BamTools::BamAlignment Class Reference

The main BAM alignment data structure. More...

#include <BamAlignment.h>

Classes
struct	BamAlignmentSupportData
Public Member Functions
	BamAlignment (void)
	constructor
	BamAlignment (const BamAlignment &other)
	copy constructor
	~BamAlignment (void)
	destructor
bool	IsDuplicate (void) const
bool	IsFailedQC (void) const
bool	IsFirstMate (void) const
bool	IsMapped (void) const
bool	IsMateMapped (void) const
bool	IsMateReverseStrand (void) const
bool	IsPaired (void) const
bool	IsPrimaryAlignment (void) const
bool	IsProperPair (void) const
bool	IsReverseStrand (void) const
bool	IsSecondMate (void) const
void	SetIsDuplicate (bool ok)
	Sets value of "PCR duplicate" flag to ok.
void	SetIsFailedQC (bool ok)
	Sets "failed quality control" flag to ok.
void	SetIsFirstMate (bool ok)
	Sets "alignment is first mate" flag to ok.
void	SetIsMapped (bool ok)
	Sets "alignment is mapped" flag to ok.
void	SetIsMateMapped (bool ok)
	Sets "alignment's mate is mapped" flag to ok.
void	SetIsMateReverseStrand (bool ok)
	Sets "alignment's mate mapped to reverse strand" flag to ok.
void	SetIsPaired (bool ok)
	Sets "alignment part of paired-end read" flag to ok.
void	SetIsPrimaryAlignment (bool ok)
	Sets "position is primary alignment" flag to ok.
void	SetIsProperPair (bool ok)
	Sets "alignment is part of read that satisfied paired-end resolution" flag to ok.
void	SetIsReverseStrand (bool ok)
	Sets "alignment mapped to reverse strand" flag to ok.
void	SetIsSecondMate (bool ok)
	Sets "alignment is second mate on read" flag to ok.
template<typename T >
bool	AddTag (const std::string &tag, const std::string &type, const T &value)
template<typename T >
bool	AddTag (const std::string &tag, const std::vector< T > &values)
template<typename T >
bool	EditTag (const std::string &tag, const std::string &type, const T &value)
template<typename T >
bool	EditTag (const std::string &tag, const std::vector< T > &values)
template<typename T >
bool	GetTag (const std::string &tag, T &destination) const
template<typename T >
bool	GetTag (const std::string &tag, std::vector< T > &destination) const
bool	GetTagType (const std::string &tag, char &type) const
	Retrieves the BAM tag type-code associated with requested tag name.
bool	HasTag (const std::string &tag) const
	Returns true if alignment has a record for requested tag.
void	RemoveTag (const std::string &tag)
	Removes field from BAM tags.
bool	BuildCharData (void)
	Populates alignment string fields (read name, bases, qualities, tag data).
int	GetEndPosition (bool usePadded=false, bool closedInterval=false) const
	Calculates alignment end position, based on its starting position and CIGAR data.
std::string	GetErrorString (void) const
	Returns a human-readable description of the last error that occurred.
bool	GetSoftClips (std::vector< int > &clipSizes, std::vector< int > &readPositions, std::vector< int > &genomePositions, bool usePadded=false) const
	Identifies if an alignment has a soft clip. If so, identifies the sizes of the soft clips, as well as their positions in the read and reference.
Public Attributes
std::string	Name
	read name
int32_t	Length
	length of query sequence
std::string	QueryBases
	'original' sequence (as reported from sequencing machine)
std::string	AlignedBases
	'aligned' sequence (includes any indels, padding, clipping)
std::string	Qualities
	FASTQ qualities (ASCII characters, not numeric values).
std::string	TagData
	tag data (use the provided methods to query/modify)
int32_t	RefID
	ID number for reference sequence.
int32_t	Position
	position (0-based) where alignment starts
uint16_t	Bin
	BAM (standard) index bin number for this alignment.
uint16_t	MapQuality
	mapping quality score
uint32_t	AlignmentFlag
	alignment bit-flag (use the provided methods to query/modify)
std::vector< CigarOp >	CigarData
	CIGAR operations for this alignment.
int32_t	MateRefID
	ID number for reference sequence where alignment's mate was aligned.
int32_t	MatePosition
	position (0-based) where alignment's mate starts
int32_t	InsertSize
	mate-pair insert size
std::string	Filename
	name of BAM file which this alignment comes from
Friends
class	Internal::BamReaderPrivate
class	Internal::BamWriterPrivate

Detailed Description

The main BAM alignment data structure.

