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

#include <yat/omic/BamFile.h>

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

Public Types
typedef hts_idx_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
uint64_t	n_mapped (int tid) const
uint64_t	n_unmapped (int tid) const
uint64_t	n_no_coordinate (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, hts_itr_t *iter)
	read the next BamRead 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

This class supports reading from a bam file.

Since

New in yat 0.10

Member Typedef Documentation

typedef hts_idx_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

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

uint64_t theplu::yat::omic::InBamFile::n_mapped

(

int

tid

)

const

Returns

number of mapped reads in segment tid

uint64_t theplu::yat::omic::InBamFile::n_no_coordinate

(

void

)

const

Returns

number of reads with no coordinate

uint64_t theplu::yat::omic::InBamFile::n_unmapped

(

int

tid

)

const

Typically unmapped reads have same coordinate as its mate.

Returns

number of unmapped reads with segment tid

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,
		hts_itr_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