NVBIO
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
Public Methods | List of all members
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
Writeran 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.


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