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nvbio::FASTA_inc_reader Struct Reference

Detailed description

An incremental FASTA reader, which parses the reads incrementally without ever storing them internally, and providing them to the output handler base by base.

Definition at line 69 of file fasta.h.

#include <fasta.h>

Public Methods

 FASTA_inc_reader (const char *filename, const uint32 buffer_size=64536u)
 ~FASTA_inc_reader ()
bool valid () const
template<typename Writer >
uint32 read (const uint32 n_reads, Writer &writer)
uint8 get ()

Constructor & Destructor Documentation

nvbio::FASTA_inc_reader::FASTA_inc_reader ( const char *  filename,
const uint32  buffer_size = 64536u 


Definition at line 35 of file fasta_inl.h.

nvbio::FASTA_inc_reader::~FASTA_inc_reader ( )


Definition at line 45 of file fasta_inl.h.

Member Function Documentation

uint8 nvbio::FASTA_inc_reader::get ( )

get the next character, or 255 if EOF

Definition at line 123 of file fasta_inl.h.

template<typename Writer >
uint32 nvbio::FASTA_inc_reader::read ( const uint32  n_reads,
Writer &  writer 

read a batch of bp reads

Template Parameters
Writeran output handler class, which must implement the following interface:
struct Writer
// called before starting to parse a new read
void begin_read();
// called upon completion of a single read
void end_read();
// provide the next character of the read id
void id(const char c);
// provide the next base of the read
void read(const char c);

Definition at line 74 of file fasta_inl.h.

bool nvbio::FASTA_inc_reader::valid ( ) const

return whether the file is valid

Definition at line 81 of file fasta.h.

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