#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...

bool	add_variant (vcflib::Variant &var) const

void	write_variants (ostream &out_stream, const SnarlManager *snarl_manager=nullptr)

void	vcf_fixup (vcflib::Variant &var) const
	Run vcffixup from vcflib. More...

void	set_translation (const unordered_map< nid_t, pair< string, size_t >> *translation)
	Add a translation map. More...

void	set_nested (bool nested)
	Assume writing nested snarls is enabled. More...

Protected Member Functions
void	add_allele_path_to_info (const HandleGraph *graph, vcflib::Variant &v, int allele, const Traversal &trav, bool reversed, bool one_based) const
	add a traversal to the VCF info field in the format of a GFA W-line or GAF path More...

void	add_allele_path_to_info (vcflib::Variant &v, int allele, const SnarlTraversal &trav, bool reversed, bool one_based) const
	legacy version of above More...

string	trav_string (const HandleGraph &graph, const SnarlTraversal &trav) const
	convert a traversal into an allele string More...

bool	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, int ploidy, function< string(const vector< SnarlTraversal > &, const vector< int > &, int, int, int)> trav_to_string=nullptr)

tuple< int64_t, int64_t, bool, step_handle_t, step_handle_t >	get_ref_interval (const PathPositionHandleGraph &graph, const Snarl &snarl, const string &ref_path_name) const

pair< string, int64_t >	get_ref_position (const PathPositionHandleGraph &graph, const Snarl &snarl, const string &ref_path_name, int64_t ref_path_offset) const
	used for making gaf traversal names More...

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

string	print_snarl (const HandleGraph *grpah, const handle_t &snarl_start, const handle_t &snarl_end, bool in_brackets=false) const

string	print_snarl (const Snarl &snarl, bool in_brackets=false) const
	legacy version of above More...

void	scan_snarl (const string &allele_string, function< void(const string &, Snarl &)> callback) const

void	update_nesting_info_tags (const SnarlManager *snarl_manager)

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

string	sample_name
	Sample name. More...

vector< vector< pair< pair< string, size_t >, string > > >	output_variants

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

const unordered_map< nid_t, pair< string, size_t > > *	translation

bool	include_nested

Static Protected Attributes
static const int64_t	max_vcf_line_length = 2000000000

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_allele_path_to_info() [1/2]

void vg::VCFOutputCaller::add_allele_path_to_info	(	const HandleGraph *	graph,
		vcflib::Variant &	v,
		int	allele,
		const Traversal &	trav,
		bool	reversed,
		bool	one_based
	)		const

protected

add a traversal to the VCF info field in the format of a GFA W-line or GAF path

◆ add_allele_path_to_info() [2/2]

void vg::VCFOutputCaller::add_allele_path_to_info	(	vcflib::Variant &	v,
		int	allele,
		const SnarlTraversal &	trav,
		bool	reversed,
		bool	one_based
	)		const

protected

legacy version of above

◆ add_variant()

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

Add a variant to our buffer Returns false if the variant line length exceeds VCFOutputCaller::max_vcf_line_length

◆ emit_variant()

bool 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,
		int	ploidy,
		function< string(const vector< SnarlTraversal > &, const vector< int > &, int, int, int)>	trav_to_string = `nullptr`
	)

protected

print a vcf variant return value is taken from add_variant (see above)

◆ 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< int64_t, int64_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 first returned value -1 if no traversal found

◆ get_ref_position()

pair< string, int64_t > vg::VCFOutputCaller::get_ref_position	(	const PathPositionHandleGraph &	graph,
		const Snarl &	snarl,
		const string &	ref_path_name,
		int64_t	ref_path_offset
	)		const

protected

used for making gaf traversal names

◆ print_snarl() [1/2]

string vg::VCFOutputCaller::print_snarl	(	const HandleGraph *	grpah,
		const handle_t &	snarl_start,
		const handle_t &	snarl_end,
		bool	in_brackets = `false`
	)		const

protected

print a snarl in a consistent form like >3435<12222 if in_brackets set to true, do (>3435<12222) instead (this is only used for nested caller)

◆ print_snarl() [2/2]

string vg::VCFOutputCaller::print_snarl	(	const Snarl &	snarl,
		bool	in_brackets = `false`
	)		const

protected

legacy version of above

◆ scan_snarl()

void vg::VCFOutputCaller::scan_snarl	(	const string &	allele_string,
		function< void(const string &, Snarl &)>	callback
	)		const

protected

do the opposite of above So a string that looks like AACT(>12<17)TTT would invoke the callback three times with ("AACT", Snarl), ("", Snarl(12,-17)), ("TTT", Snarl(12,-17)) The parameters are to be treated as unions: A sequence fragment if non-empty, otherwise a snarl

◆ set_nested()

void vg::VCFOutputCaller::set_nested ( bool nested )

Assume writing nested snarls is enabled.

◆ set_translation()

void vg::VCFOutputCaller::set_translation ( const unordered_map< nid_t, pair< string, size_t >> * translation )

Add a translation map.

◆ trav_string()

string vg::VCFOutputCaller::trav_string	(	const HandleGraph &	graph,
		const SnarlTraversal &	trav
	)		const

protected

convert a traversal into an allele string

◆ update_nesting_info_tags()

void vg::VCFOutputCaller::update_nesting_info_tags ( const SnarlManager * snarl_manager )

protected

◆ vcf_fixup()

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

Run vcffixup from vcflib.

◆ 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::NestedFlowCaller, vg::FlowCaller, vg::LegacyCaller, and vg::VCFGenotyper.

◆ write_variants()

void vg::VCFOutputCaller::write_variants	(	ostream &	out_stream,
		const SnarlManager *	snarl_manager = `nullptr`
	)

Sort then write variants in the buffer snarl_manager needed if include_nested is true

Member Data Documentation

◆ include_nested

bool vg::VCFOutputCaller::include_nested

protected

◆ 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

◆ max_vcf_line_length

const int64_t vg::VCFOutputCaller::max_vcf_line_length = 2000000000

staticprotected

◆ output_variants

vector<vector<pair<pair<string, size_t>, string> > > vg::VCFOutputCaller::output_variants

mutableprotected

output buffers (1/thread) (for sorting) variants stored as strings (and position key pairs) because vcflib::Variant in-memory struct so huge

◆ output_vcf

vcflib::VariantCallFile vg::VCFOutputCaller::output_vcf

mutableprotected

output vcf

◆ sample_name

string vg::VCFOutputCaller::sample_name

protected

Sample name.

◆ translation

const unordered_map<nid_t, pair<string, size_t> >* vg::VCFOutputCaller::translation

protected

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

src/graph_caller.hpp
src/graph_caller.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ VCFOutputCaller()

◆ ~VCFOutputCaller()

Member Function Documentation

◆ add_allele_path_to_info() [1/2]

◆ add_allele_path_to_info() [2/2]

◆ add_variant()

◆ emit_variant()

◆ flatten_common_allele_ends()

◆ get_ref_interval()

◆ get_ref_position()

◆ print_snarl() [1/2]

◆ print_snarl() [2/2]

◆ scan_snarl()

◆ set_nested()

◆ set_translation()

◆ trav_string()

◆ update_nesting_info_tags()

◆ vcf_fixup()

◆ vcf_header()

◆ write_variants()

Member Data Documentation

◆ include_nested

◆ max_uncalled_alleles

◆ max_vcf_line_length

◆ output_variants

◆ output_vcf

◆ sample_name

◆ translation