#include <graph_caller.hpp>

Inheritance diagram for vg::NestedFlowCaller:

Classes
struct	CallRecord
	stuff we remember for each snarl call, to be used when genotyping its parent More...

Public Member Functions
	NestedFlowCaller (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, const vector< int > &ref_path_ploidies, AlignmentEmitter *aln_emitter, bool traversals_only, bool gaf_output, size_t trav_padding, bool genotype_snarls)

virtual	~NestedFlowCaller ()

virtual bool	call_snarl (const Snarl &snarl)
	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, 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 More...

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. 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...

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 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 More...

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 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 Types
typedef map< Snarl, CallRecord, NestedCachedPackedTraversalSupportFinder::snarl_less >	CallTable

Protected Member Functions
bool	call_snarl_recursive (const Snarl &managed_snarl, int ploidy, const string &parent_ref_path_name, pair< size_t, size_t > parent_ref_path_interval, CallTable &call_table)
	update the table of calls for each child snarl (and the input snarl) More...

bool	emit_snarl_recursive (const Snarl &managed_snarl, int ploidy, CallTable &call_table)

string	flatten_reference_allele (const string &nested_allele, const CallTable &call_table) const

string	flatten_alt_allele (const string &nested_allele, int allele, int ploidy, const CallTable &call_table) const

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	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
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...

map< string, int >	ref_ploidies
	keep traco of the ploidies (todo: just one map for all path stuff!!) More...

size_t	max_snarl_shallow_size = 50000
	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

NestedCachedPackedTraversalSupportFinder &	nested_support_finder
	a hook into the snarl_caller's nested support finder More...

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

SnarlManager &	snarl_manager
	Our snarls. More...

bool	show_progress
	Toggle progress messages. More...

Protected Attributes inherited from vg::VCFOutputCaller
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

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
Public Types inherited from vg::GraphCaller
enum	RecurseType { RecurseOnFail, RecurseAlways, RecurseNever }

Static Protected Attributes inherited from vg::VCFOutputCaller
static const int64_t	max_vcf_line_length = 2000000000

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.

todo: this is a generalization of FlowCaller and should be able to replace it entirely after testing to get rid of duplicated code.

Member Typedef Documentation

◆ CallTable

typedef map<Snarl, CallRecord, NestedCachedPackedTraversalSupportFinder::snarl_less> vg::NestedFlowCaller::CallTable

protected

Constructor & Destructor Documentation

◆ NestedFlowCaller()

vg::NestedFlowCaller::NestedFlowCaller	(	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,
		const vector< int > &	ref_path_ploidies,
		AlignmentEmitter *	aln_emitter,
		bool	traversals_only,
		bool	gaf_output,
		size_t	trav_padding,
		bool	genotype_snarls
	)

◆ ~NestedFlowCaller()

vg::NestedFlowCaller::~NestedFlowCaller ( )

virtual

Member Function Documentation

◆ call_snarl()

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

virtual

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

Implements vg::GraphCaller.

◆ call_snarl_recursive()

bool vg::NestedFlowCaller::call_snarl_recursive	(	const Snarl &	managed_snarl,
		int	ploidy,
		const string &	parent_ref_path_name,
		pair< size_t, size_t >	parent_ref_path_interval,
		CallTable &	call_table
	)

protected

update the table of calls for each child snarl (and the input snarl)

◆ emit_snarl_recursive()

bool vg::NestedFlowCaller::emit_snarl_recursive	(	const Snarl &	managed_snarl,
		int	ploidy,
		CallTable &	call_table
	)

protected

emit the vcf of all reference-spanning snarls The call_table needs to be completely resolved

◆ flatten_alt_allele()

string vg::NestedFlowCaller::flatten_alt_allele	(	const string &	nested_allele,
		int	allele,
		int	ploidy,
		const CallTable &	call_table
	)		const

protected

◆ flatten_reference_allele()

string vg::NestedFlowCaller::flatten_reference_allele	(	const string &	nested_allele,
		const CallTable &	call_table
	)		const

protected

transform the nested allele string from something like AAC<6_10>TTT to a proper string by recursively resolving the nested snarls into alleles

◆ vcf_header()

string vg::NestedFlowCaller::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::NestedFlowCaller::alignment_emitter

protected

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

◆ gaf_output

bool vg::NestedFlowCaller::gaf_output

protected

toggle whether to output vcf or gaf

◆ genotype_snarls

bool vg::NestedFlowCaller::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::NestedFlowCaller::graph

protected

the graph

◆ max_snarl_shallow_size

size_t vg::NestedFlowCaller::max_snarl_shallow_size = 50000

protected

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

◆ nested_support_finder

NestedCachedPackedTraversalSupportFinder& vg::NestedFlowCaller::nested_support_finder

protected

a hook into the snarl_caller's nested support finder

◆ ref_offsets

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

protected

keep track of offsets in the reference paths

◆ ref_path_set

unordered_set<string> vg::NestedFlowCaller::ref_path_set

protected

◆ ref_paths

vector<string> vg::NestedFlowCaller::ref_paths

protected

keep track of the reference paths

◆ ref_ploidies

map<string, int> vg::NestedFlowCaller::ref_ploidies

protected

keep traco of the ploidies (todo: just one map for all path stuff!!)

◆ traversal_finder

TraversalFinder& vg::NestedFlowCaller::traversal_finder

protected

the traversal finder

◆ traversals_only

bool vg::NestedFlowCaller::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

Classes

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ CallTable

Constructor & Destructor Documentation

◆ NestedFlowCaller()

◆ ~NestedFlowCaller()

Member Function Documentation

◆ call_snarl()

◆ call_snarl_recursive()

◆ emit_snarl_recursive()

◆ flatten_alt_allele()

◆ flatten_reference_allele()

◆ vcf_header()

Member Data Documentation

◆ alignment_emitter

◆ gaf_output

◆ genotype_snarls

◆ graph

◆ max_snarl_shallow_size

◆ nested_support_finder

◆ ref_offsets

◆ ref_path_set

◆ ref_paths

◆ ref_ploidies

◆ traversal_finder

◆ traversals_only