nvbio::io::SequenceDataFile_TXT_gz Struct Reference

Detailed description

Definition at line 105 of file sequence_txt.h.

#include <sequence_txt.h>

Inheritance diagram for nvbio::io::SequenceDataFile_TXT_gz:

Public Methods
	SequenceDataFile_TXT_gz (const char *read_file_name, const Options &options, const uint32 buffer_size=64536u)
	~SequenceDataFile_TXT_gz ()
virtual FileState	fillBuffer (void)
virtual bool	gets (char *buffer, int len)
virtual bool	rewind ()

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 }
Static Public Members inherited from nvbio::io::SequenceDataFile
static const uint32	LONG_READ = 32*1024
Proteced Methods inherited from nvbio::io::SequenceDataFile_TXT
	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)
Protected Members inherited from nvbio::io::SequenceDataFile_TXT
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
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)

Member Function Documentation

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

inlinevirtual

Implements nvbio::io::SequenceDataFile_TXT.

Definition at line 118 of file sequence_txt.h.

---

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