nvbio::io::ReadDataFile_FASTQ_parser Struct Reference

Detailed description

Definition at line 51 of file reads_fastq.h.

#include <reads_fastq.h>

Inheritance diagram for nvbio::io::ReadDataFile_FASTQ_parser:

Proteced Methods
	ReadDataFile_FASTQ_parser (const char *read_file_name, const QualityEncoding quality_encoding, const uint32 max_reads, const uint32 max_read_len, const ReadEncoding flags, const uint32 buffer_size=64536u)
virtual int	nextChunk (ReadDataRAM *output, uint32 max_reads, uint32 max_bps)
virtual FileState	fillBuffer (void)=0
Proteced Methods inherited from nvbio::io::ReadDataFile
	ReadDataFile (const uint32 max_reads, const uint32 truncate_read_len, const ReadEncoding flags)

Protected Members
const char *	m_file_name
QualityEncoding	m_quality_encoding
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< uint8 >	m_read_bp
std::vector< uint8 >	m_read_q
Protected Members inherited from nvbio::io::ReadDataFile
uint32	m_max_reads
ReadEncoding	m_flags
uint32	m_loaded
FileState	m_file_state

Additional Inherited Members
Public Types inherited from nvbio::io::ReadDataFile
enum	FileState {   FILE_NOT_READY, FILE_OPEN_FAILED, FILE_OK, FILE_EOF,   FILE_STREAM_ERROR, FILE_PARSE_ERROR }
Public Methods inherited from nvbio::io::ReadDataFile
virtual	~ReadDataFile ()
virtual ReadData *	next (const uint32 batch_size, const uint32 batch_bps)
virtual bool	is_ok (void)
Public Members inherited from nvbio::io::ReadDataStream
uint32	m_truncate_read_len
Static Public Members inherited from nvbio::io::ReadDataFile
static const uint32	LONG_READ = 32*1024

Constructor & Destructor Documentation

nvbio::io::ReadDataFile_FASTQ_parser::ReadDataFile_FASTQ_parser ( const char *  read_file_name, const QualityEncoding  quality_encoding, const uint32  max_reads, const uint32  max_read_len, const ReadEncoding  flags, const uint32  buffer_size = 64536u  )

inlineprotected

Definition at line 54 of file reads_fastq.h.

Member Function Documentation

virtual FileState nvbio::io::ReadDataFile_FASTQ_parser::fillBuffer ( void  )

protectedpure virtual

Implemented in nvbio::io::ReadDataFile_FASTQ_gz.

Member Data Documentation

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

protected

Definition at line 92 of file reads_fastq.h.

uint32 nvbio::io::ReadDataFile_FASTQ_parser::m_buffer_pos

protected

Definition at line 94 of file reads_fastq.h.

uint32 nvbio::io::ReadDataFile_FASTQ_parser::m_buffer_size

protected

Definition at line 93 of file reads_fastq.h.

uint8 nvbio::io::ReadDataFile_FASTQ_parser::m_error_char

protected

Definition at line 100 of file reads_fastq.h.

const char* nvbio::io::ReadDataFile_FASTQ_parser::m_file_name

protected

Definition at line 87 of file reads_fastq.h.

uint32 nvbio::io::ReadDataFile_FASTQ_parser::m_line

protected

Definition at line 97 of file reads_fastq.h.

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

protected

Definition at line 103 of file reads_fastq.h.

QualityEncoding nvbio::io::ReadDataFile_FASTQ_parser::m_quality_encoding

protected

Definition at line 89 of file reads_fastq.h.

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

protected

Definition at line 104 of file reads_fastq.h.

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

protected

Definition at line 105 of file reads_fastq.h.

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

• E:/git/nvbio/nvbio/io/reads/reads_fastq.h
• E:/git/nvbio/nvbio/io/reads/reads_fastq.cpp