gkarrays::singleReadIterator Class Reference

#include <readsReader.h>

Inheritance diagram for gkarrays::singleReadIterator:

List of all members.

Public Member Functions
	singleReadIterator (char *filename, uint k=0, uint length=0, bool printWarnings=false, bool autoDiscard=true, bool autoFirstIteration=true)
	singleReadIterator (kseq_t *seq, uint k=0, uint length=0)
	singleReadIterator (const singleReadIterator &mit)
	~singleReadIterator ()
virtual readIterator &	operator++ ()
virtual singleReadIterator	operator++ (int)
virtual kseq_t &	operator* ()
virtual char *	getName ()
virtual char *	getQuality ()
virtual char *	getSequence ()
virtual uint	getReadNumber ()
virtual size_t	getLength ()
virtual bool	isFinished ()
bool	isDiscarded ()
void	setAutoDiscard (bool value)

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Detailed Description

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

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Constructor & Destructor Documentation

gkarrays::singleReadIterator::singleReadIterator	(	char *	filename,
		uint	k = 0,
		uint	length = 0,
		bool	printWarnings = false,
		bool	autoDiscard = true,
		bool	autoFirstIteration = true
	)

Constructor. Reads are retrieved from the given file.

Parameters:

filename,:	file 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
autoDiscard,:	if true skip automatically bad reads
autoFirstIteration,:	automatically perform the first iteration (meaning that it initializes the data structure)

gkarrays::singleReadIterator::singleReadIterator	(	kseq_t *	seq,
		uint	k = 0,
		uint	length = 0
	)

Constructor. singleReadIterator starts at the given sequence.

Parameters:

seq,:	the sequence to start at.
k,:	k-mer length used (0 if unknown or not applicable)
length,:	Read length (0 for variable)

gkarrays::singleReadIterator::singleReadIterator

(

const singleReadIterator &

mit

)

Copy constructor

gkarrays::singleReadIterator::~singleReadIterator

(

)

Destructor

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Member Function Documentation

size_t gkarrays::singleReadIterator::getLength

(

)

[virtual]

Returns:

the length of the read

Implements gkarrays::readIterator.

char * gkarrays::singleReadIterator::getName

(

)

[virtual]

Returns:

the name of the read

Implements gkarrays::readIterator.

char * gkarrays::singleReadIterator::getQuality

(

)

[virtual]

Returns:

the quality of the read

Implements gkarrays::readIterator.

uint gkarrays::singleReadIterator::getReadNumber

(

)

[virtual]

Returns:

the number of the read in the file

Implements gkarrays::readIterator.

char * gkarrays::singleReadIterator::getSequence

(

)

[virtual]

Returns:

the sequence of the read

Implements gkarrays::readIterator.

bool gkarrays::singleReadIterator::isDiscarded

(

)

Returns:

true if real tag length is inferior to k or to wanted length

bool gkarrays::singleReadIterator::isFinished

(

)

[virtual]

Returns:

true iff we have read the whole file

Implements gkarrays::readIterator.

kseq_t & gkarrays::singleReadIterator::operator*

(

)

[virtual]

Returns:

the kseq_t related to the current read

Implements gkarrays::readIterator.

readIterator & gkarrays::singleReadIterator::operator++

(

)

[virtual]

Go to next sequence prefix

Implements gkarrays::readIterator.

singleReadIterator gkarrays::singleReadIterator::operator++

(

int

)

[virtual]

Go to next sequence postfix

void gkarrays::singleReadIterator::setAutoDiscard

(

bool

value

)

Parameters:

value

Value to set AutoDiscard mode

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

• readsReader.h
• readsReader.cpp