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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_streamthe 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)


Definition at line 100 of file fastq_inl.h.

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


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 ( )

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
Writerthe 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.

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