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`
	)

inline

constructor

Definition at line 35 of file fasta_inl.h.

nvbio::FASTA_inc_reader::~FASTA_inc_reader ( )

inline

destructor

Definition at line 45 of file fasta_inl.h.

Member Function Documentation

uint8 nvbio::FASTA_inc_reader::get ( )

inline

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

Writer an 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

inline

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:

E:/git/nvbio/nvbio/fasta/fasta.h
E:/git/nvbio/nvbio/fasta/fasta_inl.h

Detailed description

Public Methods

Constructor & Destructor Documentation

Member Function Documentation