vg::SnarlCaller Class Reference

#include <snarl_caller.hpp>

Inheritance diagram for vg::SnarlCaller:

Classes
struct	CallInfo

Public Member Functions
virtual	~SnarlCaller ()
virtual pair< vector< int >, unique_ptr< CallInfo > >	genotype (const Snarl &snarl, const vector< SnarlTraversal > &traversals, int ref_trav_idx, int ploidy, const string &ref_path_name, pair< size_t, size_t > ref_range)=0
virtual void	update_vcf_info (const Snarl &snarl, const vector< SnarlTraversal > &traversals, const vector< int > &genotype, const unique_ptr< CallInfo > &call_info, const string &sample_name, vcflib::Variant &variant)=0
	Update INFO and FORMAT fields of the called variant. More...
virtual void	update_vcf_header (string &header) const =0
	Define any header fields needed by the above. More...
virtual function< bool(const SnarlTraversal &, int iteration)>	get_skip_allele_fn () const
	Optional method used for pruning searches. More...

Detailed Description

SnarlCaller: Given a list of traversals through a site, come up with a genotype come up with a genotype

Constructor & Destructor Documentation

~SnarlCaller()

vg::SnarlCaller::~SnarlCaller ( )

virtual

Member Function Documentation

genotype()

virtual pair<vector<int>, unique_ptr<CallInfo> > vg::SnarlCaller::genotype ( const Snarl &  snarl, const vector< SnarlTraversal > &  traversals, int  ref_trav_idx, int  ploidy, const string &  ref_path_name, pair< size_t, size_t >  ref_range  )

pure virtual

Get the genotype of a site snarl : site traversals : all traversals to consider ref_trav_idx : index of reference path traversal in traversals (in case it needs special treatment) ref_path : the reference path associated with the snarl ref_range : the interval along the reference path (forward coordinates) spanned by snarl

Implemented in vg::PoissonSupportSnarlCaller, and vg::RatioSupportSnarlCaller.

get_skip_allele_fn()

function< bool(const SnarlTraversal &, int)> vg::SnarlCaller::get_skip_allele_fn ( ) const

virtual

Optional method used for pruning searches.

Reimplemented in vg::SupportBasedSnarlCaller.

update_vcf_header()

virtual void vg::SnarlCaller::update_vcf_header ( string &  header ) const

pure virtual

Define any header fields needed by the above.

Implemented in vg::PoissonSupportSnarlCaller, and vg::RatioSupportSnarlCaller.

update_vcf_info()

virtual void vg::SnarlCaller::update_vcf_info ( const Snarl &  snarl, const vector< SnarlTraversal > &  traversals, const vector< int > &  genotype, const unique_ptr< CallInfo > &  call_info, const string &  sample_name, vcflib::Variant &  variant  )

pure virtual

Update INFO and FORMAT fields of the called variant.

Implemented in vg::PoissonSupportSnarlCaller, vg::RatioSupportSnarlCaller, and vg::SupportBasedSnarlCaller.

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

• src/snarl_caller.hpp
• src/snarl_caller.cpp