vg
tools for working with variation graphs
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vg::GAFOutputCaller Class Reference

#include <graph_caller.hpp>

Inheritance diagram for vg::GAFOutputCaller:
vg::FlowCaller vg::NestedFlowCaller 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.
 
virtual ~GAFOutputCaller ()
 
void emit_gaf_traversals (const PathHandleGraph &graph, const string &snarl_name, const vector< SnarlTraversal > &travs, int64_t ref_trav_idx, const string &ref_path_name, int64_t ref_path_position, const TraversalSupportFinder *support_finder=nullptr)
 print the GAF traversals
 
void emit_gaf_variant (const PathHandleGraph &graph, const string &snarl_name, const vector< SnarlTraversal > &travs, const vector< int > &genotype, int64_t ref_trav_idx, const string &ref_path_name, int64_t ref_path_position, const TraversalSupportFinder *support_finder=nullptr)
 print the GAF genotype
 
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
 

Protected Attributes

AlignmentEmitteremitter
 
string gaf_sample_name
 Sample name.
 
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.
 

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 string & snarl_name,
const vector< SnarlTraversal > & travs,
int64_t ref_trav_idx,
const string & ref_path_name,
int64_t ref_path_position,
const TraversalSupportFinder * support_finder = nullptr )

print the GAF traversals

◆ emit_gaf_variant()

void vg::GAFOutputCaller::emit_gaf_variant ( const PathHandleGraph & graph,
const string & snarl_name,
const vector< SnarlTraversal > & travs,
const vector< int > & genotype,
int64_t ref_trav_idx,
const string & ref_path_name,
int64_t ref_path_position,
const TraversalSupportFinder * support_finder = nullptr )

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: