theplu::yat::omic::BamReadIterator Class Reference

class to iterate through a InBamFile More...

#include <yat/omic/BamReadIterator.h>

Inheritance diagram for theplu::yat::omic::BamReadIterator:

Public Member Functions
	BamReadIterator (void)
	Contructs end of file iterator.
	BamReadIterator (InBamFile &in)
	BamReadIterator (InBamFile &in, int32_t tid, int32_t start, int32_t end)
	BamReadIterator (InBamFile &in, int32_t tid, int32_t start=0)
	BamReadIterator (InBamFile &in, const BamRegion &region)
	BamReadIterator (InBamFile &in, const std::vector< BamRegion > &regions)

Friends
class	boost::iterator_core_access

Detailed Description

class to iterate through a InBamFile

Iterator is a single pass Input Iterator which means iterator can only be used read bam file. If creating two iterators working on the same InBamFile, the iterators are not independent of each other. Incrementing one, the behaviour of the other is undefined.

Iterator can either be constructed to iterate over entire bam file or if a region is specified only over that region. When no more elements are available, iterator turns into a end-of-file iterator and is no longer dereferencable.

See also

InBamFile

Since

New in yat 0.10

Constructor & Destructor Documentation

BamReadIterator() [1/5]

theplu::yat::omic::BamReadIterator::BamReadIterator ( InBamFile &  in )

explicit

Creates an iterator pointing to first BamRead in InBamFile.

Parameters

in	file to iterate over

BamReadIterator() [2/5]

theplu::yat::omic::BamReadIterator::BamReadIterator	(	InBamFile &	in,
		int32_t	tid,
		int32_t	start,
		int32_t	end
	)

Iterator that walks over specified region. Iterator iterates over all BamReads in file in that overlap with specified region and then it turns into an end-of-region iterator.

This function requires an index file is available, see InBamFile::index().

All reads iterated over overlap with defined region, in other words, iter->tid == tid; iter->pos() < end and iter->end()

start

Parameters

in	file to iterate over
tid	segment (chromosome) to iterate over
start	left most position of specified region
end	right most position of specified region

See also

For use with large chromosomes for with int32_t is not sufficient, see BamReadIterator(InBamFile&, const BamRegion&);

BamReadIterator() [3/5]

theplu::yat::omic::BamReadIterator::BamReadIterator	(	InBamFile &	in,
		int32_t	tid,
		int32_t	start = 0
	)

Iterator that walks from tid:start to end of chromosome and then it turns into an end-of-region iterator.

This function requires an index file is available, see InBamFile::index().

All reads iterated over overlap with defined region, in other words, iter->tid == tid; iter->end() > start

Parameters

in	file to iterate over
tid	segment (chromosome) to iterate over
start	left most position of specified region

Since

New in yat 0.15

See also

For use with large chromosomes for with int32_t is not sufficient, see BamReadIterator(InBamFile&, const BamRegion&);

BamReadIterator() [4/5]

theplu::yat::omic::BamReadIterator::BamReadIterator	(	InBamFile &	in,
		const BamRegion &	region
	)

Iterator that walks over specified region. Iterator iterates over all BamReads in file in that overlap with specified region and then it turns into an end-of-region iterator.

This function requires an index file is available, see InBamFile::index().

All reads iterated over overlap with defined region, in other words, iter->tid == tid; iter->pos() < end and iter->end()

start

Parameters

in	file to iterate over
region	defining the genomic region

Since

New in yat 0.21

BamReadIterator() [5/5]

theplu::yat::omic::BamReadIterator::BamReadIterator	(	InBamFile &	in,
		const std::vector< BamRegion > &	regions
	)

Create an iterator that can be used to iterate over reads from multiple regions. The reads are iterated over in a sorted fashion and reads are not multiple times even if regions is sorted and/or have overlapping regions.

Since

New in yat 0.21

---

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

• yat/omic/BamReadIterator.h