#include <graph_caller.hpp>

Inheritance diagram for vg::FlowCaller:

Public Member Functions
	FlowCaller (const PathPositionHandleGraph &graph, SupportBasedSnarlCaller &snarl_caller, SnarlManager &snarl_manager, const string &sample_name, TraversalFinder &traversal_finder, const vector< string > &ref_paths, const vector< size_t > &ref_path_offsets, AlignmentEmitter *aln_emitter, bool traversals_only, bool gaf_output, size_t trav_padding, bool genotype_snarls)

virtual	~FlowCaller ()

virtual bool	call_snarl (const Snarl &snarl, int ploidy)
	Call a given snarl, and print the output to out_stream. More...

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...

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, int ploidy, bool recurse_on_fail=true)

virtual void	call_top_level_chains (const HandleGraph &graph, int ploidy, size_t max_edges, size_t max_trivial, bool recurse_on_fail=true)

Public Member Functions inherited from vg::VCFOutputCaller
	VCFOutputCaller (const string &sample_name)

virtual	~VCFOutputCaller ()

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...

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. More...

virtual	~GAFOutputCaller ()

void	emit_gaf_traversals (const PathHandleGraph &graph, const vector< SnarlTraversal > &travs)
	print the GAF traversals More...

void	emit_gaf_variant (const HandleGraph &graph, const Snarl &snarl, const vector< SnarlTraversal > &traversals, const vector< int > &genotype)
	print the GAF genotype More...

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 More...

Protected Attributes
const PathPositionHandleGraph &	graph
	the graph More...

TraversalFinder &	traversal_finder
	the traversal finder More...

vector< string >	ref_paths
	keep track of the reference paths More...

unordered_set< string >	ref_path_set

map< string, size_t >	ref_offsets
	keep track of offsets in the reference paths More...

size_t	max_snarl_edges = 500000
	until we support nested snarls, cap snarl size we attempt to process More...

AlignmentEmitter *	alignment_emitter

bool	traversals_only
	toggle whether to genotype or just output the traversals More...

bool	gaf_output
	toggle whether to output vcf or gaf More...

bool	genotype_snarls

Protected Attributes inherited from vg::GraphCaller
SnarlCaller &	snarl_caller
	Our Genotyper. More...

SnarlManager &	snarl_manager
	Our snarls. More...

Protected Attributes inherited from vg::VCFOutputCaller
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...

Protected Attributes inherited from vg::GAFOutputCaller
AlignmentEmitter *	emitter

string	gaf_sample_name
	Sample name. More...

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. More...

Additional Inherited Members
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. More...

Protected Member Functions inherited from vg::VCFOutputCaller
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

Detailed Description

FlowCaller : Uses any traversals finder (ex, FlowTraversalFinder) to find traversals, and calls those based on how much support they have.
Should work on any graph but will not report cyclic traversals. Does not (yet, anyway) support nested calling, so the entire site is processes in one shot. Designed to replace LegacyCaller, as it should miss fewer obviously good traversals, and is not dependent on old protobuf-based structures.

Constructor & Destructor Documentation

◆ FlowCaller()

vg::FlowCaller::FlowCaller	(	const PathPositionHandleGraph &	graph,
		SupportBasedSnarlCaller &	snarl_caller,
		SnarlManager &	snarl_manager,
		const string &	sample_name,
		TraversalFinder &	traversal_finder,
		const vector< string > &	ref_paths,
		const vector< size_t > &	ref_path_offsets,
		AlignmentEmitter *	aln_emitter,
		bool	traversals_only,
		bool	gaf_output,
		size_t	trav_padding,
		bool	genotype_snarls
	)

◆ ~FlowCaller()

vg::FlowCaller::~FlowCaller ( )

virtual

Member Function Documentation

◆ call_snarl()

bool vg::FlowCaller::call_snarl	(	const Snarl &	snarl,
		int	ploidy
	)

virtual

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

Implements vg::GraphCaller.

◆ vcf_header()

string vg::FlowCaller::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

◆ alignment_emitter

AlignmentEmitter* vg::FlowCaller::alignment_emitter

protected

alignment emitter. if not null, traversals will be output here and no genotyping will be done

◆ gaf_output

bool vg::FlowCaller::gaf_output

protected

toggle whether to output vcf or gaf

◆ genotype_snarls

bool vg::FlowCaller::genotype_snarls

protected

toggle whether to genotype every snarl (by default, uncalled snarls are skipped, and coordinates are flattened out to minimize variant size – this turns all that off)

◆ graph

const PathPositionHandleGraph& vg::FlowCaller::graph

protected

the graph

◆ max_snarl_edges

size_t vg::FlowCaller::max_snarl_edges = 500000

protected

until we support nested snarls, cap snarl size we attempt to process

◆ ref_offsets

map<string, size_t> vg::FlowCaller::ref_offsets

protected

keep track of offsets in the reference paths

◆ ref_path_set

unordered_set<string> vg::FlowCaller::ref_path_set

protected

◆ ref_paths

vector<string> vg::FlowCaller::ref_paths

protected

keep track of the reference paths

◆ traversal_finder

TraversalFinder& vg::FlowCaller::traversal_finder

protected

the traversal finder

◆ traversals_only

bool vg::FlowCaller::traversals_only

protected

toggle whether to genotype or just output the traversals

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

src/graph_caller.hpp
src/graph_caller.cpp

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FlowCaller()

◆ ~FlowCaller()

Member Function Documentation

◆ call_snarl()

◆ vcf_header()

Member Data Documentation

◆ alignment_emitter

◆ gaf_output

◆ genotype_snarls

◆ graph

◆ max_snarl_edges

◆ ref_offsets

◆ ref_path_set

◆ ref_paths

◆ traversal_finder

◆ traversals_only