vg::GAFSorterFile Struct Reference

#include <gaf_sorter.hpp>

Public Member Functions
	GAFSorterFile ()
	Default constructor that creates a compressed temporary file. More...
	GAFSorterFile (const std::string &name, std::unique_ptr< std::vector< std::string >> header_lines, const std::string &gbwt_file, bool bidirectional_gbwt)
	~GAFSorterFile ()
	If the file is temporary, the destructor removes the file. More...
	GAFSorterFile (const GAFSorterFile &)=delete
GAFSorterFile &	operator= (const GAFSorterFile &)=delete
	GAFSorterFile (GAFSorterFile &&)=default
GAFSorterFile &	operator= (GAFSorterFile &&)=default
std::pair< std::ostream *, std::unique_ptr< std::ostream > >	open_output ()
void	write (const GAFSorterRecord &record, std::ostream &out)
std::pair< std::istream *, std::unique_ptr< std::istream > >	open_input ()
void	read (GAFSorterRecord &record, std::istream &in)
bool	is_std_in_out () const
void	remove_temporary ()
	Removes the file if it is temporary. More...

Public Attributes
std::string	name
	File name. More...
std::unique_ptr< std::vector< std::string > >	header_lines
	Header lines that should be written to a raw GAF file. More...
std::string	gbwt_file
	File name for the GBWT index, if any. More...
bool	bidirectional_gbwt
	Should the GBWT index be bidirectional? More...
size_t	records
	Number of records. More...
bool	temporary
	Is this a temporary file created with temp_file::create()? More...
bool	compressed
	Is this file compressed? More...
bool	raw_gaf
	Is this a raw GAF file? More...
bool	removed
	Has the file been removed? More...
bool	ok
	Success flag. More...

Detailed Description

A file of GAFSorterRecords or GAF lines.

The records are sorted in increasing order by key. The object is movable but not copyable.

Constructor & Destructor Documentation

GAFSorterFile() [1/4]

vg::GAFSorterFile::GAFSorterFile

(

)

Default constructor that creates a compressed temporary file.

GAFSorterFile() [2/4]

vg::GAFSorterFile::GAFSorterFile	(	const std::string &	name,
		std::unique_ptr< std::vector< std::string >>	header_lines,
		const std::string &	gbwt_file,
		bool	bidirectional_gbwt
	)

Constructor that creates a raw GAF file with the given name, header, and a GBWT index that may be bidirectional. Takes ownership of the header lines.

~GAFSorterFile()

vg::GAFSorterFile::~GAFSorterFile

(

)

If the file is temporary, the destructor removes the file.

GAFSorterFile() [3/4]

vg::GAFSorterFile::GAFSorterFile ( const GAFSorterFile &  )

delete

GAFSorterFile() [4/4]

vg::GAFSorterFile::GAFSorterFile ( GAFSorterFile &&  )

default

Member Function Documentation

is_std_in_out()

bool vg::GAFSorterFile::is_std_in_out ( ) const

inline

Returns true if the file is actually stdin/stdout. In that case, open_input() should not be called.

open_input()

std::pair< std::istream *, std::unique_ptr< std::istream > > vg::GAFSorterFile::open_input

(

)

Returns an input stream to the file. The first return value is the actual stream. The second return value is a unique pointer which may contain a newly created stream. Sets the success flag.

open_output()

std::pair< std::ostream *, std::unique_ptr< std::ostream > > vg::GAFSorterFile::open_output

(

)

Returns an output stream to the file. The first return value is the actual stream. The second return value is a unique pointer which may contain a newly created stream. If this is a raw GAF file, header lines are written to the output. Sets the success flag.

operator=() [1/2]

GAFSorterFile& vg::GAFSorterFile::operator= ( const GAFSorterFile &  )

delete

operator=() [2/2]

GAFSorterFile& vg::GAFSorterFile::operator= ( GAFSorterFile &&  )

default

read()

void vg::GAFSorterFile::read ( GAFSorterRecord &  record, std::istream &  in  )

inline

Reads the next record from the file, assuming that this is not a raw GAF file. Sets the success flag.

remove_temporary()

void vg::GAFSorterFile::remove_temporary

(

)

Removes the file if it is temporary.

write()

void vg::GAFSorterFile::write ( const GAFSorterRecord &  record, std::ostream &  out  )

inline

Writes the record to the file. Updates the number of records and sets the success flag.

Member Data Documentation

bidirectional_gbwt

bool vg::GAFSorterFile::bidirectional_gbwt

Should the GBWT index be bidirectional?

compressed

bool vg::GAFSorterFile::compressed

Is this file compressed?

gbwt_file

std::string vg::GAFSorterFile::gbwt_file

File name for the GBWT index, if any.

header_lines

std::unique_ptr<std::vector<std::string> > vg::GAFSorterFile::header_lines

Header lines that should be written to a raw GAF file.

name

std::string vg::GAFSorterFile::name

File name.

ok

bool vg::GAFSorterFile::ok

Success flag.

raw_gaf

bool vg::GAFSorterFile::raw_gaf

Is this a raw GAF file?

records

size_t vg::GAFSorterFile::records

Number of records.

removed

bool vg::GAFSorterFile::removed

Has the file been removed?

temporary

bool vg::GAFSorterFile::temporary

Is this a temporary file created with temp_file::create()?

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

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