vg::AugRefCover Class Reference

#include <augref.hpp>

Classes
struct	RankedFragment

Public Member Functions
void	clear (MutablePathMutableHandleGraph *graph)
void	compute (const PathHandleGraph *graph, SnarlManager *snarl_manager, const unordered_set< path_handle_t > &reference_paths, int64_t minimum_length)
void	load (const PathHandleGraph *graph, const unordered_set< path_handle_t > &reference_paths)
void	apply (MutablePathMutableHandleGraph *mutable_graph)
void	set_augref_sample (const string &sample_name)
const string &	get_augref_sample () const
void	set_verbose (bool verbose)
bool	get_verbose () const
int64_t	get_rank (nid_t node_id) const
const vector< pair< step_handle_t, step_handle_t > > &	get_intervals () const
const pair< step_handle_t, step_handle_t > *	get_interval (nid_t node_id) const
int64_t	get_num_ref_intervals () const
void	write_augref_segments (ostream &os)

Static Public Member Functions
static string	make_augref_name (const string &base_path_name, int64_t augref_index)
static bool	is_augref_name (const string &path_name)
static string	parse_base_path (const string &augref_name)
static int64_t	parse_augref_index (const string &augref_name)

Static Public Attributes
static const string	augref_suffix = "_alt"

Protected Member Functions
void	compute_snarl (const Snarl &snarl, PathTraversalFinder &path_trav_finder, int64_t minimum_length, vector< pair< step_handle_t, step_handle_t >> &thread_augref_intervals, unordered_map< nid_t, int64_t > &thread_node_to_interval, nid_t top_snarl_start, nid_t top_snarl_end, vector< pair< nid_t, nid_t >> &thread_snarl_bounds)
vector< pair< int64_t, int64_t > >	get_uncovered_intervals (const vector< step_handle_t > &trav, const unordered_map< nid_t, int64_t > &thread_node_to_interval)
bool	add_interval (vector< pair< step_handle_t, step_handle_t >> &thread_augref_intervals, unordered_map< nid_t, int64_t > &thread_node_to_interval, const pair< step_handle_t, step_handle_t > &new_interval, bool global=false, vector< pair< nid_t, nid_t >> *snarl_bounds_vec=nullptr, pair< nid_t, nid_t > snarl_bounds={0, 0})
void	defragment_intervals ()
void	filter_short_intervals (int64_t minimum_length)
optional< step_handle_t >	try_extend_forward (step_handle_t start_step, path_handle_t path, const pair< step_handle_t, step_handle_t > &other_interval)
optional< step_handle_t >	try_extend_backward (step_handle_t start_step, path_handle_t path, const pair< step_handle_t, step_handle_t > &other_interval)
int64_t	get_coverage (const vector< step_handle_t > &trav, const pair< int64_t, int64_t > &uncovered_interval)
void	forwardize_augref_paths (MutablePathMutableHandleGraph *mutable_graph)
void	fill_uncovered_nodes (int64_t minimum_length)
vector< pair< int64_t, nid_t > >	get_reference_nodes (nid_t node_id, bool first) const
void	verify_cover () const
void	copy_base_paths_to_sample (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 > >	augref_intervals
vector< pair< nid_t, nid_t > >	interval_snarl_bounds
int64_t	num_ref_intervals = 0
unordered_map< nid_t, int64_t >	node_to_interval
unordered_map< string, int64_t >	base_path_augref_counter
string	augref_sample_name
bool	verbose = false
bool	rank_by_name = false

Member Function Documentation

add_interval()

bool vg::AugRefCover::add_interval ( vector< pair< step_handle_t, step_handle_t >> &  thread_augref_intervals, unordered_map< nid_t, int64_t > &  thread_node_to_interval, const pair< step_handle_t, step_handle_t > &  new_interval, bool  global = false, vector< pair< nid_t, nid_t >> *  snarl_bounds_vec = nullptr, pair< nid_t, nid_t >  snarl_bounds = {0, 0}  )

protected

apply()

void vg::AugRefCover::apply

(

MutablePathMutableHandleGraph *

mutable_graph

)

clear()

void vg::AugRefCover::clear

(

MutablePathMutableHandleGraph *

graph

)

compute()

void vg::AugRefCover::compute	(	const PathHandleGraph *	graph,
		SnarlManager *	snarl_manager,
		const unordered_set< path_handle_t > &	reference_paths,
		int64_t	minimum_length
	)

compute_snarl()

void vg::AugRefCover::compute_snarl ( const Snarl &  snarl, PathTraversalFinder &  path_trav_finder, int64_t  minimum_length, vector< pair< step_handle_t, step_handle_t >> &  thread_augref_intervals, unordered_map< nid_t, int64_t > &  thread_node_to_interval, nid_t  top_snarl_start, nid_t  top_snarl_end, vector< pair< nid_t, nid_t >> &  thread_snarl_bounds  )

protected

copy_base_paths_to_sample()

