The main BAM alignment data structure. More...

#include <BamAlignment.h>

Public Member Functions
	BamAlignment ()
	constructor More...

bool	IsDuplicate () const

bool	IsFailedQC () const

bool	IsFirstMate () const

bool	IsMapped () const

bool	IsMateMapped () const

bool	IsMateReverseStrand () const

bool	IsPaired () const

bool	IsSupplementary () const

bool	IsPrimaryAlignment () const

bool	IsProperPair () const

bool	IsReverseStrand () const

bool	IsSecondMate () const

void	SetIsDuplicate (bool ok)
	Sets value of "PCR duplicate" flag to ok. More...

void	SetIsFailedQC (bool ok)
	Sets "failed quality control" flag to ok. More...

void	SetIsFirstMate (bool ok)
	Sets "alignment is first mate" flag to ok. More...

void	SetIsMapped (bool ok)
	Sets "alignment is mapped" flag to ok. More...

void	SetIsMateMapped (bool ok)
	Sets "alignment's mate is mapped" flag to ok. More...

void	SetIsMateReverseStrand (bool ok)
	Sets "alignment's mate mapped to reverse strand" flag to ok. More...

void	SetIsPaired (bool ok)
	Sets "alignment part of paired-end read" flag to ok. More...

void	SetIsPrimaryAlignment (bool ok)
	Sets "position is primary alignment" flag to ok. More...

void	SetIsProperPair (bool ok)
	Sets "alignment is part of read that satisfied paired-end resolution" flag to ok. More...

void	SetIsReverseStrand (bool ok)
	Sets "alignment mapped to reverse strand" flag to ok. More...

void	SetIsSecondMate (bool ok)
	Sets "alignment is second mate on read" flag to ok. More...

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

std::vector< std::string >	GetTagNames () const
	Retrieves the BAM tag names. More...

bool	GetTagType (const std::string &tag, char &type) const
	Retrieves the BAM tag type-code associated with requested tag name. More...

bool	GetArrayTagType (const std::string &tag, char &type) const
	Retrieves the BAM tag type-code for the array elements associated with requested tag name. More...

bool	HasTag (const std::string &tag) const
	Returns true if alignment has a record for requested tag. More...

void	RemoveTag (const std::string &tag)
	Removes field from BAM tags. More...

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

int	GetEndPosition (bool usePadded=false, bool closedInterval=false) const
	Calculates alignment end position, based on its starting position and CIGAR data. More...

std::string	GetErrorString () const
	Returns a human-readable description of the last error that occurred. More...

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. More...

Public Attributes
std::string	Name
	read name More...

int32_t	Length
	length of query sequence More...

std::string	QueryBases
	'original' sequence (as reported from sequencing machine) More...

std::string	AlignedBases
	'aligned' sequence (includes any indels, padding, clipping) More...

std::string	Qualities
	FASTQ qualities (ASCII characters, not numeric values) More...

std::string	TagData
	tag data (use the provided methods to query/modify) More...

int32_t	RefID
	ID number for reference sequence. More...

int32_t	Position
	position (0-based) where alignment starts More...

uint16_t	Bin
	BAM (standard) index bin number for this alignment. More...

uint16_t	MapQuality
	mapping quality score More...

uint32_t	AlignmentFlag
	alignment bit-flag (use the provided methods to query/modify) More...

std::vector< CigarOp >	CigarData
	CIGAR operations for this alignment. More...

int32_t	MateRefID
	ID number for reference sequence where alignment's mate was aligned. More...

int32_t	MatePosition
	position (0-based) where alignment's mate starts More...

int32_t	InsertSize
	mate-pair insert size More...

std::string	Filename
	name of BAM file which this alignment comes from More...

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::BamAlignment ( )

constructor

Member Function Documentation

◆ AddTag() [1/2]

template<typename T >

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

◆ AddTag() [2/2]

template<typename T >

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

◆ BuildCharData()

bool BamAlignment::BuildCharData ( )

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)

◆ EditTag() [1/2]

template<typename T >

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

◆ EditTag() [2/2]

template<typename T >

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

◆ GetArrayTagType()

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

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

Parameters

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

Returns: true if found. False if not found, or if tag is not an array type.

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

◆ GetEndPosition()

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

◆ GetErrorString()

std::string BamAlignment::GetErrorString ( ) 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

◆ GetSoftClips()

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

◆ GetTag() [1/2]

template<typename T >

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

◆ GetTag() [2/2]

template<typename T >

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

◆ GetTagNames()

std::vector< std::string > BamAlignment::GetTagNames ( ) const

Retrieves the BAM tag names.

When paired with GetTagType() and GetTag(), this method allows you to iterate over an alignment's tag data without knowing the names (or types) beforehand.

Returns: vector containing all tag names found (empty if none available)

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

◆ GetTagType()

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.

