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().
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.
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::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().

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.

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