gkarrays::pairedEndReadIterator Class Reference

#include <readsReader.h>

Inheritance diagram for gkarrays::pairedEndReadIterator:

List of all members.

Public Member Functions
	pairedEndReadIterator (char *filename1, char *filename2, uint k=0, uint length=0, bool printWarnings=false)
	pairedEndReadIterator (const pairedEndReadIterator &mit)
virtual	~pairedEndReadIterator ()
virtual readIterator &	operator++ ()
virtual pairedEndReadIterator	operator++ (int)
virtual kseq_t &	operator* ()
virtual size_t	getLength ()
virtual char *	getName ()
readIterator &	getPair ()
virtual char *	getQuality ()
virtual uint	getReadNumber ()
virtual char *	getSequence ()
virtual bool	isFinished ()
bool	isTheFirstMemberOfPair ()

---

Detailed Description

pairedEndReadIterator allows to retrieve information on each read by traversing them in order, one after one in the case of paired-end reads. If the k-mer length or the read length are given, only reads that are long enough to fulfill those values are considered.

---

Constructor & Destructor Documentation

gkarrays::pairedEndReadIterator::pairedEndReadIterator	(	char *	filename1,
		char *	filename2,
		uint	k = 0,
		uint	length = 0,
		bool	printWarnings = false
	)

Constructor. Reads are retrieved from the given file.

Parameters:

filename1,:	file we must iterate on
filename2,:	second file (for paired-end) we must iterate on
k,:	k-mer length used (0 if unknown or not applicable)
length,:	Read length (0 for variable)
printWarnings,:	if true print warnings when skipping a read

gkarrays::pairedEndReadIterator::pairedEndReadIterator

(

const pairedEndReadIterator &

mit

)

Copy constructor

gkarrays::pairedEndReadIterator::~pairedEndReadIterator

(

)

[virtual]

Destructor

---

Member Function Documentation

size_t gkarrays::pairedEndReadIterator::getLength

(

)

[virtual]

Returns:

the length of the read

Implements gkarrays::readIterator.

char * gkarrays::pairedEndReadIterator::getName

(

)

[virtual]

Returns:

the name of the read

Implements gkarrays::readIterator.

readIterator & gkarrays::pairedEndReadIterator::getPair

(

)

Returns:

the paired iterator with the current one

char * gkarrays::pairedEndReadIterator::getQuality

(

)

[virtual]

Returns:

the quality of the read

Implements gkarrays::readIterator.

uint gkarrays::pairedEndReadIterator::getReadNumber

(

)

[virtual]

Returns:

the number of the read in the file

Implements gkarrays::readIterator.

char * gkarrays::pairedEndReadIterator::getSequence

(

)

[virtual]

Returns:

the sequence of the read

Implements gkarrays::readIterator.

bool gkarrays::pairedEndReadIterator::isFinished

(

)

[virtual]

Returns:

true iff we have read the whole file

Implements gkarrays::readIterator.

bool gkarrays::pairedEndReadIterator::isTheFirstMemberOfPair

(

)

Returns:

true if the current read is the first member of the pair

kseq_t & gkarrays::pairedEndReadIterator::operator*

(

)

[virtual]

Returns:

the kseq_t related to the current read

Implements gkarrays::readIterator.

readIterator & gkarrays::pairedEndReadIterator::operator++

(

)

[virtual]

Go to next sequence prefix

Implements gkarrays::readIterator.

pairedEndReadIterator gkarrays::pairedEndReadIterator::operator++

(

int

)

[virtual]

Go to next sequence postfix

---

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

• readsReader.h
• readsReader.cpp