theplu::yat::omic::BamPairIterator2< Base > Class Template Reference

#include <yat/omic/BamPairIterator2.h>

Inheritance diagram for theplu::yat::omic::BamPairIterator2< Base >:

Public Member Functions
	BamPairIterator2 (void)
	default constructor
	BamPairIterator2 (Base begin, Base end)
BamPairIterator2::pointer	operator-> (void) const

Friends
class	boost::iterator_core_access

Detailed Description

template<typename Base>
class theplu::yat::omic::BamPairIterator2< Base >

Type Requirments:

• Base is a Readable Iterator
• Base is a Single Pass Iterator
• value_type is BamRead

This iterator works on a sorted range [begin, end) and provides a covenient way to access the pairs rather than the reads individually. The pairs are iterated such that they appear sorted with respect to first().

If read pairs with large isize (tlen) are included the iterator will consumer a lot of memory because iterator does store virtually all reads in the underlying range between the current first() and its mate, second().

Note that BamPairIterator2 is a single-pass iterator, i.e., once it is incremented the behaviour of its copies is undefined.

See also

BamPairBuffer

Since

New in yat 0.18

Constructor & Destructor Documentation

BamPairIterator2()

template<typename Base >

theplu::yat::omic::BamPairIterator2< Base >::BamPairIterator2 ( Base  begin, Base  end  )

explicit

Creates an iterator that will work on [begin, end).

Note

Input range [begin, end ) must be sorted or behaviour is undefined.

Member Function Documentation

operator->()

template<typename Base>

BamPairIterator2::pointer theplu::yat::omic::BamPairIterator2< Base >::operator-> ( void  ) const

inline

This is workaround implementation of operator-> when implementation in base class (boost) does not compile. This implementation may be slow, so when using old boost it often prefereble to use operator*.

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

• yat/omic/BamPairIterator2.h