snarls.hpp File Reference

#include <iostream>
#include <cstdint>
#include <stdio.h>
#include <unordered_map>
#include <unordered_set>
#include <fstream>
#include <deque>
#include <vg/io/protobuf_emitter.hpp>
#include <vg/io/protobuf_iterator.hpp>
#include "vg.hpp"
#include "handle.hpp"
#include <vg/vg.pb.h>
#include "hash_map.hpp"
#include "cactus.hpp"

Classes
class	vg::SnarlFinder
class	vg::HandleGraphSnarlFinder
struct	vg::ChainIterator
class	vg::NetGraph
class	vg::SnarlManager
struct	vg::SnarlManager::SnarlRecord
struct	std::hash< const vg::Snarl >
	hash function for Snarls More...

Namespaces
	vg
	std
	Hash functor to hash NodeSides using std::hash.

Typedefs
using	vg::Chain = vector< pair< const Snarl *, bool > >

Functions
bool	vg::start_backward (const Chain &chain)
bool	vg::end_backward (const Chain &chain)
Visit	vg::get_start_of (const Chain &chain)
Visit	vg::get_end_of (const Chain &chain)
ChainIterator	vg::chain_begin (const Chain &chain)
ChainIterator	vg::chain_end (const Chain &chain)
ChainIterator	vg::chain_rbegin (const Chain &chain)
ChainIterator	vg::chain_rend (const Chain &chain)
ChainIterator	vg::chain_rcbegin (const Chain &chain)
ChainIterator	vg::chain_rcend (const Chain &chain)
ChainIterator	vg::chain_begin_from (const Chain &chain, const Snarl *start_snarl, bool snarl_orientation)
ChainIterator	vg::chain_end_from (const Chain &chain, const Snarl *start_snarl, bool snarl_orientation)
NodeTraversal	vg::to_node_traversal (const Visit &visit, const VG &graph)
NodeTraversal	vg::to_rev_node_traversal (const Visit &visit, const VG &graph)
NodeSide	vg::to_left_side (const Visit &visit)
	Converts a Visit to a node or snarl into a NodeSide for its left side. More...
NodeSide	vg::to_right_side (const Visit &visit)
	Converts a Visit to a node or snarl into a NodeSide for its right side. More...
Visit	vg::to_visit (const NodeTraversal &node_traversal)
	Converts a NodeTraversal to a Visit. More...
Visit	vg::to_visit (const Mapping &mapping, bool make_full_node_match=false)
Visit	vg::to_visit (id_t node_id, bool is_reverse)
	Make a Visit from a node ID and an orientation. More...
Visit	vg::to_visit (const Snarl &snarl)
	Make a Visit from a snarl to traverse. More...
Visit	vg::to_visit (const handlegraph::HandleGraph &graph, const handle_t &handle)
	Make a Visit from a handle in a HandleGraph. More...
Visit	vg::reverse (const Visit &visit)
	Get the reversed version of a visit. More...
Visit	vg::to_rev_visit (const NodeTraversal &node_traversal)
	Converts a NodeTraversal to a Visit in the opposite orientation. More...
Mapping	vg::to_mapping (const Visit &visit, std::function< size_t(id_t)> node_length)
Mapping	vg::to_mapping (const Visit &visit, const HandleGraph &vg)
Alignment	vg::to_alignment (const SnarlTraversal &trav, const HandleGraph &graph)
	Convert a snarl traversal into an alignment. More...
void	vg::transfer_boundary_info (const Snarl &from, Snarl &to)
	Copies the boundary Visits from one Snarl into another. More...
edge_t	vg::to_edge (const handlegraph::HandleGraph &graph, const Visit &v1, const Visit &v2)
	Make an edge_t from a pair of visits. More...
bool	vg::operator== (const Visit &a, const Visit &b)
bool	vg::operator!= (const Visit &a, const Visit &b)
bool	vg::operator< (const Visit &a, const Visit &b)
ostream &	vg::operator<< (ostream &out, const Visit &visit)
bool	vg::operator== (const SnarlTraversal &a, const SnarlTraversal &b)
bool	vg::operator!= (const SnarlTraversal &a, const SnarlTraversal &b)
bool	vg::operator< (const SnarlTraversal &a, const SnarlTraversal &b)
bool	vg::operator== (const Snarl &a, const Snarl &b)
bool	vg::operator!= (const Snarl &a, const Snarl &b)
bool	vg::operator< (const Snarl &a, const Snarl &b)
ostream &	vg::operator<< (ostream &out, const Snarl &snarl)
NodeTraversal	vg::to_node_traversal (const Visit &visit, VG &graph)
NodeTraversal	vg::to_rev_node_traversal (const Visit &visit, VG &graph)

Detailed Description

Contains object to own Snarls and keep track of their tree relationships as well as utility functions that interact with snarls.