theplu::yat::omic::InBamFile Class Reference

#include <yat/omic/BamFile.h>

Inheritance diagram for theplu::yat::omic::InBamFile:

Public Types
typedef bam_index_t	index_type

Public Member Functions
	InBamFile (void)
	Default constructor.
	InBamFile (const std::string &fn)
virtual	~InBamFile (void)
	destructor
const BamHeader &	header (void) const
const index_type *	index (void) const
void	open (const std::string &fn)
	Open an input bam file. More...
bool	read (BamRead &read)
	read the next BamRead More...
bool	read (BamRead &read, bam_iter_t iter)
	read the next BamRead 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

This class supports reading from a bam file.

Since

New in yat 0.10

Member Typedef Documentation

typedef bam_index_t theplu::yat::omic::InBamFile::index_type

Struct describing bam index.

If compiled against htslib, hts_idx_t. If compiled against libbam, bam_index_t.

Since

New in yat 0.13

See Also

function index(void) const

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

protectedinherited

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

theplu::yat::omic::InBamFile::InBamFile ( const std::string &  fn )

explicit

Create an input file

Parameters

fn	string specifying the filename

See Also

open(const std::string&)

Member Function Documentation

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

inlineprotectedinherited

filename of bam file

The filename is set in open_base().

const BamHeader& theplu::yat::omic::InBamFile::header

(

void

)

const

Returns

header

const index_type* theplu::yat::omic::InBamFile::index

(

void

)

const

Returns

index associated with BamFile

First time this function is called an index file is loaded from disk. If bam file is named 'foo.bam', the index file should be named 'foo.bam.bai'. If no such file exists or this bam file reads from stdin, this function throws.

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

inherited

Returns

true iff open

void theplu::yat::omic::InBamFile::open

(

const std::string &

fn

)

Open an input bam file.

Open a bam file named fn. If fn is "-", stdin is used.

Parameters

fn	string specifying the filename

void theplu::yat::omic::BamFile< InBamFile >::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

Note

aux is ignored when compiling against htslib

bool theplu::yat::omic::InBamFile::read

(

BamRead &

read

)

read the next BamRead

Returns

true on success

bool theplu::yat::omic::InBamFile::read	(	BamRead &	read,
		bam_iter_t	iter
	)

read the next BamRead

This function is used in BamReadIterator. Typically it is more convenient to read bams via a BamReadIterator than through this function directly.

Returns

true on success

Member Data Documentation

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

protectedinherited

bam file handler

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

• yat/omic/BamFile.h