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_snarls (const Region &region, SnarlManager &snarl_manager, MutablePathMutableHandleGraph &subgraph)
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)
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
	)

Extract a connected component starting from an id set. Processes path metadata and creates subpaths.

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. Processes path metadata and creates subpaths.

extract_snarls()

void vg::PathChunker::extract_snarls	(	const Region &	region,
		SnarlManager &	snarl_manager,
		MutablePathMutableHandleGraph &	subgraph
	)

Extract the region along the given path, and any snarls fully contained in it. This will often give more intuitive results than messing with context steps, which can run way outside the region of interest

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 region of the target path (which can be different because we expand context and don't cut nodes) are written to out_region. If the target path goes through the extracted region multiple times, only the extended bounds of the visit containing the target region are produced.

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