#include <vcf_genotyper.hpp>

Inheritance diagram for vg::VCFGenotyper:

Public Member Functions
	VCFGenotyper (const PathHandleGraph &graph, SnarlCaller &snarl_caller, SnarlManager &snarl_manager, vcflib::VariantCallFile &variant_file, const string &sample_name, const vector< string > &ref_paths, const vector< int > &ref_path_ploidies, FastaReference ref_fasta, FastaReference ins_fasta, AlignmentEmitter *aln_emitter, bool traversals_only, bool gaf_output, size_t trav_padding)
virtual	~VCFGenotyper ()
virtual bool	call_snarl (const Snarl &snarl)
	Call a given snarl, and print the output to out_stream.
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).
Public Member Functions inherited from vg::GraphCaller
	GraphCaller (SnarlCaller &snarl_caller, SnarlManager &snarl_manager)
virtual	~GraphCaller ()
virtual void	call_top_level_snarls (const HandleGraph &graph, RecurseType recurse_type=RecurseOnFail)
virtual void	call_top_level_chains (const HandleGraph &graph, size_t max_edges, size_t max_trivial, RecurseType recurise_type=RecurseOnFail)
void	set_show_progress (bool show_progress)
	toggle progress messages
Public Member Functions inherited from vg::VCFOutputCaller
	VCFOutputCaller (const string &sample_name)
virtual	~VCFOutputCaller ()
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.
void	set_translation (const unordered_map< nid_t, pair< string, size_t > > *translation)
	Add a translation map.
void	set_nested (bool nested)
	Assume writing nested snarls is enabled.
void	set_allele_merge (double threshold, int64_t min_len)
unordered_set< string >	get_output_contigs () const
string	prune_header_contigs (const string &header, const unordered_set< string > &keep) const
Public Member Functions inherited from vg::GAFOutputCaller
	GAFOutputCaller (AlignmentEmitter *emitter, const string &sample_name, const vector< string > &ref_paths, size_t trav_padding)
	The emitter object is created and owned by external forces.
virtual	~GAFOutputCaller ()
void	emit_gaf_traversals (const PathHandleGraph &graph, const string &snarl_name, const vector< SnarlTraversal > &travs, int64_t ref_trav_idx, const string &ref_path_name, int64_t ref_path_position, const TraversalSupportFinder *support_finder=nullptr)
	print the GAF traversals
void	emit_gaf_variant (const PathHandleGraph &graph, const string &snarl_name, const vector< SnarlTraversal > &travs, const vector< int > &genotype, int64_t ref_trav_idx, const string &ref_path_name, int64_t ref_path_position, const TraversalSupportFinder *support_finder=nullptr)
	print the GAF genotype
SnarlTraversal	pad_traversal (const PathHandleGraph &graph, const SnarlTraversal &trav) const
	pad a traversal with (first found) reference path, adding up to trav_padding to each side

Protected Member Functions
tuple< string, size_t, size_t >	get_ref_positions (const vector< vcflib::Variant * > &variants) const
	get path positions bounding a set of variants
virtual unordered_map< string, size_t >	scan_contig_lengths () const
	munge out the contig lengths from the VCF header
Protected Member Functions inherited from vg::GraphCaller
vector< Chain >	break_chain (const HandleGraph &graph, const Chain &chain, size_t max_edges, size_t max_trivial)
	Break up a chain into bits that we want to call using size heuristics.
Protected Member Functions inherited from vg::VCFOutputCaller
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
void	add_allele_path_to_info (vcflib::Variant &v, int allele, const SnarlTraversal &trav, bool reversed, bool one_based) const
	legacy version of above
string	trav_string (const HandleGraph &graph, const SnarlTraversal &trav) const
	convert a traversal into an allele string
bool	merge_similar_alleles (const PathPositionHandleGraph &graph, const vector< SnarlTraversal > &site_traversals, vector< int > &site_genotype, const string &sample_name, vcflib::Variant &out_variant) const
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
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
string	print_flipped_snarl (const Snarl &snarl, bool in_brackets=false) const
	The same as above, but print the snarl as if its orientation has been flipped.
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
const PathHandleGraph &	graph
	the graph
vcflib::VariantCallFile &	input_vcf
	input VCF to genotype, must have been loaded etc elsewhere
VCFTraversalFinder	traversal_finder
bool	traversals_only
	toggle whether to genotype or just output the traversals
bool	gaf_output
	toggle whether to output vcf or gaf
unordered_map< string, int >	path_to_ploidy
	the ploidies
Protected Attributes inherited from vg::GraphCaller
SnarlCaller &	snarl_caller
	Our Genotyper.
SnarlManager &	snarl_manager
	Our snarls.
bool	show_progress
	Toggle progress messages.
Protected Attributes inherited from vg::VCFOutputCaller
vcflib::VariantCallFile	output_vcf
	output vcf
string	sample_name
	Sample name.
vector< vector< pair< pair< string, size_t >, string > > >	output_variants
vector< unordered_map< string, SuppressedRef > >	suppressed_ref_info
size_t	max_uncalled_alleles = 5
	print up to this many uncalled alleles when doing ref-genotpes in -a mode
const unordered_map< nid_t, pair< string, size_t > > *	translation
bool	include_nested
double	allele_merge_threshold = 1.0
int64_t	allele_merge_min_len = 0
Protected Attributes inherited from vg::GAFOutputCaller
AlignmentEmitter *	emitter
string	gaf_sample_name
	Sample name.
size_t	trav_padding = 0
unordered_set< string >	ref_paths
	Reference paths are used to pad out traversals. If there are none, then first path found is used.

