#include <deconstructor.hpp>

Inheritance diagram for vg::Deconstructor:

Classes
struct	NestingInfo

Public Member Functions
	Deconstructor ()

	~Deconstructor ()

void	deconstruct (vector< string > refpaths, const PathPositionHandleGraph graph, SnarlManager snarl_manager, bool include_nested, int context_jaccard_window, bool untangle_traversals, bool keep_conflicted, bool strict_conflicts, bool long_ref_contig, double cluster_threshold=1.0, gbwt::GBWT *gbwt=nullptr, bool nested_decomposition=false, bool star_allele=false)

Public Member Functions inherited from vg::VCFOutputCaller
	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...

Private Member Functions
string	get_vcf_header ()

string	add_contigs_to_vcf_header (const string &vcf_header) const

void	deconstruct_graph (SnarlManager *snarl_manager)

void	deconstruct_graph_top_down (SnarlManager *snarl_manager)

bool	deconstruct_site (const handle_t &snarl_start, const handle_t &snarl_end, const NestingInfo in_nesting_info=nullptr, vector< NestingInfo > out_nesting_infos=nullptr) const

void	get_traversals (const handle_t &snarl_start, const handle_t &snarl_end, vector< Traversal > &out_travs, vector< string > &out_trav_path_names, vector< pair< step_handle_t, step_handle_t >> &out_trav_steps) const

unordered_map< string, vector< int > >	add_star_traversals (vector< Traversal > &travs, vector< string > &trav_names, vector< vector< int >> &trav_clusters, vector< pair< double, int64_t >> &trav_cluster_info, const unordered_map< string, vector< int >> &parent_haplotypes) const

vector< int >	get_alleles (vcflib::Variant &v, const vector< Traversal > &travs, const vector< pair< step_handle_t, step_handle_t >> &trav_steps, int ref_path_idx, const vector< vector< int >> &trav_clusters, char prev_char, bool use_start) const

void	get_genotypes (vcflib::Variant &v, const vector< string > &names, const vector< int > &trav_to_allele, const vector< pair< double, int64_t >> &trav_to_cluster_info) const

pair< vector< int >, bool >	choose_traversals (const string &sample_name, const vector< int > &travs, const vector< int > &trav_to_allele, const vector< string > &trav_to_name, const vector< int > &gbwt_phases) const

vector< nid_t >	get_context (step_handle_t start_step, step_handle_t end_step) const

Private Attributes
const PathPositionHandleGraph *	graph

gbwt::GBWT *	gbwt

unique_ptr< PathTraversalFinder >	path_trav_finder

unique_ptr< GBWTTraversalFinder >	gbwt_trav_finder

unordered_set< string >	gbwt_reference_samples

unordered_map< string, pair< int, int > >	gbwt_sample_to_phase_range

set< string >	ref_paths

vector< unordered_set< path_handle_t > >	off_ref_paths

set< string >	ref_samples

bool	long_ref_contig = false

set< string >	sample_names

const unordered_map< string, pair< string, int > > *	path_to_sample_phase

unordered_map< string, int >	sample_ploidys

int	path_jaccard_window = 10000

bool	untangle_allele_traversals = false

bool	strict_conflict_checking = false

bool	show_path_info = false

bool	keep_conflicted_genotypes = false

double	cluster_threshold = 1.0

bool	nested_decomposition = false

bool	star_allele = false

Additional Inherited Members
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 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

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

Constructor & Destructor Documentation

◆ Deconstructor()

vg::Deconstructor::Deconstructor ( )

◆ ~Deconstructor()

vg::Deconstructor::~Deconstructor ( )

Member Function Documentation

◆ add_contigs_to_vcf_header()

string vg::Deconstructor::add_contigs_to_vcf_header ( const string & vcf_header ) const

private

◆ add_star_traversals()

unordered_map< string, vector< int > > vg::Deconstructor::add_star_traversals	(	vector< Traversal > &	travs,
		vector< string > &	trav_names,
		vector< vector< int >> &	trav_clusters,
		vector< pair< double, int64_t >> &	trav_cluster_info,
		const unordered_map< string, vector< int >> &	parent_haplotypes
	)		const

private

◆ choose_traversals()

pair< vector< int >, bool > vg::Deconstructor::choose_traversals	(	const string &	sample_name,
		const vector< int > &	travs,
		const vector< int > &	trav_to_allele,
		const vector< string > &	trav_to_name,
		const vector< int > &	gbwt_phases
	)		const

private

◆ deconstruct()

void vg::Deconstructor::deconstruct	(	vector< string >	ref_paths,
		const PathPositionHandleGraph *	graph,
		SnarlManager *	snarl_manager,
		bool	include_nested,
		int	context_jaccard_window,
		bool	untangle_traversals,
		bool	keep_conflicted,
		bool	strict_conflicts,
		bool	long_ref_contig,
		double	cluster_threshold = `1.0`,
		gbwt::GBWT *	gbwt = `nullptr`,
		bool	nested_decomposition = `false`,
		bool	star_allele = `false`
	)

Convenience wrapper function for deconstruction of multiple paths.

