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NAME

Sanger::CGP::Vagrent::Data::Substitution - Data object representing a substitution

DESCRIPTION

This is a data class describing a substitution variant plotted to a genome.

It inherits from Sanger::CGP::Vagrent::Data::AbstractGenomicPosition and Sanger::CGP::Vagrent::Data::AbstractVariation

METHODS

Constructor

new

Usage :
 my $cplx = Sanger::CGP::Vagrent::Data::Substitution->new(%params);
Function :

Builds a new Sanger::CGP::Vagrent::Data::Substitution object

Returns :

Sanger::CGP::Vagrent::Data::Substitution object initialized with parameter values

Params :

Same as the constructor from Sanger::CGP::Vagrent::Data::AbstractGenomicPosition plus

 wt => the wildtype sequence
 mt => the mutant/variant sequence

Attributes

getWt

Usage :
 my $seq = $sub->getWt;
Function :

Returns the wildtype sequence string

Returns :

String - DNA sequence

getMt

Usage :
 my $seq = $sub->getMt;
Function :

Returns the mutated/variant sequence string

Returns :

String - DNA sequence

Functions

toString

Usage :
 print $variant->toString;
Function :

Returns a simple string representation of the variant in hgvs genomic syntax

Returns :

String

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