Group of exons from the same gene. More...

#include <isoseqAlgn.hpp>

Public Member Functions
	ExonGroup ()=default
	Default constructor.
	ExonGroup (std::string geneName, const char strand, std::set< std::pair< hts_pos_t, hts_pos_t > > &exonSet)
	Constructor with lines from a GFF file.
	ExonGroup (std::string geneName, const char strand, const std::vector< std::string > &exonLinesFomGFF)
	Constructor with exon lines from a GFF file.
	ExonGroup (const ExonGroup &toCopy)=default
	Copy constructor.
ExonGroup &	operator= (const ExonGroup &toCopy)=default
	Copy assignment operator.
	ExonGroup (ExonGroup &&toMove) noexcept=default
	Move constructor.
ExonGroup &	operator= (ExonGroup &&toMove) noexcept=default
	Move assignment operator.
	~ExonGroup ()=default
	Destructor.
bool	empty () const noexcept
	Is the object empty?
std::string	geneName () const
	Report the gene name.
size_t	nExons () const noexcept
	Number of exons in the gene.
char	strand () const noexcept
	Strand ID.
std::pair< hts_pos_t, hts_pos_t >	at (const size_t &idx) const
	Range covered by a given exon.
std::pair< hts_pos_t, hts_pos_t >	geneSpan () const noexcept
	Gene span.
std::pair< hts_pos_t, hts_pos_t >	firstExonSpan () const noexcept
	First exon span.
hts_pos_t	firstExonLength () const noexcept
	First exon length.
uint32_t	firstExonAfter (const hts_pos_t &position) const noexcept
	Index of the first exon after a given position.
uint32_t	firstOverlappingExon (const hts_pos_t &position) const noexcept
	Index of the first exon overlapping a given position.
uint32_t	lastExonBefore (const hts_pos_t &position) const noexcept
	Index of the last exon before a given position.
uint32_t	lastOverlappingExon (const hts_pos_t &position) const noexcept
	Index of the last exon overlapping a given position.
std::pair< hts_pos_t, hts_pos_t >	getFirstIntronSpan () const
	First intron span.
std::vector< float >	getExonCoverageQuality (const BAMrecord &alignment) const
	Get read coverage quality per exon.
std::vector< float >	getBestExonCoverageQuality (const BAMrecord &alignment) const
	Get best read coverage quality per exon.

Detailed Description

Group of exons from the same gene.

Gathers exons belonging to all transcripts of a gene.

Constructor & Destructor Documentation

◆ ExonGroup() [1/4]

isaSpace::ExonGroup::ExonGroup	(	std::string	geneName,
		const char	strand,
		std::set< std::pair< hts_pos_t, hts_pos_t > > &	exonSet )

Constructor with lines from a GFF file.

The exon set is ordered by the exon starts. The first exon can be the first or the last, depending on the strand. The strand is assumed positive, unless explicitly specified as negative by passing the - character.

Parameters

[in]	geneName	gene name
[in]	strand	mRNA strand
[in]	exonSet	set of exons from the same gene

◆ ExonGroup() [2/4]

isaSpace::ExonGroup::ExonGroup	(	std::string	geneName,
		const char	strand,
		const std::vector< std::string > &	exonLinesFomGFF )

Constructor with exon lines from a GFF file.

Uses lines exon from a GFF file that belong to the same gene.

Parameters

[in]	geneName	gene name
[in]	strand	mRNA strand
[in]	exonLinesFomGFF	GFF file exon lines

◆ ExonGroup() [3/4]

isaSpace::ExonGroup::ExonGroup ( const ExonGroup & toCopy )

default

Copy constructor.

Parameters

[in] toCopy object to copy

◆ ExonGroup() [4/4]

isaSpace::ExonGroup::ExonGroup ( ExonGroup && toMove )

defaultnoexcept

Move constructor.

Parameters

[in] toMove object to move

Member Function Documentation

◆ at()

std::pair< hts_pos_t, hts_pos_t > isaSpace::ExonGroup::at ( const size_t & idx ) const

inlinenodiscard

Range covered by a given exon.

Parameters

[in] idx exon index

Returns: the exon start and end nucleotide position pair

◆ empty()

bool isaSpace::ExonGroup::empty ( ) const

inlinenodiscardnoexcept

Is the object empty?

Returns: true is the object has no exons

◆ firstExonAfter()

uint32_t isaSpace::ExonGroup::firstExonAfter ( const hts_pos_t & position ) const

nodiscardnoexcept

Index of the first exon after a given position.

0-based index of the first exon found entirely after the given position. Equal to the index of the last exon if the position is after the last exon.

