◆ SamReadGroupConstIterator

◆ SamReadGroupContainer

◆ SamReadGroupIterator

◆ SamSequenceConstIterator

◆ SamSequenceContainer

◆ SamSequenceIterator

Function Documentation

◆ BamAlignment::AddTag< std::string >()

◆ BamAlignment::GetTag< std::string >()

◆ FileExists()

◆ operator==() [1/3]

◆ operator==() [2/3]

◆ operator==() [3/3]

◆ PackUnsignedInt()

◆ PackUnsignedShort()

◆ SwapEndian_16() [1/2]

◆ SwapEndian_16() [2/2]

◆ SwapEndian_16p()

◆ SwapEndian_32() [1/2]

◆ SwapEndian_32() [2/2]

◆ SwapEndian_32p()

◆ SwapEndian_64() [1/2]

◆ SwapEndian_64() [2/2]

◆ SwapEndian_64p()

◆ SystemIsBigEndian()

◆ UnpackDouble()

◆ UnpackFloat()

◆ UnpackSignedInt()

◆ UnpackSignedShort()

◆ UnpackUnsignedInt()

◆ UnpackUnsignedShort()