vg::GAFSorterRecord Struct Reference

#include <gaf_sorter.hpp>

Public Types
enum	key_type { key_node_interval, key_gbwt_pos, key_hash }
	Types of keys that can be derived from the value. More...

Public Member Functions
	GAFSorterRecord ()
	Default constructor. More...
	GAFSorterRecord (std::string &&value, key_type type)
	Constructor that consumes the given value and sets the key. More...
bool	operator< (const GAFSorterRecord &another) const
	Records are sorted by key in ascending order. More...
void	flip_key ()
void	set_key (key_type type)
	Sets a key of the given type, or MISSING_KEY if the key cannot be derived. More...
bool	serialize (std::ostream &out) const
	Serializes the record to a stream. Returns true on success. More...
bool	write_line (std::ostream &out) const
	Writes the underlying GAF line to a stream. Returns true on success. More...
bool	deserialize (std::istream &in)
	Deserializes the record from a stream. Returns true on success. More...
bool	read_line (std::istream &in, key_type type)
	Reads a GAF line from a stream and sets the key. Returns true on success. More...
str_view	get_field (size_t field) const
	Returns a view of the given 0-based field, or an empty string if the field is missing. More...
void	for_each_field (const std::function< bool(size_t, str_view)> &lambda) const
gbwt::vector_type	as_gbwt_path (bool *ok=nullptr) const

Public Attributes
std::uint64_t	key
	Integer key. More...
std::string	value
	GAF line. More...

Static Public Attributes
static std::hash< std::string >	hasher
	Hasher used for random shuffling. More...
constexpr static std::uint64_t	MISSING_KEY = std::numeric_limits<std::uint64_t>::max()
	Missing key. Records without a key are sorted to the end. More...
const static std::string	GBWT_OFFSET_TAG = "GB:i:"
constexpr static size_t	STRAND_FIELD = 4
	0-based field number for the strand/orientation in a GAF line. More...
constexpr static size_t	PATH_FIELD = 5
	0-based field number for the path in a GAF line. More...
constexpr static size_t	MANDATORY_FIELDS = 12
	Number of mandatory fields in a GAF line. More...

Detailed Description

A record corresponding to a single line (alignment) in a GAF file. The record contains an integer key and the original line. Various types of keys can be derived from the value, but the line is not parsed beyond that.

Member Enumeration Documentation

key_type

enum vg::GAFSorterRecord::key_type

Types of keys that can be derived from the value.

Enumerator
key_node_interval	(minimum node id, maximum node id) in the path.
key_gbwt_pos	GBWT starting position for the forward orientation. Derived from the path and tag "GB:i:".
key_hash	Hash of the value for random shuffling.

Constructor & Destructor Documentation

GAFSorterRecord() [1/2]

vg::GAFSorterRecord::GAFSorterRecord ( )

inline

Default constructor.

GAFSorterRecord() [2/2]

vg::GAFSorterRecord::GAFSorterRecord ( std::string &&  value, key_type  type  )

inline

Constructor that consumes the given value and sets the key.

Member Function Documentation

as_gbwt_path()

gbwt::vector_type vg::GAFSorterRecord::as_gbwt_path

(

bool *

ok = nullptr

)

const

Returns the path as a GBWT path in forward orientation. If an ok flag is given, sets it to false and prints an error message if the path could not be parsed.

deserialize()

bool vg::GAFSorterRecord::deserialize

(

std::istream &

in

)

Deserializes the record from a stream. Returns true on success.

flip_key()

void vg::GAFSorterRecord::flip_key ( )

inline

Flips they key to reverse the order. Sorting is based on ascending order, while priority queues return the largest element first.

for_each_field()

void vg::GAFSorterRecord::for_each_field

(

const std::function< bool(size_t, str_view)> &

lambda

)

const

Calls the given function with a 0-based field index and the field value. Stops if the function returns false.

get_field()

str_view vg::GAFSorterRecord::get_field

(

size_t

field

)

const

Returns a view of the given 0-based field, or an empty string if the field is missing.

operator<()

bool vg::GAFSorterRecord::operator< ( const GAFSorterRecord &  another ) const

inline

Records are sorted by key in ascending order.

read_line()

bool vg::GAFSorterRecord::read_line	(	std::istream &	in,
		key_type	type
	)

Reads a GAF line from a stream and sets the key. Returns true on success.

serialize()

bool vg::GAFSorterRecord::serialize

(

std::ostream &

out

)

const

Serializes the record to a stream. Returns true on success.

set_key()

void vg::GAFSorterRecord::set_key

(

key_type

type

)

Sets a key of the given type, or MISSING_KEY if the key cannot be derived.

write_line()

bool vg::GAFSorterRecord::write_line

(

std::ostream &

out

)

const

Writes the underlying GAF line to a stream. Returns true on success.

Member Data Documentation

GBWT_OFFSET_TAG

const std::string vg::GAFSorterRecord::GBWT_OFFSET_TAG = "GB:i:"

static

Node offset for the GBWT starting position of the forward orientation may be stored in this tag.

hasher

std::hash<std::string> vg::GAFSorterRecord::hasher

static

Hasher used for random shuffling.

key

std::uint64_t vg::GAFSorterRecord::key

Integer key.

MANDATORY_FIELDS

constexpr size_t vg::GAFSorterRecord::MANDATORY_FIELDS = 12

staticconstexpr

Number of mandatory fields in a GAF line.

MISSING_KEY

constexpr std::uint64_t vg::GAFSorterRecord::MISSING_KEY = std::numeric_limits<std::uint64_t>::max()

staticconstexpr

Missing key. Records without a key are sorted to the end.

PATH_FIELD

constexpr size_t vg::GAFSorterRecord::PATH_FIELD = 5

staticconstexpr

0-based field number for the path in a GAF line.

STRAND_FIELD

constexpr size_t vg::GAFSorterRecord::STRAND_FIELD = 4

staticconstexpr

0-based field number for the strand/orientation in a GAF line.

value

std::string vg::GAFSorterRecord::value

GAF line.

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

• src/gaf_sorter.hpp
• src/gaf_sorter.cpp