theplu::yat::omic::BamFile< Derived > Class Template Reference

#include <yat/omic/BamFile.h>

Inheritance diagram for theplu::yat::omic::BamFile< Derived >:

Public Member Functions
	BamFile (void)
virtual	~BamFile (void)
	Destructor. 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

template<typename Derived>
class theplu::yat::omic::BamFile< Derived >

Base class for bam files

Since

New in yat 0.10

Constructor & Destructor Documentation

BamFile()

template<class Derived >

theplu::yat::omic::BamFile< Derived >::BamFile

(

void

)

Default Constructor

~BamFile()

template<class Derived >

theplu::yat::omic::BamFile< Derived >::~BamFile ( void  )

virtual

Destructor.

Closes file if it is open.

Member Function Documentation

build_index_base()

template<class Derived >

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

protected

Since

New in yat 0.15

filename()

template<typename Derived>

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

inlineprotected

filename of bam file

The filename is set in open_base().

have_index()

template<class Derived >

bool theplu::yat::omic::BamFile< Derived >::have_index

(

void

)

const

Returns

true if file has an index file

Since

New in yat 0.15

is_open()

template<class Derived >

bool theplu::yat::omic::BamFile< Derived >::is_open

(

void

)

const

Returns

true iff open

open_base() [1/2]

template<class Derived >

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

protected

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]

template<class Derived >

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

protected

open a bam file named fn with mode mode

See also

sam_open in htslib

Since

New in yat 0.18

Member Data Documentation

sf_

template<typename Derived>

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

protected

bam file handler

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

• yat/omic/BamFile.h