vg::SupportBasedSnarlCaller Class Reference

#include <snarl_caller.hpp>

Inheritance diagram for vg::SupportBasedSnarlCaller:

Public Member Functions
	SupportBasedSnarlCaller (const PathHandleGraph &graph, SnarlManager &snarl_manager, TraversalSupportFinder &support_finder)
virtual	~SupportBasedSnarlCaller ()
virtual void	update_vcf_info (const Snarl &snarl, const vector< SnarlTraversal > &traversals, const vector< int > &genotype, const unique_ptr< CallInfo > &call_info, const string &sample_name, vcflib::Variant &variant)
	Update INFO and FORMAT fields of the called variant.
void	set_min_supports (double min_mad_for_call, double min_support_for_call, double min_site_support)
	Set some of the parameters.
TraversalSupportFinder &	get_support_finder () const
	Get the traversal support finder.
virtual int	get_min_total_support_for_call () const
	Get the minimum total support for call.
virtual function< bool(const SnarlTraversal &, int iteration)>	get_skip_allele_fn () const
	Use min_alt_path_support threshold as cutoff.
Public Member Functions inherited from vg::SnarlCaller
virtual	~SnarlCaller ()
virtual pair< vector< int >, unique_ptr< CallInfo > >	genotype (const Snarl &snarl, const vector< SnarlTraversal > &traversals, int ref_trav_idx, int ploidy, const string &ref_path_name, pair< size_t, size_t > ref_range)=0
virtual void	update_vcf_header (string &header) const =0
	Define any header fields needed by the above.

Static Protected Member Functions
static int	get_best_support (const vector< Support > &supports, const vector< int > &skips)
	Get the best support out of a list of supports, ignoring skips.
static double	support_val (const Support &support)
	Relic from old code.

Protected Attributes
const PathHandleGraph &	graph
SnarlManager &	snarl_manager
TraversalSupportFinder &	support_finder
	Get support from traversals.
int	min_total_support_for_call = 2
size_t	min_mad_for_filter = 1
size_t	min_site_depth = 4
double	min_alt_path_support = 0.5

Detailed Description

Interface for a caller that relies on a TraversalSupportFinder and has a few very basic support-based cutoffs Not every exciting but is currently required for the LegacySupportCaller which needs this to interface with the RepresentativeTraversalFinder

Constructor & Destructor Documentation

SupportBasedSnarlCaller()

vg::SupportBasedSnarlCaller::SupportBasedSnarlCaller	(	const PathHandleGraph &	graph,
		SnarlManager &	snarl_manager,
		TraversalSupportFinder &	support_finder )

~SupportBasedSnarlCaller()

vg::SupportBasedSnarlCaller::~SupportBasedSnarlCaller ( )

virtual

Member Function Documentation

get_best_support()

int vg::SupportBasedSnarlCaller::get_best_support ( const vector< Support > & supports, const vector< int > & skips )

staticprotected

Get the best support out of a list of supports, ignoring skips.

get_min_total_support_for_call()

int vg::SupportBasedSnarlCaller::get_min_total_support_for_call ( ) const

virtual

Get the minimum total support for call.

get_skip_allele_fn()

function< bool(const SnarlTraversal &, int)> vg::SupportBasedSnarlCaller::get_skip_allele_fn ( ) const

virtual

Use min_alt_path_support threshold as cutoff.

Reimplemented from vg::SnarlCaller.

get_support_finder()

TraversalSupportFinder & vg::SupportBasedSnarlCaller::get_support_finder

(

)

const

Get the traversal support finder.

set_min_supports()

void vg::SupportBasedSnarlCaller::set_min_supports	(	double	min_mad_for_call,
		double	min_support_for_call,
		double	min_site_support )

Set some of the parameters.

support_val()

double vg::SupportBasedSnarlCaller::support_val ( const Support & support )

inlinestaticprotected

Relic from old code.

update_vcf_info()

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

virtual

Update INFO and FORMAT fields of the called variant.

Implements vg::SnarlCaller.

Reimplemented in vg::PoissonSupportSnarlCaller, and vg::RatioSupportSnarlCaller.

Member Data Documentation

graph

const PathHandleGraph& vg::SupportBasedSnarlCaller::graph

protected

min_alt_path_support

double vg::SupportBasedSnarlCaller::min_alt_path_support = 0.5

protected

used only for pruning alleles in the VCFTraversalFinder: minimum support of an allele's alt-path for it to be considered in the brute-force enumeration

min_mad_for_filter

size_t vg::SupportBasedSnarlCaller::min_mad_for_filter = 1

protected

what's the minimum ref or alt allele depth to give a PASS in the filter column? Also used as a min actual support for a second-best allele call

min_site_depth

size_t vg::SupportBasedSnarlCaller::min_site_depth = 4

protected

what's the minimum total support (over all alleles) of the site to make a call

min_total_support_for_call

int vg::SupportBasedSnarlCaller::min_total_support_for_call = 2

protected

What's the minimum integer number of reads that must support a call? We don't necessarily want to call a SNP as het because we have a single

snarl_manager

SnarlManager& vg::SupportBasedSnarlCaller::snarl_manager

protected

support_finder

TraversalSupportFinder& vg::SupportBasedSnarlCaller::support_finder

protected

Get support from traversals.

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

• src/snarl_caller.hpp
• src/snarl_caller.cpp