Provides methods to query/modify BAM alignment data fields.

Constructor & Destructor Documentation

BamAlignment::BamAlignment ( void )

constructor

BamAlignment::BamAlignment ( const BamAlignment & other )

copy constructor

BamAlignment::~BamAlignment ( void )

destructor

Member Function Documentation

template<typename T >

bool BamTools::BamAlignment::AddTag	(	const std::string &	tag,
		const std::vector< T > &	values
	)			`[inline]`

template<typename T >

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

bool BamAlignment::BuildCharData ( void )

Populates alignment string fields (read name, bases, qualities, tag data).

An alignment retrieved using BamReader::GetNextAlignmentCore() lacks this data. Using that method makes parsing much quicker when only positional data is required.

However, if you later want to access the character data fields from such an alignment, use this method to populate those fields. Provides ability to do 'lazy evaluation' of alignment parsing.

Returns:: true if character data populated successfully (or was already available to begin with)

template<typename T >

bool BamTools::BamAlignment::EditTag	(	const std::string &	tag,
		const std::vector< T > &	values
	)			`[inline]`

template<typename T >

bool BamTools::BamAlignment::EditTag	(	const std::string &	tag,
		const std::string &	type,
		const T &	value
	)			`[inline]`

int BamAlignment::GetEndPosition	(	bool	usePadded = `false`,
		bool	closedInterval = `false`
	)			const

Calculates alignment end position, based on its starting position and CIGAR data.

Warning:: The position returned now represents a zero-based, HALF-OPEN interval. In previous versions of BamTools (0.x & 1.x) all intervals were treated as zero-based, CLOSED.

Parameters:

`[in]`	usePadded	Allow inserted bases to affect the reported position. Default is false, so that reported position stays synced with reference coordinates.
`[in]`	closedInterval	Setting this to true will return a 0-based end coordinate. Default is false, so that his value represents a standard, half-open interval.

Returns:: alignment end position

std::string BamAlignment::GetErrorString ( void ) const

Returns a human-readable description of the last error that occurred.

This method allows elimination of STDERR pollution. Developers of client code may choose how the messages are displayed to the user, if at all.

Returns:: error description

bool BamAlignment::GetSoftClips	(	std::vector< int > &	clipSizes,
		std::vector< int > &	readPositions,
		std::vector< int > &	genomePositions,
		bool	usePadded = `false`
	)			const

Identifies if an alignment has a soft clip. If so, identifies the sizes of the soft clips, as well as their positions in the read and reference.

Parameters:

`[out]`	clipSizes	vector of the sizes of each soft clip in the alignment
`[out]`	readPositions	vector of the 0-based read locations of each soft clip in the alignment. These positions are basically indexes within the read, not genomic positions.
`[out]`	genomePositions	vector of the 0-based genome locations of each soft clip in the alignment
`[in]`	usePadded	inserted bases affect reported position. Default is false, so that reported position stays 'sync-ed' with reference coordinates.

Returns:: true if any soft clips were found in the alignment

template<typename T >

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

template<typename T >

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

bool BamAlignment::GetTagType	(	const std::string &	tag,
		char &	type
	)			const

Retrieves the BAM tag type-code associated with requested tag name.

Parameters:

`[in]`	tag	2-character tag name
`[out]`	type	retrieved (1-character) type-code

Returns:: true if found

See also:: http://samtools.sourceforge.net/SAM1.pdf for more details on reserved tag names, supported tag types, etc.

bool BamAlignment::HasTag ( const std::string & tag ) const

Returns true if alignment has a record for requested tag.

