#include <mcmc_caller.hpp>

Inheritance diagram for vg::MCMCCaller:

Public Member Functions
	MCMCCaller (const PathPositionHandleGraph *path_position_handle_graph, PhasedGenome &genome, SnarlManager &snarl_manager, const string &sample_name, const vector< string > &ref_paths, const vector< size_t > &ref_path_offsets, const vector< size_t > &ref_path_lengths, ostream &out_stream=cout)

virtual	~MCMCCaller ()

void	call_top_level_snarls (bool recurse_on_fail=true)

virtual string	vcf_header (const PathPositionHandleGraph &graph, const vector< string > &ref_paths, const vector< size_t > &contig_length_overrides) const
	print vcf header More...

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...

Public Attributes
PhasedGenome &	genome

SnarlManager &	snarl_manager

const string	sample_name = "SAMPLE"

const vector< size_t >	ref_path_offsets = {}

const vector< size_t >	ref_path_lengths = {}

ostream &	out_stream

const SnarlTraversal	trav

Protected Member Functions
void	update_vcf_info (const Snarl &snarl, const vector< SnarlTraversal > &traversals, const vector< int > &genotype, const string &sample_name, vcflib::Variant &variant) const
	Update INFO and FORMAT fields of the called variant. More...

void	emit_variant (const Snarl &snarl, const vector< int > &genotype, SnarlTraversal ref_trav, const string &ref_path_name, const vector< SnarlTraversal > &haplo_travs) const
	print a vcf variant More...

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

bool	is_traversable (const Snarl &snarl)
	check if a site can be handled More...

pair< size_t, bool >	get_ref_position (const Snarl &snarl, const string &ref_path_name) const
	get position of reference path More...

void	flatten_common_allele_ends (vcflib::Variant &variant, bool backward) const
	clean up the alleles to not share common prefixes / suffixes 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 *	path_position_handle_graph
	path position handle graph More...

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

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

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

Constructor & Destructor Documentation

◆ MCMCCaller()

vg::MCMCCaller::MCMCCaller	(	const PathPositionHandleGraph *	path_position_handle_graph,
		PhasedGenome &	genome,
		SnarlManager &	snarl_manager,
		const string &	sample_name,
		const vector< string > &	ref_paths,
		const vector< size_t > &	ref_path_offsets,
		const vector< size_t > &	ref_path_lengths,
		ostream &	out_stream = `cout`
	)

MCMCCaller : Inherits from VCFOutputCaller

keep track of offsets in the reference paths

◆ ~MCMCCaller()

vg::MCMCCaller::~MCMCCaller ( )

virtual

Member Function Documentation

◆ call_snarl()

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

protected

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

◆ call_top_level_snarls()

void vg::MCMCCaller::call_top_level_snarls ( bool recurse_on_fail = true )

Run call_snarl() on every top-level snarl in the manager. For any that return false, try the children, etc. (when recurse_on_fail true) Snarls are processed in parallel

◆ emit_variant()

void vg::MCMCCaller::emit_variant	(	const Snarl &	snarl,
		const vector< int > &	genotype,
		SnarlTraversal	ref_trav,
		const string &	ref_path_name,
		const vector< SnarlTraversal > &	haplo_travs
	)		const

protected

print a vcf variant

◆ flatten_common_allele_ends()

void vg::MCMCCaller::flatten_common_allele_ends	(	vcflib::Variant &	variant,
		bool	backward
	)		const

protected

clean up the alleles to not share common prefixes / suffixes

◆ get_ref_position()

pair< size_t, bool > vg::MCMCCaller::get_ref_position	(	const Snarl &	snarl,
		const string &	ref_path_name
	)		const

protected

get position of reference path

◆ is_traversable()

bool vg::MCMCCaller::is_traversable ( const Snarl & snarl )

protected

check if a site can be handled

◆ update_vcf_info()

void vg::MCMCCaller::update_vcf_info	(	const Snarl &	snarl,
		const vector< SnarlTraversal > &	traversals,
		const vector< int > &	genotype,
		const string &	sample_name,
		vcflib::Variant &	variant
	)		const

protected

Update INFO and FORMAT fields of the called variant.

◆ vcf_header()

string vg::MCMCCaller::vcf_header	(	const PathPositionHandleGraph &	graph,
		const vector< string > &	ref_paths,
		const vector< size_t > &	contig_length_overrides
	)		const

virtual

print vcf header

Member Data Documentation

◆ genome

PhasedGenome& vg::MCMCCaller::genome

◆ out_stream

ostream& vg::MCMCCaller::out_stream

◆ path_position_handle_graph

const PathPositionHandleGraph* vg::MCMCCaller::path_position_handle_graph

protected

path position handle graph

◆ ref_offsets

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

protected

keep track of offsets in the reference paths

◆ ref_path_lengths

const vector<size_t> vg::MCMCCaller::ref_path_lengths = {}

◆ ref_path_offsets

const vector<size_t> vg::MCMCCaller::ref_path_offsets = {}

◆ ref_paths

vector<string> vg::MCMCCaller::ref_paths

protected

keep track of the reference paths

◆ sample_name

const string vg::MCMCCaller::sample_name = "SAMPLE"

◆ snarl_manager

SnarlManager& vg::MCMCCaller::snarl_manager

◆ trav

const SnarlTraversal vg::MCMCCaller::trav

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

src/mcmc_caller.hpp
src/mcmc_caller.cpp

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ MCMCCaller()

◆ ~MCMCCaller()

Member Function Documentation

◆ call_snarl()

◆ call_top_level_snarls()

◆ emit_variant()

◆ flatten_common_allele_ends()

◆ get_ref_position()

◆ is_traversable()

◆ update_vcf_info()

◆ vcf_header()

Member Data Documentation

◆ genome

◆ out_stream

◆ path_position_handle_graph

◆ ref_offsets

◆ ref_path_lengths

◆ ref_path_offsets

◆ ref_paths

◆ sample_name

◆ snarl_manager

◆ trav