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	is_open (void) const

Protected Types
typedef samfile_t	samFile
	only defined when compiling against old bamlib More...

Protected Member Functions
void	open_base (const std::string &fn, const std::string &mode, const void *aux)
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

Member Typedef Documentation

template<typename Derived>

typedef samfile_t theplu::yat::omic::BamFile< Derived >::samFile

protected

only defined when compiling against old bamlib

Old samtools 0.1.xx had a struct samfile_t, which in htslib has changed to samFile

Constructor & Destructor Documentation

template<class Derived >

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

(

void

)

Default Constructor

template<class Derived >

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

virtual

Destructor.

Closes file if it is open.

Member Function Documentation

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().

template<class Derived >

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

(

void

)

const

Returns

true iff open

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

samopen

Note

aux is ignored when compiling against htslib

Member Data Documentation

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