vg::PathChunker Class Reference

#include <chunker.hpp>

Public Member Functions
	PathChunker (const PathPositionHandleGraph *graph=NULL)
	~PathChunker ()
void	extract_subgraph (const Region &region, int64_t context, int64_t length, bool forward_only, MutablePathMutableHandleGraph &subgraph, Region &out_region)
void	extract_path_component (const string &path_name, MutablePathMutableHandleGraph &subgraph, Region &out_region)
void	extract_component (const unordered_set< nid_t > &node_ids, MutablePathMutableHandleGraph &subgraph, bool subpath_naming)
void	extract_id_range (vg::id_t start, vg::id_t end, int64_t context, int64_t length, bool forward_only, MutablePathMutableHandleGraph &subgraph, Region &out_region)
set< pair< pair< id_t, bool >, pair< id_t, bool > > >	get_path_edge_index (step_handle_t start_step, step_handle_t end_step, int64_t context) const

Public Attributes
const PathPositionHandleGraph *	graph

Detailed Description

Chunk up a graph along a path, using a given number of context expansion steps to fill out the chunks. Most of the work done by exising xg functions.

Constructor & Destructor Documentation

PathChunker()

vg::PathChunker::PathChunker

(

const PathPositionHandleGraph *

graph = NULL

)

~PathChunker()

vg::PathChunker::~PathChunker

(

)

Member Function Documentation

extract_component()

void vg::PathChunker::extract_component	(	const unordered_set< nid_t > &	node_ids,
		MutablePathMutableHandleGraph &	subgraph,
		bool	subpath_naming
	)

Extract a connected component starting from an id set

extract_id_range()

void vg::PathChunker::extract_id_range	(	vg::id_t	start,
		vg::id_t	end,
		int64_t	context,
		int64_t	length,
		bool	forward_only,
		MutablePathMutableHandleGraph &	subgraph,
		Region &	out_region
	)

Like above, but use (inclusive) id range instead of region on path.

extract_path_component()

void vg::PathChunker::extract_path_component	(	const string &	path_name,
		MutablePathMutableHandleGraph &	subgraph,
		Region &	out_region
	)

Extract a connected component containing a given path

extract_subgraph()

void vg::PathChunker::extract_subgraph	(	const Region &	region,
		int64_t	context,
		int64_t	length,
		bool	forward_only,
		MutablePathMutableHandleGraph &	subgraph,
		Region &	out_region
	)

Extract subgraph corresponding to given path region into its own vg graph, and send it to out_stream. The boundaries of the extracted graph (which can be different because we expand context and don't cut nodes) are written to out_region. If forward_only set, context is only expanded in the forward direction

NOTE: we follow convention of Region coordinates being 0-based inclusive.

get_path_edge_index()

set< pair< pair< id_t, bool >, pair< id_t, bool > > > vg::PathChunker::get_path_edge_index	(	step_handle_t	start_step,
		step_handle_t	end_step,
		int64_t	context
	)		const

Get a set of all edges in the graph along a path region (to check for discontinuities later on)

Member Data Documentation

graph

const PathPositionHandleGraph* vg::PathChunker::graph

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

• src/chunker.hpp
• src/chunker.cpp