xg.hpp File Reference

#include <iostream>
#include <fstream>
#include <map>
#include <queue>
#include <omp.h>
#include <unordered_map>
#include <unordered_set>
#include <string>
#include <functional>
#include <utility>
#include <tuple>
#include <sys/types.h>
#include <dirent.h>
#include <sdsl/bit_vectors.hpp>
#include <sdsl/enc_vector.hpp>
#include <sdsl/dac_vector.hpp>
#include <sdsl/vlc_vector.hpp>
#include <sdsl/wavelet_trees.hpp>
#include <sdsl/csa_wt.hpp>
#include <sdsl/suffix_arrays.hpp>
#include <handlegraph/types.hpp>
#include <handlegraph/iteratee.hpp>
#include <handlegraph/util.hpp>
#include <handlegraph/handle_graph.hpp>
#include <handlegraph/serializable_handle_graph.hpp>
#include <handlegraph/path_position_handle_graph.hpp>
#include <mmmultimap.hpp>

Classes
class	xg::XGFormatError
class	xg::XG
class	xg::XGPath

Namespaces
	xg
	xg::temp_file

Typedefs
using	xg::nid_t = handlegraph::nid_t
typedef std::tuple< nid_t, bool, size_t >	xg::pos_t

Functions
pos_t	xg::make_pos_t (const nid_t &id, bool is_rev, const size_t &off)
nid_t	xg::id (const pos_t &pos)
	Extract the id of the node a pos_t is on. More...
bool	xg::is_rev (const pos_t &pos)
	Return true if a pos_t is on the reverse strand of its node. More...
size_t	xg::offset (const pos_t &pos)
	Get the offset along the selected strand of the node from a pos_t. More...
nid_t &	xg::get_id (pos_t &pos)
	Get a reference to the Node ID of a pos_t. More...
bool &	xg::get_is_rev (pos_t &pos)
	Get a reference to the reverse flag of a pos_t. More...
size_t &	xg::get_offset (pos_t &pos)
	Get a reference to the offset field of a pos_t, which counts along the selected strand of the node. More...
bool	xg::is_empty (const pos_t &pos)
	Return true if a pos_t is unset. More...
pos_t	xg::reverse (const pos_t &pos, size_t node_length)
pos_t	xg::reverse_base_pos (const pos_t &pos, size_t node_length)
	Reverse a pos_t and get a pos_t at the same base, going the other direction. More...
std::ostream &	xg::operator<< (std::ostream &out, const pos_t &pos)
	Print a pos_t to a stream. More...
char	xg::reverse_complement (const char &c)
std::string	xg::reverse_complement (const std::string &seq)
void	xg::reverse_complement_in_place (std::string &seq)
std::string	xg::temp_file::create (const std::string &base)
	Create a temporary file starting with the given base name. More...
std::string	xg::temp_file::create ()
	Create a temporary file. More...
void	xg::temp_file::remove (const std::string &filename)
	Remove a temporary file. More...
void	xg::temp_file::forget ()
	Forget about all current temporary files and directories without deleting them. More...
void	xg::temp_file::set_dir (const std::string &new_temp_dir)
	Set a temp dir, overriding system defaults and environment variables. More...
std::string	xg::temp_file::get_dir ()
	Get the current temp dir. More...
int	xg::get_thread_count (void)
	Uses OMP to get the count of threads. More...