Additional Inherited Members
Public Types inherited from vg::GraphCaller
enum	RecurseType { RecurseOnFail , RecurseAlways , RecurseNever }
Static Protected Member Functions inherited from vg::VCFOutputCaller
static bool	snarl_traversal_to_handles (const HandleGraph &graph, const SnarlTraversal &trav, Traversal &out_trav)
static int64_t	allele_core_length (const vector< string > &alleles)
static string	nesting_info_headers ()
Static Protected Attributes inherited from vg::VCFOutputCaller
static const int64_t	max_vcf_line_length = 2000000000

Detailed Description

VCFGenotyper : Genotype variants in a given VCF file

Constructor & Destructor Documentation

◆ VCFGenotyper()

vg::VCFGenotyper::VCFGenotyper	(	const PathHandleGraph &	graph,
		SnarlCaller &	snarl_caller,
		SnarlManager &	snarl_manager,
		vcflib::VariantCallFile &	variant_file,
		const string &	sample_name,
		const vector< string > &	ref_paths,
		const vector< int > &	ref_path_ploidies,
		FastaReference *	ref_fasta,
		FastaReference *	ins_fasta,
		AlignmentEmitter *	aln_emitter,
		bool	traversals_only,
		bool	gaf_output,
		size_t	trav_padding )

◆ ~VCFGenotyper()

vg::VCFGenotyper::~VCFGenotyper ( )

virtual

Member Function Documentation

◆ call_snarl()

bool vg::VCFGenotyper::call_snarl ( const Snarl & snarl )

virtual

Call a given snarl, and print the output to out_stream.

Implements vg::GraphCaller.

◆ get_ref_positions()

tuple< string, size_t, size_t > vg::VCFGenotyper::get_ref_positions ( const vector< vcflib::Variant * > & variants ) const

protected

get path positions bounding a set of variants

◆ scan_contig_lengths()

unordered_map< string, size_t > vg::VCFGenotyper::scan_contig_lengths ( ) const

protectedvirtual

munge out the contig lengths from the VCF header

◆ vcf_header()

string vg::VCFGenotyper::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 from vg::VCFOutputCaller.

Member Data Documentation

◆ gaf_output

bool vg::VCFGenotyper::gaf_output

protected

toggle whether to output vcf or gaf

◆ graph

const PathHandleGraph& vg::VCFGenotyper::graph

protected

the graph

◆ input_vcf

vcflib::VariantCallFile& vg::VCFGenotyper::input_vcf

protected

input VCF to genotype, must have been loaded etc elsewhere

◆ path_to_ploidy

unordered_map<string, int> vg::VCFGenotyper::path_to_ploidy

protected

the ploidies

◆ traversal_finder

VCFTraversalFinder vg::VCFGenotyper::traversal_finder

protected

traversal finder uses alt paths to map VCF alleles from input_vcf back to traversals in the snarl

◆ traversals_only

bool vg::VCFGenotyper::traversals_only

protected

toggle whether to genotype or just output the traversals

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

src/vcf_genotyper.hpp
src/vcf_genotyper.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ VCFGenotyper()

◆ ~VCFGenotyper()

Member Function Documentation

◆ call_snarl()

◆ get_ref_positions()

◆ scan_contig_lengths()

◆ vcf_header()

Member Data Documentation

◆ gaf_output

◆ graph

◆ input_vcf

◆ path_to_ploidy

◆ traversal_finder

◆ traversals_only