nvbio::FASTA_reader Struct Reference

Detailed description

A non-incremental FASTA reader, which parses the reads atomically and provides them to the output handler one by one.

Definition at line 124 of file fasta.h.

#include <fasta.h>

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

Constructor & Destructor Documentation

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

inline

constructor

Definition at line 136 of file fasta_inl.h.

nvbio::FASTA_reader::~FASTA_reader ( )

inline

destructor

Definition at line 147 of file fasta_inl.h.

Member Function Documentation

uint8 nvbio::FASTA_reader::get ( )

inline

get the next character, or 255 if EOF

Definition at line 241 of file fasta_inl.h.

template<typename Writer >

uint32 nvbio::FASTA_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 whenever a new read has been parsed
    void push_back(
        const char*     id,
        const uint32    read_length,
        const uint8*    read);
}

Definition at line 182 of file fasta_inl.h.

void nvbio::FASTA_reader::rewind ( )

inline

rewind the file

Definition at line 156 of file fasta_inl.h.

bool nvbio::FASTA_reader::valid ( ) const

inline

return whether the file is valid

Definition at line 136 of file fasta.h.

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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