vg::GraphCaller Class Reference

#include <graph_caller.hpp>

Inheritance diagram for vg::GraphCaller:

Public Types
enum	RecurseType { RecurseOnFail, RecurseAlways, RecurseNever }

Public Member Functions
	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)
virtual bool	call_snarl (const Snarl &snarl)=0
	Call a given snarl, and print the output to out_stream. More...
void	set_show_progress (bool show_progress)
	toggle progress messages More...

Protected Member Functions
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 Attributes
SnarlCaller &	snarl_caller
	Our Genotyper. More...
SnarlManager &	snarl_manager
	Our snarls. More...
bool	show_progress
	Toggle progress messages. More...

Detailed Description

GraphCaller: Use the snarl decomposition to call snarls in a graph

Member Enumeration Documentation

RecurseType

enum vg::GraphCaller::RecurseType

Enumerator
RecurseOnFail
RecurseAlways
RecurseNever

Constructor & Destructor Documentation

GraphCaller()

vg::GraphCaller::GraphCaller	(	SnarlCaller &	snarl_caller,
		SnarlManager &	snarl_manager
	)

~GraphCaller()

vg::GraphCaller::~GraphCaller ( )

virtual

Member Function Documentation

break_chain()

vector< Chain > vg::GraphCaller::break_chain ( const HandleGraph &  graph, const Chain &  chain, size_t  max_edges, size_t  max_trivial  )

protected

Break up a chain into bits that we want to call using size heuristics.

call_snarl()

virtual bool vg::GraphCaller::call_snarl ( const Snarl &  snarl )

pure virtual

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

Implemented in vg::NestedFlowCaller, vg::FlowCaller, vg::LegacyCaller, and vg::VCFGenotyper.

call_top_level_chains()

void vg::GraphCaller::call_top_level_chains ( const HandleGraph &  graph, size_t  max_edges, size_t  max_trivial, RecurseType  recurise_type = RecurseOnFail  )

virtual

For every chain, cut it up into pieces using max_edges and max_trivial to cap the size of each piece then make a fake snarl for each chain piece and call it. If a fake snarl fails to call, It's child chains will be recursed on (if selected)_

call_top_level_snarls()

void vg::GraphCaller::call_top_level_snarls ( const HandleGraph &  graph, RecurseType  recurse_type = RecurseOnFail  )

virtual

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

set_show_progress()

void vg::GraphCaller::set_show_progress

(

bool

show_progress

)

toggle progress messages

Member Data Documentation

show_progress

bool vg::GraphCaller::show_progress

protected

Toggle progress messages.

snarl_caller

SnarlCaller& vg::GraphCaller::snarl_caller

protected

Our Genotyper.

snarl_manager

SnarlManager& vg::GraphCaller::snarl_manager

protected

Our snarls.

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

• src/graph_caller.hpp
• src/graph_caller.cpp