◆ HasTag()

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

◆ IsDuplicate()

bool BamAlignment::IsDuplicate ( ) const

Returns: true if this read is a PCR duplicate

◆ IsFailedQC()

bool BamAlignment::IsFailedQC ( ) const

Returns: true if this read failed quality control

◆ IsFirstMate()

bool BamAlignment::IsFirstMate ( ) const

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

◆ IsMapped()

bool BamAlignment::IsMapped ( ) const

Returns: true if alignment is mapped

◆ IsMateMapped()

bool BamAlignment::IsMateMapped ( ) const

Returns: true if alignment's mate is mapped

◆ IsMateReverseStrand()

bool BamAlignment::IsMateReverseStrand ( ) const

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

◆ IsPaired()

bool BamAlignment::IsPaired ( ) const

Returns: true if alignment part of paired-end read

◆ IsPrimaryAlignment()

bool BamAlignment::IsPrimaryAlignment ( ) const

Returns: true if reported position is primary alignment

◆ IsProperPair()

bool BamAlignment::IsProperPair ( ) const

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

◆ IsReverseStrand()

bool BamAlignment::IsReverseStrand ( ) const

Returns: true if alignment mapped to reverse strand

◆ IsSecondMate()

bool BamAlignment::IsSecondMate ( ) const

Returns: true if alignment is second mate on read

◆ IsSupplementary()

bool BamAlignment::IsSupplementary ( ) const

Returns: true if this read is supplementary

◆ RemoveTag()

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

Removes field from BAM tags.

Parameters

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

◆ SetIsDuplicate()

void BamAlignment::SetIsDuplicate ( bool ok )

Sets value of "PCR duplicate" flag to ok.

◆ SetIsFailedQC()

void BamAlignment::SetIsFailedQC ( bool ok )

Sets "failed quality control" flag to ok.

◆ SetIsFirstMate()

void BamAlignment::SetIsFirstMate ( bool ok )

Sets "alignment is first mate" flag to ok.

◆ SetIsMapped()

void BamAlignment::SetIsMapped ( bool ok )

Sets "alignment is mapped" flag to ok.

◆ SetIsMateMapped()

void BamAlignment::SetIsMateMapped ( bool ok )

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

◆ SetIsMateReverseStrand()

void BamAlignment::SetIsMateReverseStrand ( bool ok )

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

◆ SetIsPaired()

void BamAlignment::SetIsPaired ( bool ok )

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

◆ SetIsPrimaryAlignment()

void BamAlignment::SetIsPrimaryAlignment ( bool ok )

Sets "position is primary alignment" flag to ok.

◆ SetIsProperPair()

void BamAlignment::SetIsProperPair ( bool ok )

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

◆ SetIsReverseStrand()

void BamAlignment::SetIsReverseStrand ( bool ok )

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

◆ SetIsSecondMate()

void BamAlignment::SetIsSecondMate ( bool ok )

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

Friends And Related Function Documentation

◆ Internal::BamReaderPrivate

friend class Internal::BamReaderPrivate

friend

◆ Internal::BamWriterPrivate

friend class Internal::BamWriterPrivate

friend

Member Data Documentation

◆ AlignedBases

BamAlignment::AlignedBases

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

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

◆ AlignmentFlag

BamAlignment::AlignmentFlag

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

◆ Bin

BamAlignment::Bin

BAM (standard) index bin number for this alignment.

◆ CigarData

BamAlignment::CigarData

CIGAR operations for this alignment.

◆ Filename

BamAlignment::Filename

name of BAM file which this alignment comes from

◆ InsertSize

BamAlignment::InsertSize

mate-pair insert size

◆ Length

BamAlignment::Length

length of query sequence

◆ MapQuality

BamAlignment::MapQuality

mapping quality score

◆ MatePosition

BamAlignment::MatePosition

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

◆ MateRefID

BamAlignment::MateRefID

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

◆ Name

BamAlignment::Name

read name

◆ Position

BamAlignment::Position

position (0-based) where alignment starts

◆ Qualities

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.

◆ 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 "*").

◆ RefID

BamAlignment::RefID

ID number for reference sequence.

◆ TagData

BamAlignment::TagData

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

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

Public Member Functions

Public Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ BamAlignment()

Member Function Documentation

◆ AddTag() [1/2]

◆ AddTag() [2/2]

◆ BuildCharData()

◆ EditTag() [1/2]

◆ EditTag() [2/2]

◆ GetArrayTagType()

◆ GetEndPosition()

◆ GetErrorString()

◆ GetSoftClips()

◆ GetTag() [1/2]

◆ GetTag() [2/2]

◆ GetTagNames()

◆ GetTagType()

◆ HasTag()

◆ IsDuplicate()

◆ IsFailedQC()

◆ IsFirstMate()

◆ IsMapped()

◆ IsMateMapped()

◆ IsMateReverseStrand()

◆ IsPaired()

◆ IsPrimaryAlignment()

◆ IsProperPair()

◆ IsReverseStrand()

◆ IsSecondMate()

◆ IsSupplementary()

◆ RemoveTag()

◆ SetIsDuplicate()

◆ SetIsFailedQC()

◆ SetIsFirstMate()

◆ SetIsMapped()

◆ SetIsMateMapped()

◆ SetIsMateReverseStrand()

◆ SetIsPaired()

◆ SetIsPrimaryAlignment()

◆ SetIsProperPair()

◆ SetIsReverseStrand()

◆ SetIsSecondMate()

Friends And Related Function Documentation

◆ Internal::BamReaderPrivate

◆ Internal::BamWriterPrivate

Member Data Documentation

◆ AlignedBases

◆ AlignmentFlag

◆ Bin

◆ CigarData

◆ Filename

◆ InsertSize

◆ Length

◆ MapQuality

◆ MatePosition

◆ MateRefID

◆ Name

◆ Position

◆ Qualities

◆ QueryBases

◆ RefID

◆ TagData