Summary of a BAM record set. More...

#include <isoseqAlgn.hpp>

Public Member Functions
	BAMrecord ()=default
	Default constructor.
	BAMrecord (const bam1_t alignmentRecord, const sam_hdr_t samHeader)
	Constructor with data.
	BAMrecord (const BAMrecord &toCopy)=default
	Copy constructor.
BAMrecord &	operator= (const BAMrecord &toCopy)=default
	Copy assignment operator.
	BAMrecord (BAMrecord &&toMove) noexcept=default
	Move constructor.
BAMrecord &	operator= (BAMrecord &&toMove) noexcept=default
	Move assignment operator.
	~BAMrecord ()=default
	Destructor.
void	addSecondaryAlignment (const bam1_t alignmentRecord, const sam_hdr_t samHeader, const hts_pos_t localWindow=500 '000)
	Add a secondary alignment record.
std::string	getReadName () const
	Output read name.
hts_pos_t	getMapStart () const noexcept
	Map start position.
hts_pos_t	getMapEnd () const noexcept
	Map end position.
hts_pos_t	getmRNAstart () const noexcept
	mRNA start position
bool	isRevComp () const noexcept
	Is the read reverse-complemented?
bool	isMapped () const noexcept
	Is the read mapped?
bool	hasSecondaryAlignments () const noexcept
	Are there any secondary alignments?
bool	hasLocalSecondaryAlignments () const noexcept
	Are there any local secondary alignments?
uint16_t	secondaryAlignmentCount () const noexcept
	Count of all secondary alignments regardless of position.
uint16_t	localSecondaryAlignmentCount () const noexcept
	Count of secondary alignments overlapping the primary.
uint16_t	localReversedSecondaryAlignmentCount () const noexcept
	Count of reversed secondary alignments overlapping the primary.
hts_pos_t	getReadLength () const noexcept
	Read length.
std::vector< uint32_t >	getCIGARvector () const
	CIGAR vector.
std::string	getCIGARstring () const
	CIGAR string.
uint32_t	getFirstCIGAR () const noexcept
	Get the first cigar element with strand reversal.
std::string	getReferenceName () const
	Get reference name.
MappedReadMatchStatus	getBestReferenceMatchStatus () const
	Best reference-centric match status.
std::vector< std::pair< float, hts_pos_t > >	getReadCentricMatchStatus () const
	Reference match status along the read.
std::vector< MappedReadInterval >	getPoorlyMappedRegions (const BinomialWindowParameters &windowParameters) const
	Identify unmapped portions of the read.
std::string	getSequenceAndQuality (const MappedReadInterval &segmentBoundaries) const
	Get a segment of the sequence and the ASCII quality score.

Detailed Description

Summary of a BAM record set.

Stores relevant information from BAM format alignment records.

Constructor & Destructor Documentation

◆ BAMrecord() [1/3]

isaSpace::BAMrecord::BAMrecord	(	const bam1_t *	alignmentRecord,
		const sam_hdr_t *	samHeader )

Constructor with data.

Constructs an object from an HTSLIB alignment record and the corresponding header.

Parameters

[in]	alignmentRecord	pointer to a read alignment record
[in]	samHeader	pointer to the corresponding BAM/SAM header

◆ BAMrecord() [2/3]

isaSpace::BAMrecord::BAMrecord ( const BAMrecord & toCopy )

default

Copy constructor.

Parameters

[in] toCopy object to copy

◆ BAMrecord() [3/3]

isaSpace::BAMrecord::BAMrecord ( BAMrecord && toMove )

defaultnoexcept

Move constructor.

Parameters

[in] toMove object to move

Member Function Documentation

◆ addSecondaryAlignment()

void isaSpace::BAMrecord::addSecondaryAlignment	(	const bam1_t *	alignmentRecord,
		const sam_hdr_t *	samHeader,
		const hts_pos_t	localWindow = 500 '000 )

Add a secondary alignment record.

Adds information from a secondary alignment record if it is a local secondary alignment. Otherwise, only increments the total number of secondary alignments.

Parameters

[in]	alignmentRecord	pointer to a read alignment record
[in]	samHeader	pointer to the corresponding BAM/SAM header
[in]	localWindow	window size for a secondary alignment to be considered local

◆ getBestReferenceMatchStatus()

MappedReadMatchStatus isaSpace::BAMrecord::getBestReferenceMatchStatus ( ) const

nodiscard

Best reference-centric match status.

For each position, best match among all primary and secondary alignments.

Returns: match status with map start

◆ getCIGARstring()

std::string isaSpace::BAMrecord::getCIGARstring ( ) const

nodiscard

CIGAR string.

Reversed if the read is reverse-complemented.

Returns: CIGAR string

◆ getCIGARvector()

std::vector< uint32_t > isaSpace::BAMrecord::getCIGARvector ( ) const

inlinenodiscard

CIGAR vector.

Orientation independent of strand

Returns: CIGAR vector

◆ getFirstCIGAR()

uint32_t isaSpace::BAMrecord::getFirstCIGAR ( ) const

nodiscardnoexcept

Get the first cigar element with strand reversal.

Returns: first CIGAR vector element or 0 if none

◆ getMapEnd()

hts_pos_t isaSpace::BAMrecord::getMapEnd ( ) const

inlinenodiscardnoexcept

Map end position.

Position of the first past the mapped region of the reference.

