#include <graph_caller.hpp>

Inheritance diagram for vg::VCFOutputCaller:

Public Member Functions
	VCFOutputCaller (const string &sample_name)

virtual	~VCFOutputCaller ()

virtual string	vcf_header (const PathHandleGraph &graph, const vector< string > &contigs, const vector< size_t > &contig_length_overrides) const
	Write the vcf header (version and contigs and basic info) More...

void	add_variant (vcflib::Variant &var) const
	Add a variant to our buffer. More...

void	write_variants (ostream &out_stream) const
	Sort then write variants in the buffer. More...

Protected Attributes
vcflib::VariantCallFile	output_vcf
	output vcf More...

string	sample_name
	Sample name. More...

vector< vector< vcflib::Variant > >	output_variants
	output buffers (1/thread) (for sorting) More...

Detailed Description

Helper class that vcf writers can inherit from to for some common code to output sorted VCF

Constructor & Destructor Documentation

◆ VCFOutputCaller()

vg::VCFOutputCaller::VCFOutputCaller ( const string & sample_name )

◆ ~VCFOutputCaller()

vg::VCFOutputCaller::~VCFOutputCaller ( )

virtual

Member Function Documentation

◆ add_variant()

void vg::VCFOutputCaller::add_variant ( vcflib::Variant & var ) const

Add a variant to our buffer.

◆ vcf_header()

string vg::VCFOutputCaller::vcf_header	(	const PathHandleGraph &	graph,
		const vector< string > &	contigs,
		const vector< size_t > &	contig_length_overrides
	)		const

virtual

Write the vcf header (version and contigs and basic info)

Reimplemented in vg::LegacyCaller, and vg::VCFGenotyper.

◆ write_variants()

void vg::VCFOutputCaller::write_variants ( ostream & out_stream ) const

Sort then write variants in the buffer.

Member Data Documentation

◆ output_variants

vector<vector<vcflib::Variant> > vg::VCFOutputCaller::output_variants

mutableprotected

output buffers (1/thread) (for sorting)

◆ output_vcf

vcflib::VariantCallFile vg::VCFOutputCaller::output_vcf

mutableprotected

output vcf

◆ sample_name

string vg::VCFOutputCaller::sample_name

protected

Sample name.

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

src/graph_caller.hpp
src/graph_caller.cpp

Public Member Functions

Protected Attributes