kaori::FastqReader< Pointer_ > Class Template Reference

Stream reads from a FASTQ file. More...

#include <FastqReader.hpp>

Public Member Functions
	FastqReader (Pointer_ p)
bool	operator() ()
const std::vector< char > &	get_sequence () const
const std::vector< char > &	get_name () const

Detailed Description

template<typename Pointer_>
class kaori::FastqReader< Pointer_ >

Stream reads from a FASTQ file.

Pretty much what it says on the tin. Multi-line sequence and quality strings are supported. The name of each read is only considered up to the first whitespace.

Template Parameters

Pointer_

Pointer to a class that serves as a source of input bytes. The pointed-to class should satisfy the byteme::Reader interface; it may also be a concrete byteme::Reader subclass to enable devirtualization. Either a smart or raw pointer may be supplied depending on how the caller wants to manage the lifetime of the pointed-to object.

Constructor & Destructor Documentation

FastqReader()

template<typename Pointer_ >

kaori::FastqReader< Pointer_ >::FastqReader ( Pointer_ p )

inline

Parameters

p	Pointer to a text stream.

Member Function Documentation

get_name()

template<typename Pointer_ >

const std::vector< char > & kaori::FastqReader< Pointer_ >::get_name ( ) const

inline

Returns

Vector containing the name for the current read. Note that the name is considered to end at the first whitespace on the line. This should only be called if load() returns true.

get_sequence()

template<typename Pointer_ >

const std::vector< char > & kaori::FastqReader< Pointer_ >::get_sequence ( ) const

inline

Returns

Vector containing the sequence for the current read. This should only be called if load() returns true.

operator()()

template<typename Pointer_ >

bool kaori::FastqReader< Pointer_ >::operator() ( )

inline

Extract details for the next read in the file.

Returns

Whether or not a record was successfully extracted. If true, get_sequence() and get_name() may be used. If false, the end of the file was reached.

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

• kaori/FastqReader.hpp