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

protected

defragment_intervals()

void vg::AugRefCover::defragment_intervals ( )

protected

fill_uncovered_nodes()

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

protected

filter_short_intervals()

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

protected

forwardize_augref_paths()

void vg::AugRefCover::forwardize_augref_paths ( MutablePathMutableHandleGraph *  mutable_graph )

protected

get_augref_sample()

const string & vg::AugRefCover::get_augref_sample

(

)

const

get_coverage()

int64_t vg::AugRefCover::get_coverage ( const vector< step_handle_t > &  trav, const pair< int64_t, int64_t > &  uncovered_interval  )

protected

get_interval()

const pair< step_handle_t, step_handle_t > * vg::AugRefCover::get_interval

(

nid_t

node_id

)

const

get_intervals()

const vector< pair< step_handle_t, step_handle_t > > & vg::AugRefCover::get_intervals

(

)

const

get_num_ref_intervals()

int64_t vg::AugRefCover::get_num_ref_intervals

(

)

const

get_rank()

int64_t vg::AugRefCover::get_rank

(

nid_t

node_id

)

const

get_reference_nodes()

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

protected

get_uncovered_intervals()

vector< pair< int64_t, int64_t > > vg::AugRefCover::get_uncovered_intervals ( const vector< step_handle_t > &  trav, const unordered_map< nid_t, int64_t > &  thread_node_to_interval  )

protected

get_verbose()

bool vg::AugRefCover::get_verbose

(

)

const

is_augref_name()

bool vg::AugRefCover::is_augref_name ( const string &  path_name )

static

load()

void vg::AugRefCover::load	(	const PathHandleGraph *	graph,
		const unordered_set< path_handle_t > &	reference_paths
	)

make_augref_name()

string vg::AugRefCover::make_augref_name ( const string &  base_path_name, int64_t  augref_index  )

static

parse_augref_index()

int64_t vg::AugRefCover::parse_augref_index ( const string &  augref_name )

static

parse_base_path()

string vg::AugRefCover::parse_base_path ( const string &  augref_name )

static

set_augref_sample()

void vg::AugRefCover::set_augref_sample

(

const string &

sample_name

)

set_verbose()

void vg::AugRefCover::set_verbose

(

bool

verbose

)

try_extend_backward()

optional< step_handle_t > vg::AugRefCover::try_extend_backward ( step_handle_t  start_step, path_handle_t  path, const pair< step_handle_t, step_handle_t > &  other_interval  )

protected

try_extend_forward()

optional< step_handle_t > vg::AugRefCover::try_extend_forward ( step_handle_t  start_step, path_handle_t  path, const pair< step_handle_t, step_handle_t > &  other_interval  )

protected

verify_cover()

void vg::AugRefCover::verify_cover ( ) const

protected

write_augref_segments()

void vg::AugRefCover::write_augref_segments

(

ostream &

os

)

Member Data Documentation

augref_intervals

vector<pair<step_handle_t, step_handle_t> > vg::AugRefCover::augref_intervals

protected

augref_sample_name

string vg::AugRefCover::augref_sample_name

protected

augref_suffix

const string vg::AugRefCover::augref_suffix = "_alt"

static

base_path_augref_counter

unordered_map<string, int64_t> vg::AugRefCover::base_path_augref_counter

mutableprotected

graph

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

protected

interval_snarl_bounds

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

protected

node_to_interval

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

protected

num_ref_intervals

int64_t vg::AugRefCover::num_ref_intervals = 0

protected

rank_by_name

bool vg::AugRefCover::rank_by_name = false

protected

verbose

bool vg::AugRefCover::verbose = false

protected

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

• src/augref.hpp
• src/augref.cpp