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

class to iterate through a InBamFile More...

#include </scratch/bob/jari/tmp/pristine/yat-0.10.x/yat/omic/BamReadIterator.h>

List of all members.

Classes
class	Actor
class	AllActor
class	IndexActor
struct	IndexDestroyer

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)

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

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

explicit

Creates an iterator pointing to first BamRead in InBamFile.

Parameters:

in	file to iterate over

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

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

---

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

• /scratch/bob/jari/tmp/pristine/yat-0.10.x/yat/omic/BamReadIterator.h