vg::VCFOutputCaller Class Reference

#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 Member Functions
void	emit_variant (const PathPositionHandleGraph &graph, SnarlCaller &snarl_caller, const Snarl &snarl, const vector< SnarlTraversal > &called_traversals, const vector< int > &genotype, int ref_trav_idx, const unique_ptr< SnarlCaller::CallInfo > &call_info, const string &ref_path_name, int ref_offset, bool genotype_snarls) const
	print a vcf variant More...
tuple< size_t, size_t, bool, step_handle_t, step_handle_t >	get_ref_interval (const PathPositionHandleGraph &graph, const Snarl &snarl, const string &ref_path_name) const
void	flatten_common_allele_ends (vcflib::Variant &variant, bool backward, size_t len_override) const

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...
size_t	max_uncalled_alleles = 5
	print up to this many uncalled alleles when doing ref-genotpes in -a mode 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.

emit_variant()

void vg::VCFOutputCaller::emit_variant ( const PathPositionHandleGraph &  graph, SnarlCaller &  snarl_caller, const Snarl &  snarl, const vector< SnarlTraversal > &  called_traversals, const vector< int > &  genotype, int  ref_trav_idx, const unique_ptr< SnarlCaller::CallInfo > &  call_info, const string &  ref_path_name, int  ref_offset, bool  genotype_snarls  ) const

protected

print a vcf variant

flatten_common_allele_ends()

void vg::VCFOutputCaller::flatten_common_allele_ends ( vcflib::Variant &  variant, bool  backward, size_t  len_override  ) const

protected

clean up the alleles to not share common prefixes / suffixes if len_override given, just do that many bases without thinking

get_ref_interval()

tuple< size_t, size_t, bool, step_handle_t, step_handle_t > vg::VCFOutputCaller::get_ref_interval ( const PathPositionHandleGraph &  graph, const Snarl &  snarl, const string &  ref_path_name  ) const

protected

get the interval of a snarl from our reference path using the PathPositionHandleGraph interface the bool is true if the snarl's backward on the path

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::FlowCaller, 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

max_uncalled_alleles

size_t vg::VCFOutputCaller::max_uncalled_alleles = 5

protected

print up to this many uncalled alleles when doing ref-genotpes in -a mode

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.

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

• src/graph_caller.hpp
• src/graph_caller.cpp