yat  0.14.5pre
Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
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 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

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


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

Generated on Tue Sep 26 2017 02:33:29 for yat by  doxygen 1.8.5