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Proteced Methods | Protected Members | List of all members
nvbio::io::SequenceDataFile_FASTQ_parser Struct Referenceabstract

Detailed description

SequenceDataFile from a FASTQ file contains the code to parse FASTQ files and dump the results into a SequenceDataRAM object file access is done via derived classes

Definition at line 53 of file sequence_fastq.h.

#include <sequence_fastq.h>

Inheritance diagram for nvbio::io::SequenceDataFile_FASTQ_parser:
nvbio::io::SequenceDataFile nvbio::io::SequenceDataInputStream nvbio::io::SequenceDataFile_FASTQ_gz

Proteced Methods

 SequenceDataFile_FASTQ_parser (const char *read_file_name, const SequenceDataFile::Options &options, const uint32 buffer_size=64536u)
virtual int nextChunk (struct SequenceDataEncoder *output, uint32 max_reads, uint32 max_bps)
virtual FileState fillBuffer (void)=0
virtual bool gets (char *buffer, int len)=0
- Proteced Methods inherited from nvbio::io::SequenceDataFile
 SequenceDataFile (const Options &options)

Protected Members

const char * m_file_name
std::vector< char > m_buffer
uint32 m_buffer_size
uint32 m_buffer_pos
uint32 m_line
uint8 m_error_char
std::vector< char > m_name
std::vector< uint8m_read_bp
std::vector< uint8m_read_q
- Protected Members inherited from nvbio::io::SequenceDataFile
Options m_options
uint32 m_loaded
FileState m_file_state

Additional Inherited Members

- Public Types inherited from nvbio::io::SequenceDataFile
enum  FileState {
- Public Methods inherited from nvbio::io::SequenceDataFile
virtual ~SequenceDataFile ()
virtual int next (struct SequenceDataEncoder *encoder, const uint32 batch_size, const uint32 batch_bps)
virtual bool is_ok (void)
- Static Public Members inherited from nvbio::io::SequenceDataFile
static const uint32 LONG_READ = 32*1024

Constructor & Destructor Documentation

nvbio::io::SequenceDataFile_FASTQ_parser::SequenceDataFile_FASTQ_parser ( const char *  read_file_name,
const SequenceDataFile::Options options,
const uint32  buffer_size = 64536u 

Definition at line 56 of file sequence_fastq.h.

Member Function Documentation

virtual FileState nvbio::io::SequenceDataFile_FASTQ_parser::fillBuffer ( void  )
protectedpure virtual
virtual bool nvbio::io::SequenceDataFile_FASTQ_parser::gets ( char *  buffer,
int  len 
protectedpure virtual

Member Data Documentation

std::vector<char> nvbio::io::SequenceDataFile_FASTQ_parser::m_buffer

Definition at line 91 of file sequence_fastq.h.

uint32 nvbio::io::SequenceDataFile_FASTQ_parser::m_buffer_pos

Definition at line 93 of file sequence_fastq.h.

uint32 nvbio::io::SequenceDataFile_FASTQ_parser::m_buffer_size

Definition at line 92 of file sequence_fastq.h.

uint8 nvbio::io::SequenceDataFile_FASTQ_parser::m_error_char

Definition at line 99 of file sequence_fastq.h.

const char* nvbio::io::SequenceDataFile_FASTQ_parser::m_file_name

Definition at line 88 of file sequence_fastq.h.

uint32 nvbio::io::SequenceDataFile_FASTQ_parser::m_line

Definition at line 96 of file sequence_fastq.h.

std::vector<char> nvbio::io::SequenceDataFile_FASTQ_parser::m_name

Definition at line 102 of file sequence_fastq.h.

std::vector<uint8> nvbio::io::SequenceDataFile_FASTQ_parser::m_read_bp

Definition at line 103 of file sequence_fastq.h.

std::vector<uint8> nvbio::io::SequenceDataFile_FASTQ_parser::m_read_q

Definition at line 104 of file sequence_fastq.h.

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