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

#include <graph_caller.hpp>

Inheritance diagram for vg::GAFOutputCaller:
vg::FlowCaller vg::VCFGenotyper

Public Member Functions

 GAFOutputCaller (AlignmentEmitter *emitter, const string &sample_name, const vector< string > &ref_paths, size_t trav_padding)
 The emitter object is created and owned by external forces. More...
 
virtual ~GAFOutputCaller ()
 
void emit_gaf_traversals (const PathHandleGraph &graph, const vector< SnarlTraversal > &travs)
 print the GAF traversals More...
 
void emit_gaf_variant (const HandleGraph &graph, const Snarl &snarl, const vector< SnarlTraversal > &traversals, const vector< int > &genotype)
 print the GAF genotype More...
 
SnarlTraversal pad_traversal (const PathHandleGraph &graph, const SnarlTraversal &trav) const
 pad a traversal with (first found) reference path, adding up to trav_padding to each side More...
 

Protected Attributes

AlignmentEmitteremitter
 
string gaf_sample_name
 Sample name. More...
 
size_t trav_padding = 0
 
unordered_set< string > ref_paths
 Reference paths are used to pad out traversals. If there are none, then first path found is used. More...
 

Detailed Description

Helper class for outputing snarl traversals as GAF

Constructor & Destructor Documentation

◆ GAFOutputCaller()

vg::GAFOutputCaller::GAFOutputCaller ( AlignmentEmitter emitter,
const string &  sample_name,
const vector< string > &  ref_paths,
size_t  trav_padding 
)

The emitter object is created and owned by external forces.

◆ ~GAFOutputCaller()

vg::GAFOutputCaller::~GAFOutputCaller ( )
virtual

Member Function Documentation

◆ emit_gaf_traversals()

void vg::GAFOutputCaller::emit_gaf_traversals ( const PathHandleGraph graph,
const vector< SnarlTraversal > &  travs 
)

print the GAF traversals

◆ emit_gaf_variant()

void vg::GAFOutputCaller::emit_gaf_variant ( const HandleGraph graph,
const Snarl snarl,
const vector< SnarlTraversal > &  traversals,
const vector< int > &  genotype 
)

print the GAF genotype

◆ pad_traversal()

SnarlTraversal vg::GAFOutputCaller::pad_traversal ( const PathHandleGraph graph,
const SnarlTraversal trav 
) const

pad a traversal with (first found) reference path, adding up to trav_padding to each side

Member Data Documentation

◆ emitter

AlignmentEmitter* vg::GAFOutputCaller::emitter
protected

◆ gaf_sample_name

string vg::GAFOutputCaller::gaf_sample_name
protected

Sample name.

◆ ref_paths

unordered_set<string> vg::GAFOutputCaller::ref_paths
protected

Reference paths are used to pad out traversals. If there are none, then first path found is used.

◆ trav_padding

size_t vg::GAFOutputCaller::trav_padding = 0
protected

Add padding from reference paths to traversals to make them at least this long (only in emit_gaf_traversals(), not emit_gaf_variant)


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