Parameters:

[in] tag 2-character tag name

Returns:: true if alignment has a record for tag

bool BamAlignment::IsDuplicate ( void ) const

Returns:: true if this read is a PCR duplicate

bool BamAlignment::IsFailedQC ( void ) const

Returns:: true if this read failed quality control

bool BamAlignment::IsFirstMate ( void ) const

Returns:: true if alignment is first mate on paired-end read

bool BamAlignment::IsMapped ( void ) const

Returns:: true if alignment is mapped

bool BamAlignment::IsMateMapped ( void ) const

Returns:: true if alignment's mate is mapped

bool BamAlignment::IsMateReverseStrand ( void ) const

Returns:: true if alignment's mate mapped to reverse strand

bool BamAlignment::IsPaired ( void ) const

Returns:: true if alignment part of paired-end read

bool BamAlignment::IsPrimaryAlignment ( void ) const

Returns:: true if reported position is primary alignment

bool BamAlignment::IsProperPair ( void ) const

Returns:: true if alignment is part of read that satisfied paired-end resolution

bool BamAlignment::IsReverseStrand ( void ) const

Returns:: true if alignment mapped to reverse strand

bool BamAlignment::IsSecondMate ( void ) const

Returns:: true if alignment is second mate on read

void BamAlignment::RemoveTag ( const std::string & tag )

Removes field from BAM tags.

Parameters:

[in] tag 2-character name of field to remove

void BamAlignment::SetIsDuplicate ( bool ok )

Sets value of "PCR duplicate" flag to ok.

void BamAlignment::SetIsFailedQC ( bool ok )

Sets "failed quality control" flag to ok.

void BamAlignment::SetIsFirstMate ( bool ok )

Sets "alignment is first mate" flag to ok.

void BamAlignment::SetIsMapped ( bool ok )

Sets "alignment is mapped" flag to ok.

void BamAlignment::SetIsMateMapped ( bool ok )

Sets "alignment's mate is mapped" flag to ok.

void BamAlignment::SetIsMateReverseStrand ( bool ok )

Sets "alignment's mate mapped to reverse strand" flag to ok.

void BamAlignment::SetIsPaired ( bool ok )

Sets "alignment part of paired-end read" flag to ok.

void BamAlignment::SetIsPrimaryAlignment ( bool ok )

Sets "position is primary alignment" flag to ok.

void BamAlignment::SetIsProperPair ( bool ok )

Sets "alignment is part of read that satisfied paired-end resolution" flag to ok.

void BamAlignment::SetIsReverseStrand ( bool ok )

Sets "alignment mapped to reverse strand" flag to ok.

void BamAlignment::SetIsSecondMate ( bool ok )

Sets "alignment is second mate on read" flag to ok.

Friends And Related Function Documentation

friend class Internal::BamReaderPrivate [friend]

friend class Internal::BamWriterPrivate [friend]

Member Data Documentation

BamAlignment::AlignedBases

'aligned' sequence (includes any indels, padding, clipping)

This field will be completely empty after reading from BamReader/BamMultiReader when QueryBases is empty.

BamAlignment::AlignmentFlag

alignment bit-flag (use the provided methods to query/modify)

BamAlignment::Bin

BAM (standard) index bin number for this alignment.

BamAlignment::CigarData

CIGAR operations for this alignment.

BamAlignment::Filename

name of BAM file which this alignment comes from

BamAlignment::InsertSize

mate-pair insert size

BamAlignment::Length

length of query sequence

BamAlignment::MapQuality

mapping quality score

BamAlignment::MatePosition

position (0-based) where alignment's mate starts

BamAlignment::MateRefID

ID number for reference sequence where alignment's mate was aligned.

BamAlignment::Name

read name

BamAlignment::Position

position (0-based) where alignment starts

BamAlignment::Qualities

FASTQ qualities (ASCII characters, not numeric values).

Note:: Setting this field to "*" indicates to BamWriter that the quality scores are not to be stored, but instead will be output as a sequence of '0xFF'. Otherwise, QueryBases must not be a "*" and the length of this field should equal the length of QueryBases.

BamAlignment::QueryBases

'original' sequence (as reported from sequencing machine)

Note:: Setting this field to "*" indicates that the sequence is not to be stored on output. In this case, the contents of the Qualities field should be invalidated as well (cleared or marked as "*").

BamAlignment::RefID

ID number for reference sequence.

BamAlignment::TagData

tag data (use the provided methods to query/modify)

The documentation for this class was generated from the following files:

BamTools::BamAlignment Class Reference

Classes

Public Member Functions

Public Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation