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

#include <yat/omic/BamPairIterator.h>

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

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

Friends
class	boost::iterator_core_access

Related Functions
(Note that these are not member functions.)
template<typename Base >
BamPairIterator< Base >	bam_pair_iterator (Base base, Base end)
template<typename Base >
BamPairIterator< Base >	bam_pair_iterator (Base end)
template<typename Base >
BamPairIterator2< Base >	bam_pair_iterator2 (Base base, Base end)
template<typename Base >
BamPairIterator2< Base >	bam_pair_iterator2 (Base end)

Detailed Description

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

Since

New in yat 0.12

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 convenient way to access the pairs rather than the reads individually. When BamPairIterator is incremented, rather than just step to next element in [begin, end), BamPairIterator keeps stepping until it finds a read whose mate it has already seen, and operator* return the pair of BamReads.

The resulting iterator is sorted with respect to second().

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

Constructor & Destructor Documentation

BamPairIterator()

template<typename Base >

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

explicit

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

See also

bam_pair_iterator

Note

Input range [first, last ) must be sorted or behaviour is undefined.

Member Function Documentation

operator->()

template<typename Base>

BamPairIterator::pointer theplu::yat::omic::BamPairIterator< 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*.

Friends And Related Function Documentation

bam_pair_iterator() [1/2]

template<typename Base >

BamPairIterator< Base > bam_pair_iterator ( Base  base, Base  end  )

related

Convenient function to create BamPairIterator

bam_pair_iterator() [2/2]

template<typename Base >

BamPairIterator< Base > bam_pair_iterator ( Base  end )

related

Convenient function to create BamPairIterator that works on empty range. Equivalent to bam_pair_iterator(end, end).

bam_pair_iterator2() [1/2]

template<typename Base >

BamPairIterator2< Base > bam_pair_iterator2 ( Base  base, Base  end  )

related

Convenient function to create BamPairIterator

bam_pair_iterator2() [2/2]

template<typename Base >

BamPairIterator2< Base > bam_pair_iterator2 ( Base  end )

related

Convenient function to create BamPairIterator that works on empty range. Equivalent to bam_pair_iterator(end, end).

---

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

• yat/omic/BamPairIterator.h
• yat/omic/BamPairIterator2.h