xg Namespace Reference

Namespaces
	temp_file

Classes
class	XG
class	XGFormatError
class	XGPath

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

Functions
int	dna3bit (char c)
char	revdna3bit (int i)
int	get_thread_count (void)
	Uses OMP to get the count of threads. More...
pos_t	make_pos_t (const nid_t &id, bool is_rev, const size_t &off)
nid_t	id (const pos_t &pos)
	Extract the id of the node a pos_t is on. More...
bool	is_rev (const pos_t &pos)
	Return true if a pos_t is on the reverse strand of its node. More...
size_t	offset (const pos_t &pos)
	Get the offset along the selected strand of the node from a pos_t. More...
nid_t &	get_id (pos_t &pos)
	Get a reference to the Node ID of a pos_t. More...
bool &	get_is_rev (pos_t &pos)
	Get a reference to the reverse flag of a pos_t. More...
size_t &	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	is_empty (const pos_t &pos)
	Return true if a pos_t is unset. More...
pos_t	reverse (const pos_t &pos, size_t node_length)
pos_t	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 &	operator<< (std::ostream &out, const pos_t &pos)
	Print a pos_t to a stream. More...
char	reverse_complement (const char &c)
std::string	reverse_complement (const std::string &seq)
void	reverse_complement_in_place (std::string &seq)

Typedef Documentation

nid_t

using xg::nid_t = typedef handlegraph::nid_t

pos_t

typedef std::tuple<nid_t, bool, size_t> xg::pos_t

Function Documentation

dna3bit()

int xg::dna3bit

(

char

c

)

get_id()

nid_t& xg::get_id ( pos_t &  pos )

inline

Get a reference to the Node ID of a pos_t.

get_is_rev()

bool& xg::get_is_rev ( pos_t &  pos )

inline

Get a reference to the reverse flag of a pos_t.

get_offset()

size_t& xg::get_offset ( pos_t &  pos )

inline

Get a reference to the offset field of a pos_t, which counts along the selected strand of the node.

get_thread_count()

int xg::get_thread_count

(

void

)

Uses OMP to get the count of threads.

id()

nid_t xg::id ( const pos_t &  pos )

inline

Extract the id of the node a pos_t is on.

is_empty()

bool xg::is_empty ( const pos_t &  pos )

inline

Return true if a pos_t is unset.

is_rev()

bool xg::is_rev ( const pos_t &  pos )

inline

Return true if a pos_t is on the reverse strand of its node.

make_pos_t()

pos_t xg::make_pos_t ( const nid_t &  id, bool  is_rev, const size_t &  off  )

inline

offset()

size_t xg::offset ( const pos_t &  pos )

inline

Get the offset along the selected strand of the node from a pos_t.

operator<<()

std::ostream& xg::operator<< ( std::ostream &  out, const pos_t &  pos  )

inline

Print a pos_t to a stream.

revdna3bit()

char xg::revdna3bit

(

int

i

)

reverse()

pos_t xg::reverse ( const pos_t &  pos, size_t  node_length  )

inline

Reverse a pos_t and get a pos_t at the same point between bases, going the other direction. To get a pos_t to the same base, subtract 1 from the resulting offset or call reverse_base_pos().

reverse_base_pos()

pos_t xg::reverse_base_pos ( const pos_t &  pos, size_t  node_length  )

inline

Reverse a pos_t and get a pos_t at the same base, going the other direction.

reverse_complement() [1/2]

char xg::reverse_complement ( const char &  c )

inline

reverse_complement() [2/2]

std::string xg::reverse_complement ( const std::string &  seq )

inline

reverse_complement_in_place()

void xg::reverse_complement_in_place ( std::string &  seq )

inline