cgatools::variants::Allele Class Reference

A class that corresponds to a single allele within a locus in a Complete Genomics variant file. More...

#include <Allele.hpp>

List of all members.

Public Member Functions
	Allele ()
	Construct the Allele.
	Allele (const Locus *locus)
	Construct the Allele.
const std::vector< size_t > &	getCallOffsets () const
	Returns the offsets of the calls for this Allele within locus_->getCalls().
const Call &	getCall (size_t index) const
std::string	getAlleleSequence () const
	Returns the sequence of this Allele of this Locus, replacing "=" with the corresponding reference sequence.
std::string	getRefSequence () const
	Returns the reference sequence corresponding to this Locus, replacing "=" with the corresponding reference sequence.
const std::string &	getHapLink () const
	Returns the first hapLink specified for this Allele, in call order.
std::string	getXRef () const
	Returns the union of xRef annotations for all Calls in this Allele, joined by ";".
std::string	getAlleleFreqs () const
	Returns the union of allele frequencies for all Calls in this Allele, joined by ";".
int32_t	getMinVarScoreVAF () const
	Returns the minimum varScoreVAF of all calls in this Allele.
int32_t	getMinVarScoreEAF () const
	Returns the minimum varScoreEAF of all calls in this Allele.
std::vector< std::string >	getCombinedVarFilter () const
	Returns the union of all varFilters for all calls in this Allele.
std::vector < Call::AlternativeCall >	getAlternativeCalls () const
bool	hasNoCalls () const
	Returns true iff this Allele has one or more calls whose sequence contains N or ? characters.
void	clearCalls ()
	Clears out the set of calls associated with this Allele.
void	addCallOffset (size_t offset)
	Associates a call in locus_->getCalls() with this Allele.
void	setLocus (const Locus *locus)
	Sets the locus for this Allele.

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Detailed Description

A class that corresponds to a single allele within a locus in a Complete Genomics variant file.

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Constructor & Destructor Documentation

cgatools::variants::Allele::Allele

(

)

[inline]

Construct the Allele.

The Allele cannot be used until its locus is set and its call offsets are set.

cgatools::variants::Allele::Allele

(

const Locus *

locus

)

[inline]

Construct the Allele.

The Allele cannot be used until its call offsets are set.

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Member Function Documentation

std::string cgatools::variants::Allele::getAlleleFreqs

(

)

const

Returns the union of allele frequencies for all Calls in this Allele, joined by ";".

std::string cgatools::variants::Allele::getAlleleSequence

(

)

const

Returns the sequence of this Allele of this Locus, replacing "=" with the corresponding reference sequence.

const std::vector<size_t>& cgatools::variants::Allele::getCallOffsets

(

)

const [inline]

Returns the offsets of the calls for this Allele within locus_->getCalls().

std::vector<std::string> cgatools::variants::Allele::getCombinedVarFilter

(

)

const

Returns the union of all varFilters for all calls in this Allele.

If filters are given, PASS is excluded.

const std::string& cgatools::variants::Allele::getHapLink

(

)

const

Returns the first hapLink specified for this Allele, in call order.

std::string cgatools::variants::Allele::getRefSequence

(

)

const

Returns the reference sequence corresponding to this Locus, replacing "=" with the corresponding reference sequence.

std::string cgatools::variants::Allele::getXRef

(

)

const

Returns the union of xRef annotations for all Calls in this Allele, joined by ";".

bool cgatools::variants::Allele::hasNoCalls

(

)

const

Returns true iff this Allele has one or more calls whose sequence contains N or ? characters.

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

• Allele.hpp