theplu::yat::omic::Pileup< Iterator > Class Template Reference

#include <yat/omic/Pileup.h>

Classes
class	Entry

Public Types
typedef std::list< Entry >::const_iterator	const_iterator
typedef std::list< Entry >::const_reverse_iterator	const_reverse_iterator

Public Member Functions
	Pileup (void)
	Pileup (Iterator first, Iterator last)
const_iterator	begin (void) const
const_iterator	end (void) const
bool	good (void) const
void	increment (void)
	step to next position. More...
size_t	size (void) const
const_reverse_iterator	rbegin (void) const
const_reverse_iterator	rend (void) const
int32_t	tid (void) const
int32_t	pos (void) const
bool	skip_ref (void) const

Related Functions
(Note that these are not member functions.)
template<typename Iterator >
Pileup< Iterator >	make_pileup (Iterator first, Iterator last)

Detailed Description

template<typename Iterator>
class theplu::yat::omic::Pileup< Iterator >

Pileup takes a range of BamReads and pile them up on the current position. User can investigate the pile of reads at current (locus) position via begin() and end(), which provide access to reads at current position. The position can be incremented and in that way the user can investigate each position of the genome.

Since

new in yat 0.13

Type Requirments:

• Iterator is a Readable Iterator
• Iterator is a Single Pass Iterator
• value_type is convertible to BamRead

Member Typedef Documentation

const_iterator

template<typename Iterator>

typedef std::list<Entry>::const_iterator theplu::yat::omic::Pileup< Iterator >::const_iterator

Const iterator that can be used to iterate over reads that overlap with current position (as defined by tid() and pos()).

const_reverse_iterator

template<typename Iterator>

typedef std::list<Entry>::const_reverse_iterator theplu::yat::omic::Pileup< Iterator >::const_reverse_iterator

Same as const_iterator but iterates reversed.

See also

rbegin(void) rend(void)

Since

new in yat 0.17

Constructor & Destructor Documentation

Pileup() [1/2]

template<typename Iterator>

theplu::yat::omic::Pileup< Iterator >::Pileup ( void  )

inline

Create an empty Pileup

Pileup() [2/2]

template<typename Iterator >

theplu::yat::omic::Pileup< Iterator >::Pileup	(	Iterator	first,
		Iterator	last
	)

Create a Pileup that will use reads in range [first, last). The range must be sorted as defined by BamLessPos.

Iterator is a Readable Iterator.

Member Function Documentation

begin()

template<typename Iterator >

Pileup< Iterator >::const_iterator theplu::yat::omic::Pileup< Iterator >::begin

(

void

)

const

Returns

an iterator that points to the first Entry in Pileup.

Iteration is done in same order as range provided in constructor. Reads that do not overlap with current position (tid:pos) are ignored.

end()

template<typename Iterator >

Pileup< Iterator >::const_iterator theplu::yat::omic::Pileup< Iterator >::end

(

void

)

const

Returns

an iterator that points one past the last element in the Pileup.

good()

template<typename Iterator>

bool theplu::yat::omic::Pileup< Iterator >::good ( void  ) const

inline

Returns

true if there are more positions to increment into

increment()

template<typename Iterator >

void theplu::yat::omic::Pileup< Iterator >::increment

(

void

)

step to next position.

If any Entry has a insertion at current position, increment each Entry that has an insertion. Otherwise increment to next position and update each Entry accordingly.

If the position is not covered by any read, the Pileup fastforward to next covered locus.

pos()

template<typename Iterator>

int32_t theplu::yat::omic::Pileup< Iterator >::pos ( void  ) const

inline

Returns

position

When in a skip_ref region, the position of the next reference is returned.

rbegin()

template<typename Iterator >

Pileup< Iterator >::const_reverse_iterator theplu::yat::omic::Pileup< Iterator >::rbegin

(

void

)

const

Returns

an iterator that points to the last Entry in Pileup.

Iteration is done in reversed order; othwerwise behaves as begin(void)

Since

new in yat 0.17

rend()

template<typename Iterator >

Pileup< Iterator >::const_reverse_iterator theplu::yat::omic::Pileup< Iterator >::rend

(

void

)

const

Returns

const reverse iterator to reverse end

See also

end(void)

rbegin(void)

Since

new in yat 0.17

size()

template<typename Iterator >

size_t theplu::yat::omic::Pileup< Iterator >::size

(

void

)

const

Returns

number of reads in pileup. Reads with a deletion of the current position is also counted.

Since

new in yat 0.17

skip_ref()

template<typename Iterator >

bool theplu::yat::omic::Pileup< Iterator >::skip_ref

(

void

)

const

Returns

true if position does not exist in reference, i.e., inserted region.

tid()

template<typename Iterator>

int32_t theplu::yat::omic::Pileup< Iterator >::tid ( void  ) const

inline

Returns

template id as defined in bam file header

Friends And Related Function Documentation

make_pileup()

template<typename Iterator >

Pileup< Iterator > make_pileup ( Iterator  first, Iterator  last  )

related

Since

new in yat 0.13

---

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

• yat/omic/Pileup.h