yat  0.10.4pre
Public Member Functions | Protected Member Functions | Protected Attributes
theplu::yat::omic::OutBamFile Class Reference

#include </scratch/bob/jari/tmp/pristine/yat-0.10.x/yat/omic/BamFile.h>

Inheritance diagram for theplu::yat::omic::OutBamFile:
theplu::yat::omic::BamFile< OutBamFile > noncopyable

List of all members.

Public Member Functions

 OutBamFile (void)
 OutBamFile (const std::string &, const BamHeader &header)
 Create an output bam file.
void open (const std::string &fn, const BamHeader &hdr)
 Open an output bam file.
void write (const BamRead &read)
 write a read to output file
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

Protected Attributes

samfile_t * sf_

Detailed Description

This class supports writing to a bam file.

Since:
New in yat 0.10

Constructor & Destructor Documentation

theplu::yat::omic::OutBamFile::OutBamFile ( void  )

Create an output bam file

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&)

Member Function Documentation

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

filename of bam file

The filename is set in open_base().

bool theplu::yat::omic::BamFile< OutBamFile >::is_open ( void  ) const
inherited
Returns:
true iff open
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.

Parameters:
fnstring specifying the filename
hdrheader
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:
samopen

Member Data Documentation

samfile_t* theplu::yat::omic::BamFile< OutBamFile >::sf_
protectedinherited

bam file handler


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

Generated on Mon Nov 11 2013 09:41:45 for yat by  doxygen 1.8.1