theplu::yat::omic::OutBamFile Class Reference

#include <yat/omic/BamFile.h>

Inheritance diagram for theplu::yat::omic::OutBamFile:

Classes
class	error
	Error thrown from OutBamFile::write(const BamRead&) at failure. More...

Public Member Functions
	OutBamFile (void)
	OutBamFile (const std::string &, const BamHeader &header)
	Create an output bam file. More...
	OutBamFile (const std::string &, const BamHeader &header, unsigned int compression)
	Create an output bam file. More...
void	build_index (void) const
void	open (const std::string &fn, const BamHeader &hdr)
	Open an output bam file. More...
void	open (const std::string &fn, const BamHeader &hdr, unsigned int compression)
	Open an output bam file. More...
void	write (const BamRead &read)
	write a read to output file More...
void	close (void)
	close file
bool	have_index (void) const
bool	is_open (void) const

Protected Member Functions
void	build_index_base (void) const
void	open_base (const std::string &fn, const std::string &mode, const void *aux)
void	open_base (const std::string &fn, const std::string &mode)
const std::string &	filename (void) const
	filename of bam file More...

Protected Attributes
samFile *	sf_

Detailed Description

This class supports writing to a bam file.

Since

New in yat 0.10

Constructor & Destructor Documentation

OutBamFile() [1/3]

theplu::yat::omic::OutBamFile::OutBamFile

(

void

)

Create an output bam file

OutBamFile() [2/3]

theplu::yat::omic::OutBamFile::OutBamFile	(	const std::string &	,
		const BamHeader &	header
	)

Create an output bam file.

Equivalent to default constructor followed by a call to open(2).

See also

open(const std::string&, const BamHeader&)

OutBamFile() [3/3]

theplu::yat::omic::OutBamFile::OutBamFile	(	const std::string &	,
		const BamHeader &	header,
		unsigned int	compression
	)

Create an output bam file.

Equivalent to default constructor followed by a call to open(3).

See also

open(const std::string&, const BamHeader&, unsigned int)

Since

yat 0.12

Member Function Documentation

build_index()

void theplu::yat::omic::OutBamFile::build_index

(

void

)

const

Since

New in yat 0.15

Exceptions

if	file is open (

See also

is_open())

build_index_base()

void theplu::yat::omic::BamFile< OutBamFile >::build_index_base ( void  ) const

protectedinherited

Since

New in yat 0.15

filename()

const std::string& theplu::yat::omic::BamFile< OutBamFile >::filename ( void  ) const

inlineprotectedinherited

filename of bam file

The filename is set in open_base().

have_index()

bool theplu::yat::omic::BamFile< OutBamFile >::have_index ( void  ) const

inherited

Returns

true if file has an index file

Since

New in yat 0.15

is_open()

bool theplu::yat::omic::BamFile< OutBamFile >::is_open ( void  ) const

inherited

Returns

true iff open

open() [1/2]

void theplu::yat::omic::OutBamFile::open	(	const std::string &	fn,
		const BamHeader &	hdr
	)

Open an output bam file.

Opens an output bam file and writes the header contained in hdr. If fn is "-", stdout is used.

Parameters

fn	string specifying the filename
hdr	header

open() [2/2]

void theplu::yat::omic::OutBamFile::open	(	const std::string &	fn,
		const BamHeader &	hdr,
		unsigned int	compression
	)

Open an output bam file.

Opens an output bam file and writes the header contained in hdr. If fn is "-", stdout is used.

Parameters

fn	string specifying the filename
hdr	header
compression	a number [0,9] indicating level of compression. 9 gives highest compression and 0 indicates no compression (suitable for piping between applications).

Since

yat 0.12

open_base() [1/2]

void theplu::yat::omic::BamFile< OutBamFile >::open_base ( const std::string &  fn, const std::string &  mode, const void *  aux  )

protectedinherited

open a bam file named fn with mode mode

See also

sam_open in htslib

Note

aux is ignored when compiling against htslib

Deprecated:

Provided for backward compatibility with the yat 0.17 API. Use open_base(2) instead.

open_base() [2/2]

void theplu::yat::omic::BamFile< OutBamFile >::open_base ( const std::string &  fn, const std::string &  mode  )

protectedinherited

open a bam file named fn with mode mode

See also

sam_open in htslib

Since

New in yat 0.18

write()

void theplu::yat::omic::OutBamFile::write

(

const BamRead &

read

)

write a read to output file

Exceptions

OutBamFile::error

if write failed

Since

yat 0.12

Member Data Documentation

sf_

samFile* theplu::yat::omic::BamFile< OutBamFile >::sf_

protectedinherited

bam file handler

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The documentation for this class was generated from the following file:

• yat/omic/BamFile.h