nvbio::io::SequenceDataFile_TXT Struct Reference

Detailed description

Definition at line 52 of file sequence_txt.h.

#include <sequence_txt.h>

Inheritance diagram for nvbio::io::SequenceDataFile_TXT:

Proteced Methods
	SequenceDataFile_TXT (const char *read_file_name, const 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< uint8 >	m_read_bp
std::vector< uint8 >	m_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 {   FILE_NOT_READY, FILE_OPEN_FAILED, FILE_OK, FILE_EOF,   FILE_STREAM_ERROR, FILE_PARSE_ERROR }
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
Related Functions inherited from nvbio::io::SequenceDataInputStream
int	next (const Alphabet alphabet, SequenceDataHost *data, SequenceDataInputStream *stream, const uint32 batch_size, const uint32 batch_bps=uint32(-1))
int	append (const Alphabet alphabet, SequenceDataHost *data, SequenceDataInputStream *stream, const uint32 batch_size, const uint32 batch_bps=uint32(-1))
int	skip (SequenceDataInputStream *stream, const uint32 batch_size)
SequenceDataInputStream *	open_sequence_file (const char *sequence_file_name, const QualityEncoding qualities=Phred33, const uint32 max_seqs=uint32(-1), const uint32 max_sequence_len=uint32(-1), const SequenceEncoding flags=FORWARD, const uint32 trim3=0, const uint32 trim5=0)

Constructor & Destructor Documentation

nvbio::io::SequenceDataFile_TXT::SequenceDataFile_TXT ( const char *  read_file_name, const Options &  options, const uint32  buffer_size = 64536u  )

inlineprotected

Definition at line 55 of file sequence_txt.h.

Member Function Documentation

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

protectedpure virtual

Implemented in nvbio::io::SequenceDataFile_TXT_gz.

virtual bool nvbio::io::SequenceDataFile_TXT::gets ( char *  buffer, int  len  )

protectedpure virtual

Implemented in nvbio::io::SequenceDataFile_TXT_gz.

Member Data Documentation

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

protected

Definition at line 87 of file sequence_txt.h.

uint32 nvbio::io::SequenceDataFile_TXT::m_buffer_pos

protected

Definition at line 89 of file sequence_txt.h.

uint32 nvbio::io::SequenceDataFile_TXT::m_buffer_size

protected

Definition at line 88 of file sequence_txt.h.

uint8 nvbio::io::SequenceDataFile_TXT::m_error_char

protected

Definition at line 95 of file sequence_txt.h.

const char* nvbio::io::SequenceDataFile_TXT::m_file_name

protected

Definition at line 84 of file sequence_txt.h.

uint32 nvbio::io::SequenceDataFile_TXT::m_line

protected

Definition at line 92 of file sequence_txt.h.

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

protected

Definition at line 98 of file sequence_txt.h.

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

protected

Definition at line 99 of file sequence_txt.h.

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

protected

Definition at line 100 of file sequence_txt.h.

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

• E:/git/nvbio/nvbio/io/sequence/sequence_txt.h
• E:/git/nvbio/nvbio/io/sequence/sequence_txt.cpp