vg::GrefCover Class Reference

#include <gref.hpp>

Classes
struct	TopLevelSnarlStats

Public Member Functions
void	clear (MutablePathMutableHandleGraph *graph)
void	compute (const PathHandleGraph *graph, const bdsg::SnarlDistanceIndex *distance_index, const unordered_set< path_handle_t > &reference_paths, int64_t minimum_length)
void	apply (MutablePathMutableHandleGraph *mutable_graph)
void	set_verbose (bool verbose)
void	enforce_top_level_anchoring (const bdsg::SnarlDistanceIndex &distance_index)
void	assign_top_level_snarls (const bdsg::SnarlDistanceIndex &distance_index)
void	assign_nesting (const bdsg::SnarlDistanceIndex &distance_index)
void	write_gref_segments (ostream &os)

Static Public Member Functions
static string	make_gref_copy_name (const string &path_name)
static string	make_gref_base_name (const string &base_path_name)
static bool	is_gref_derived (const string &name)
static string	make_gref_name (const string &base_path_name, int64_t gref_index)
static bool	is_gref_name (const string &path_name)
static string	parse_base_path (const string &gref_name)
static int64_t	parse_gref_index (const string &gref_name)

Static Public Attributes
static const string	gref_prefix = "gref_"
static const string	gref_suffix = "_alt"

Protected Member Functions
void	add_interval (vector< pair< step_handle_t, step_handle_t > > &thread_gref_intervals, unordered_map< nid_t, int64_t > &thread_node_to_interval, const pair< step_handle_t, step_handle_t > &new_interval, vector< pair< nid_t, nid_t > > *snarl_bounds_vec=nullptr, pair< nid_t, nid_t > snarl_bounds={0, 0})
void	filter_short_intervals (int64_t minimum_length)
void	fill_uncovered_nodes (int64_t minimum_length)
vector< pair< int64_t, nid_t > >	get_reference_nodes (nid_t node_id, bool first) const
string	resolve_base_path_name (int64_t interval_index, path_handle_t *out_ref_path=nullptr, nid_t *out_ref_node=nullptr) const
void	verify_cover (int64_t minimum_length) const
void	verify_disjoint () const
void	copy_base_paths_to_gref (MutablePathMutableHandleGraph *mutable_graph, const unordered_set< path_handle_t > &reference_paths)

Protected Attributes
const PathHandleGraph *	graph = nullptr
vector< pair< step_handle_t, step_handle_t > >	gref_intervals
vector< pair< nid_t, nid_t > >	interval_snarl_bounds
TopLevelSnarlStats	top_level_snarl_stats
vector< int64_t >	interval_parent
vector< int64_t >	interval_level
unordered_set< nid_t >	excluded_nodes
int64_t	excluded_units = 0
int64_t	excluded_bp = 0
int64_t	num_ref_intervals = 0
unordered_map< nid_t, int64_t >	node_to_interval
unordered_map< string, int64_t >	base_path_gref_counter
bool	verbose = false

Member Function Documentation

add_interval()

void vg::GrefCover::add_interval ( vector< pair< step_handle_t, step_handle_t > > & thread_gref_intervals, unordered_map< nid_t, int64_t > & thread_node_to_interval, const pair< step_handle_t, step_handle_t > & new_interval, vector< pair< nid_t, nid_t > > * snarl_bounds_vec = nullptr, pair< nid_t, nid_t > snarl_bounds = {0, 0} )

protected

apply()

void vg::GrefCover::apply

(

MutablePathMutableHandleGraph *

mutable_graph

)

assign_nesting()

void vg::GrefCover::assign_nesting

(

const bdsg::SnarlDistanceIndex &

distance_index

)

assign_top_level_snarls()

void vg::GrefCover::assign_top_level_snarls

(

const bdsg::SnarlDistanceIndex &

distance_index

)

clear()

void vg::GrefCover::clear

(

MutablePathMutableHandleGraph *

graph

)

compute()

void vg::GrefCover::compute	(	const PathHandleGraph *	graph,
		const bdsg::SnarlDistanceIndex *	distance_index,
		const unordered_set< path_handle_t > &	reference_paths,
		int64_t	minimum_length )

copy_base_paths_to_gref()

void vg::GrefCover::copy_base_paths_to_gref ( MutablePathMutableHandleGraph * mutable_graph, const unordered_set< path_handle_t > & reference_paths )

protected

enforce_top_level_anchoring()

void vg::GrefCover::enforce_top_level_anchoring

(

const bdsg::SnarlDistanceIndex &

distance_index

)

fill_uncovered_nodes()

void vg::GrefCover::fill_uncovered_nodes ( int64_t minimum_length )

protected

filter_short_intervals()

void vg::GrefCover::filter_short_intervals ( int64_t minimum_length )

protected

get_reference_nodes()

vector< pair< int64_t, nid_t > > vg::GrefCover::get_reference_nodes ( nid_t node_id, bool first ) const

protected

is_gref_derived()

bool vg::GrefCover::is_gref_derived ( const string & name )

static

is_gref_name()

bool vg::GrefCover::is_gref_name ( const string & path_name )

static

make_gref_base_name()

string vg::GrefCover::make_gref_base_name ( const string & base_path_name )

static

make_gref_copy_name()

string vg::GrefCover::make_gref_copy_name ( const string & path_name )

static

make_gref_name()

string vg::GrefCover::make_gref_name ( const string & base_path_name, int64_t gref_index )

static

parse_base_path()

string vg::GrefCover::parse_base_path ( const string & gref_name )

static

parse_gref_index()

int64_t vg::GrefCover::parse_gref_index ( const string & gref_name )

static

resolve_base_path_name()

string vg::GrefCover::resolve_base_path_name ( int64_t interval_index, path_handle_t * out_ref_path = nullptr, nid_t * out_ref_node = nullptr ) const

protected

set_verbose()

void vg::GrefCover::set_verbose

(

bool

verbose

)

verify_cover()

void vg::GrefCover::verify_cover ( int64_t minimum_length ) const

protected

verify_disjoint()

void vg::GrefCover::verify_disjoint ( ) const

protected

write_gref_segments()

void vg::GrefCover::write_gref_segments

(

ostream &

os

)

Member Data Documentation

base_path_gref_counter

unordered_map<string, int64_t> vg::GrefCover::base_path_gref_counter

protected

excluded_bp

int64_t vg::GrefCover::excluded_bp = 0

protected

excluded_nodes

unordered_set<nid_t> vg::GrefCover::excluded_nodes

protected

excluded_units

int64_t vg::GrefCover::excluded_units = 0

protected

graph

const PathHandleGraph* vg::GrefCover::graph = nullptr

protected

gref_intervals

vector<pair<step_handle_t, step_handle_t> > vg::GrefCover::gref_intervals

protected

gref_prefix

const string vg::GrefCover::gref_prefix = "gref_"

static

gref_suffix

const string vg::GrefCover::gref_suffix = "_alt"

static

interval_level

vector<int64_t> vg::GrefCover::interval_level

protected

interval_parent

vector<int64_t> vg::GrefCover::interval_parent

protected

interval_snarl_bounds

vector<pair<nid_t, nid_t> > vg::GrefCover::interval_snarl_bounds

protected

node_to_interval

unordered_map<nid_t, int64_t> vg::GrefCover::node_to_interval

protected

num_ref_intervals

int64_t vg::GrefCover::num_ref_intervals = 0

protected

top_level_snarl_stats

TopLevelSnarlStats vg::GrefCover::top_level_snarl_stats

protected

verbose

bool vg::GrefCover::verbose = false

protected

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

• src/gref.hpp
• src/gref.cpp