nvbio::FASTQ_reader< FASTQ_stream > Struct Template Reference

Detailed description

template< typename FASTQ_stream>
struct nvbio::FASTQ_reader< FASTQ_stream >

A simple FASTQ_reader, templated over an input stream class

Template Parameters

FASTQ_stream

the templated input stream, which must provide a single method:

struct FASTQ_stream
{
    // consume and return the next character
    uint8 get();
}

Definition at line 163 of file fastq.h.

#include <fastq.h>

Public Methods
	FASTQ_reader (FASTQ_stream &stream)
	~FASTQ_reader ()
template<typename Writer >
uint32	read (const uint32 n_reads, Writer &writer)
uint8	get ()
void	error_string (char *error)

Constructor & Destructor Documentation

template<typename FASTQ_stream >

nvbio::FASTQ_reader< FASTQ_stream >::FASTQ_reader

(

FASTQ_stream &

stream)

constructor

Definition at line 100 of file fastq_inl.h.

template<typename FASTQ_stream>

nvbio::FASTQ_reader< FASTQ_stream >::~FASTQ_reader ( )

inline

destructor

Definition at line 171 of file fastq.h.

Member Function Documentation

template<typename FASTQ_stream >

void nvbio::FASTQ_reader< FASTQ_stream >::error_string

(

char *

error)

return the error string

Definition at line 234 of file fastq_inl.h.

template<typename FASTQ_stream>

uint8 nvbio::FASTQ_reader< FASTQ_stream >::get ( )

inline

get the next character, or 255 if EOF

Definition at line 193 of file fastq.h.

template<typename FASTQ_stream >

template<typename Writer >

uint32 nvbio::FASTQ_reader< FASTQ_stream >::read	(	const uint32	n_reads,
		Writer &	writer
	)

read a batch of bp reads

Template Parameters

Writer

the output FASTQ writer, which must implement the following interface struct Writer { void push_back( const uint32 read_length, const char* read_name, const uint8* bps, const uint8* qualities); }

Definition at line 110 of file fastq_inl.h.

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

• E:/git/nvbio/nvbio/fastq/fastq.h
• E:/git/nvbio/nvbio/fastq/fastq_inl.h