Parameters

[in] position genome position to test

Returns: index of the first exon after the given position

◆ firstExonLength()

hts_pos_t isaSpace::ExonGroup::firstExonLength ( ) const

nodiscardnoexcept

First exon length.

Returns: first exon length

◆ firstExonSpan()

std::pair< hts_pos_t, hts_pos_t > isaSpace::ExonGroup::firstExonSpan ( ) const

nodiscardnoexcept

First exon span.

Returns the position of the first exon, depends on the strand. First position is always smaller than the second regardless of strand, in keeping with the GFF3 specification.

Returns: first exon nucleotide position pair (1-based)

◆ firstOverlappingExon()

uint32_t isaSpace::ExonGroup::firstOverlappingExon ( const hts_pos_t & position ) const

nodiscardnoexcept

Index of the first exon overlapping a given position.

0-based index of the first exon found at least partially after the given position. Equal to the index of the last exon if the position is after the last exon.

Parameters

[in] position genome position to test

Returns: index of the first exon overlapping the given position

◆ geneName()

std::string isaSpace::ExonGroup::geneName ( ) const

inlinenodiscard

Report the gene name.

Returns: gene name

◆ geneSpan()

std::pair< hts_pos_t, hts_pos_t > isaSpace::ExonGroup::geneSpan ( ) const

nodiscardnoexcept

Gene span.

Returns the position span of the gene. First element of the pair is always smaller than the last regardless of the strand.

Returns: first and last nucleotide position (1-based) of the gene

◆ getBestExonCoverageQuality()

std::vector< float > isaSpace::ExonGroup::getBestExonCoverageQuality ( const BAMrecord & alignment ) const

nodiscard

Get best read coverage quality per exon.

Use CIGAR information, adding local secondary alignments, to extract alignment quality for each exon. Quality is the fraction of reference nucleotides covered by matching read bases.

Parameters

[in] alignment BAM alignment record

Returns: vector best alignment qualities, one per exon

◆ getExonCoverageQuality()

std::vector< float > isaSpace::ExonGroup::getExonCoverageQuality ( const BAMrecord & alignment ) const

nodiscard

Get read coverage quality per exon.

Use CIGAR information to extract alignment quality for each exon. Quality is the fraction of reference nucleotides covered by matching read bases.

Parameters

[in] alignment BAM alignment record

Returns: vector of alignment qualities, one per exon

◆ getFirstIntronSpan()

std::pair< hts_pos_t, hts_pos_t > isaSpace::ExonGroup::getFirstIntronSpan ( ) const

nodiscard

First intron span.

Smaller value first regardless of strand, but the intron is always the first in the gene, last in the sequence if the strand is negative. If there is only one exon, the start and end are reported as -1.

Returns: first intron start and end positions

◆ lastExonBefore()

uint32_t isaSpace::ExonGroup::lastExonBefore ( const hts_pos_t & position ) const

nodiscardnoexcept

Index of the last exon before a given position.

0-based index of the last exon found entirely before the given position. Equal to the index of the last exon if the position is after the last exon.

Parameters

[in] position genome position to test

Returns: index of the last exon before the given position

◆ lastOverlappingExon()

uint32_t isaSpace::ExonGroup::lastOverlappingExon ( const hts_pos_t & position ) const

nodiscardnoexcept

Index of the last exon overlapping a given position.

0-based index of the last exon found at least before after the given position. Equal to the index of the last exon if the position is after the last exon.

Parameters

[in] position genome position to test

Returns: index of the last exon overlapping the given position

◆ nExons()

size_t isaSpace::ExonGroup::nExons ( ) const

inlinenodiscardnoexcept

Number of exons in the gene.

Returns: number of exons

◆ operator=() [1/2]

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

default

Copy assignment operator.

Parameters

[in] toCopy object to copy

Returns: ExonGroup object

◆ operator=() [2/2]

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

defaultnoexcept

Move assignment operator.

Parameters

[in] toMove object to move

Returns: ExonGroup object

◆ strand()

char isaSpace::ExonGroup::strand ( ) const

inlinenodiscardnoexcept

Strand ID.

Returns: strand ID (+ or -)

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

isoseqAlgn.hpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ExonGroup() [1/4]

◆ ExonGroup() [2/4]

◆ ExonGroup() [3/4]

◆ ExonGroup() [4/4]

Member Function Documentation

◆ at()

◆ empty()

◆ firstExonAfter()

◆ firstExonLength()

◆ firstExonSpan()

◆ firstOverlappingExon()

◆ geneName()

◆ geneSpan()

◆ getBestExonCoverageQuality()

◆ getExonCoverageQuality()

◆ getFirstIntronSpan()

◆ lastExonBefore()

◆ lastOverlappingExon()

◆ nExons()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ strand()