vg
tools for working with variation graphs
Public Member Functions | Protected Attributes | List of all members
vg::GraphCaller Class Referenceabstract

#include <graph_caller.hpp>

Inheritance diagram for vg::GraphCaller:
vg::LegacyCaller vg::VCFGenotyper

Public Member Functions

 GraphCaller (SnarlCaller &snarl_caller, SnarlManager &snarl_manager, ostream &out_stream=cout)
 
virtual ~GraphCaller ()
 
virtual void call_top_level_snarls (bool recurse_on_fail=true)
 
virtual bool call_snarl (const Snarl &snarl)=0
 Call a given snarl, and print the output to out_stream. More...
 

Protected Attributes

SnarlCallersnarl_caller
 Our Genotyper. More...
 
SnarlManagersnarl_manager
 Our snarls. More...
 
ostream & out_stream
 Where all output written. More...
 

Detailed Description

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

Constructor & Destructor Documentation

◆ GraphCaller()

vg::GraphCaller::GraphCaller ( SnarlCaller snarl_caller,
SnarlManager snarl_manager,
ostream &  out_stream = cout 
)

◆ ~GraphCaller()

vg::GraphCaller::~GraphCaller ( )
virtual

Member Function Documentation

◆ 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::LegacyCaller, and vg::VCFGenotyper.

◆ call_top_level_snarls()

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

Member Data Documentation

◆ out_stream

ostream& vg::GraphCaller::out_stream
protected

Where all output written.

◆ snarl_caller

SnarlCaller& vg::GraphCaller::snarl_caller
protected

Our Genotyper.

◆ snarl_manager

SnarlManager& vg::GraphCaller::snarl_manager
protected

Our snarls.


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