◆ deconstruct_graph()

void vg::Deconstructor::deconstruct_graph ( SnarlManager * snarl_manager )

private

◆ deconstruct_graph_top_down()

void vg::Deconstructor::deconstruct_graph_top_down ( SnarlManager * snarl_manager )

private

◆ deconstruct_site()

bool vg::Deconstructor::deconstruct_site	(	const handle_t &	snarl_start,
		const handle_t &	snarl_end,
		const NestingInfo *	in_nesting_info = `nullptr`,
		vector< NestingInfo > *	out_nesting_infos = `nullptr`
	)		const

private

◆ get_alleles()

vector< int > vg::Deconstructor::get_alleles	(	vcflib::Variant &	v,
		const vector< Traversal > &	travs,
		const vector< pair< step_handle_t, step_handle_t >> &	trav_steps,
		int	ref_path_idx,
		const vector< vector< int >> &	trav_clusters,
		char	prev_char,
		bool	use_start
	)		const

private

Takes in a vector of snarltraversals, an index of the ref path among them, a vector of flags for traversals to actually use, the character before all the traversals, and a flag for whether the start should be used (???).

Returns a vector where entires are which allele number a traversal in travs ought to become in the VCF. If a traversal is flagged off, it gets a -1.

◆ get_context()

vector< nid_t > vg::Deconstructor::get_context	(	step_handle_t	start_step,
		step_handle_t	end_step
	)		const

private

◆ get_genotypes()

void vg::Deconstructor::get_genotypes	(	vcflib::Variant &	v,
		const vector< string > &	names,
		const vector< int > &	trav_to_allele,
		const vector< pair< double, int64_t >> &	trav_to_cluster_info
	)		const

private

◆ get_traversals()

void vg::Deconstructor::get_traversals	(	const handle_t &	snarl_start,
		const handle_t &	snarl_end,
		vector< Traversal > &	out_travs,
		vector< string > &	out_trav_path_names,
		vector< pair< step_handle_t, step_handle_t >> &	out_trav_steps
	)		const

private

◆ get_vcf_header()

string vg::Deconstructor::get_vcf_header ( )

private

Member Data Documentation

◆ cluster_threshold

double vg::Deconstructor::cluster_threshold = 1.0

private

◆ gbwt

gbwt::GBWT* vg::Deconstructor::gbwt

private

◆ gbwt_reference_samples

unordered_set<string> vg::Deconstructor::gbwt_reference_samples

private

◆ gbwt_sample_to_phase_range

unordered_map<string, pair<int, int> > vg::Deconstructor::gbwt_sample_to_phase_range

private

◆ gbwt_trav_finder

unique_ptr<GBWTTraversalFinder> vg::Deconstructor::gbwt_trav_finder

private

◆ graph

const PathPositionHandleGraph* vg::Deconstructor::graph

private

◆ keep_conflicted_genotypes

bool vg::Deconstructor::keep_conflicted_genotypes = false

private

◆ long_ref_contig

bool vg::Deconstructor::long_ref_contig = false

private

◆ nested_decomposition

bool vg::Deconstructor::nested_decomposition = false

private

◆ off_ref_paths

vector<unordered_set<path_handle_t> > vg::Deconstructor::off_ref_paths

mutableprivate

◆ path_jaccard_window

int vg::Deconstructor::path_jaccard_window = 10000

private

◆ path_to_sample_phase

const unordered_map<string, pair<string, int> >* vg::Deconstructor::path_to_sample_phase

private

◆ path_trav_finder

unique_ptr<PathTraversalFinder> vg::Deconstructor::path_trav_finder

private

◆ ref_paths

set<string> vg::Deconstructor::ref_paths

private

◆ ref_samples

set<string> vg::Deconstructor::ref_samples

private

◆ sample_names

set<string> vg::Deconstructor::sample_names

private

◆ sample_ploidys

unordered_map<string, int> vg::Deconstructor::sample_ploidys

private

◆ show_path_info

bool vg::Deconstructor::show_path_info = false

private

◆ star_allele

bool vg::Deconstructor::star_allele = false

private

◆ strict_conflict_checking

bool vg::Deconstructor::strict_conflict_checking = false

private

◆ untangle_allele_traversals

bool vg::Deconstructor::untangle_allele_traversals = false

private

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

src/deconstructor.hpp
src/deconstructor.cpp

Classes

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ Deconstructor()

◆ ~Deconstructor()

Member Function Documentation

◆ add_contigs_to_vcf_header()

◆ add_star_traversals()

◆ choose_traversals()

◆ deconstruct()

◆ deconstruct_graph()

◆ deconstruct_graph_top_down()

◆ deconstruct_site()

◆ get_alleles()

◆ get_context()

◆ get_genotypes()

◆ get_traversals()

◆ get_vcf_header()

Member Data Documentation

◆ cluster_threshold

◆ gbwt

◆ gbwt_reference_samples

◆ gbwt_sample_to_phase_range

◆ gbwt_trav_finder

◆ graph

◆ keep_conflicted_genotypes

◆ long_ref_contig

◆ nested_decomposition

◆ off_ref_paths

◆ path_jaccard_window

◆ path_to_sample_phase

◆ path_trav_finder

◆ ref_paths

◆ ref_samples

◆ sample_names

◆ sample_ploidys

◆ show_path_info

◆ star_allele

◆ strict_conflict_checking

◆ untangle_allele_traversals