Returns: 1-based read map end position

◆ getMapStart()

hts_pos_t isaSpace::BAMrecord::getMapStart ( ) const

inlinenodiscardnoexcept

Map start position.

Position of the first mapped nucleotide.

Returns: 1-based read map start position

◆ getmRNAstart()

hts_pos_t isaSpace::BAMrecord::getmRNAstart ( ) const

inlinenodiscardnoexcept

mRNA start position

Position of the first mRNA read nucleotide, taking into account possible reverse-complement.

Returns: 1-based read mRNA start position

◆ getPoorlyMappedRegions()

std::vector< MappedReadInterval > isaSpace::BAMrecord::getPoorlyMappedRegions ( const BinomialWindowParameters & windowParameters ) const

nodiscard

Identify unmapped portions of the read.

Returns a vector of poorly mapped portions of the read. Vector is empty if the read is mapped.

Parameters

[in] windowParameters window parameters: size and the mapped/unmapped region binomial probabilities

Returns: vector of poorly mapped region coordinates

◆ getReadCentricMatchStatus()

std::vector< std::pair< float, hts_pos_t > > isaSpace::BAMrecord::getReadCentricMatchStatus ( ) const

nodiscard

Reference match status along the read.

Parses CIGAR to track reference match/mismatch (1.0 for match, 0.0 for mismatch) status along the read, relating each read position to the corresponding reference base-1 nucleotide position. The vector start begins at the position closest to the first exon start regardless of strand.

Returns: vector of match status/reference position pairs

◆ getReadLength()

hts_pos_t isaSpace::BAMrecord::getReadLength ( ) const

inlinenodiscardnoexcept

Read length.

Returns: read length in bases

◆ getReadName()

std::string isaSpace::BAMrecord::getReadName ( ) const

inlinenodiscard

Output read name.

Returns: read name

◆ getReferenceName()

std::string isaSpace::BAMrecord::getReferenceName ( ) const

inlinenodiscard

Get reference name.

Reference sequence (e.g., chromosome) name. If absent, returns * like samtools.

Returns: reference name

◆ getSequenceAndQuality()

std::string isaSpace::BAMrecord::getSequenceAndQuality ( const MappedReadInterval & segmentBoundaries ) const

nodiscard

Get a segment of the sequence and the ASCII quality score.

Returns sequence and printable ASCII quality scores separated by a newline, with a newline at the end. Negative strand alignments are reverse-complemented to export the original strand.

Parameters

[in] segmentBoundaries read interval to retrieve

Returns: sequence and quality

◆ hasLocalSecondaryAlignments()

bool isaSpace::BAMrecord::hasLocalSecondaryAlignments ( ) const

inlinenodiscardnoexcept

Are there any local secondary alignments?

Returns: true if there are any secondary alignments overlapping the primary

◆ hasSecondaryAlignments()

bool isaSpace::BAMrecord::hasSecondaryAlignments ( ) const

inlinenodiscardnoexcept

Are there any secondary alignments?

Returns: true if there are any secondary alignments

◆ isMapped()

bool isaSpace::BAMrecord::isMapped ( ) const

inlinenodiscardnoexcept

Is the read mapped?

Returns: true if the read is mapped

◆ isRevComp()

bool isaSpace::BAMrecord::isRevComp ( ) const

inlinenodiscardnoexcept

Is the read reverse-complemented?

Returns: true if the read is reverse-complemented

◆ localReversedSecondaryAlignmentCount()

uint16_t isaSpace::BAMrecord::localReversedSecondaryAlignmentCount ( ) const

nodiscardnoexcept

Count of reversed secondary alignments overlapping the primary.

Returns: Local reversed secondary alignment count

◆ localSecondaryAlignmentCount()

uint16_t isaSpace::BAMrecord::localSecondaryAlignmentCount ( ) const

inlinenodiscardnoexcept

Count of secondary alignments overlapping the primary.

Returns: Local secondary alignment count

◆ operator=() [1/2]

BAMrecord & isaSpace::BAMrecord::operator= ( BAMrecord && toMove )

defaultnoexcept

Move assignment operator.

Parameters

[in] toMove object to move

Returns: BAMrecord object

◆ operator=() [2/2]

BAMrecord & isaSpace::BAMrecord::operator= ( const BAMrecord & toCopy )

default

Copy assignment operator.

Parameters

[in] toCopy object to copy

Returns: BAMrecord object

◆ secondaryAlignmentCount()

uint16_t isaSpace::BAMrecord::secondaryAlignmentCount ( ) const

inlinenodiscardnoexcept

Count of all secondary alignments regardless of position.

Returns: Secondary alignment count

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

isoseqAlgn.hpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ BAMrecord() [1/3]

◆ BAMrecord() [2/3]

◆ BAMrecord() [3/3]

Member Function Documentation

◆ addSecondaryAlignment()

◆ getBestReferenceMatchStatus()

◆ getCIGARstring()

◆ getCIGARvector()

◆ getFirstCIGAR()

◆ getMapEnd()

◆ getMapStart()

◆ getmRNAstart()

◆ getPoorlyMappedRegions()

◆ getReadCentricMatchStatus()

◆ getReadLength()

◆ getReadName()

◆ getReferenceName()

◆ getSequenceAndQuality()

◆ hasLocalSecondaryAlignments()

◆ hasSecondaryAlignments()

◆ isMapped()

◆ isRevComp()

◆ localReversedSecondaryAlignmentCount()

◆ localSecondaryAlignmentCount()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ secondaryAlignmentCount()