nvbio::io::SequenceDataFile Struct Reference

Detailed description

abstract file-backed SequenceDataStream

Definition at line 48 of file sequence_priv.h.

#include <sequence_priv.h>

Inheritance diagram for nvbio::io::SequenceDataFile:

Classes
struct	Options

Public Types
enum	FileState {   FILE_NOT_READY, FILE_OPEN_FAILED, FILE_OK, FILE_EOF,   FILE_STREAM_ERROR, FILE_PARSE_ERROR }

Public Methods
virtual	~SequenceDataFile ()
virtual int	next (struct SequenceDataEncoder *encoder, const uint32 batch_size, const uint32 batch_bps)
virtual bool	is_ok (void)
Public Methods inherited from nvbio::io::SequenceDataInputStream
virtual	~SequenceDataInputStream ()
virtual bool	rewind ()=0

Static Public Members
static const uint32	LONG_READ = 32*1024

Proteced Methods
	SequenceDataFile (const Options &options)
virtual int	nextChunk (struct SequenceDataEncoder *encoder, uint32 max_reads, uint32 max_bps)=0

Protected Members
Options	m_options
uint32	m_loaded
FileState	m_file_state

Additional Inherited Members
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 Enumeration Documentation

enum nvbio::io::SequenceDataFile::FileState

enum describing various possible file states

Enumerator
FILE_NOT_READY
FILE_OPEN_FAILED
FILE_OK
FILE_EOF
FILE_STREAM_ERROR
FILE_PARSE_ERROR

Definition at line 72 of file sequence_priv.h.

Constructor & Destructor Documentation

nvbio::io::SequenceDataFile::SequenceDataFile ( const Options &  options)

inlineprotected

Definition at line 88 of file sequence_priv.h.

virtual nvbio::io::SequenceDataFile::~SequenceDataFile ( )

inlinevirtual

virtual destructor

Definition at line 99 of file sequence_priv.h.

Member Function Documentation

virtual bool nvbio::io::SequenceDataFile::is_ok ( void  )

inlinevirtual

returns true if the stream is ready to read from

Implements nvbio::io::SequenceDataInputStream.

Definition at line 107 of file sequence_priv.h.

int nvbio::io::SequenceDataFile::next ( struct SequenceDataEncoder *  encoder, const uint32  batch_size, const uint32  batch_bps  )

virtual

grab the next batch of reads into a host memory buffer

Implements nvbio::io::SequenceDataInputStream.

Definition at line 44 of file sequence_priv.cpp.

virtual int nvbio::io::SequenceDataFile::nextChunk ( struct SequenceDataEncoder *  encoder, uint32  max_reads, uint32  max_bps  )

protectedpure virtual

Implemented in nvbio::io::SequenceDataFile_SAM, nvbio::io::SequenceDataFile_FASTQ_parser, nvbio::io::SequenceDataFile_TXT, nvbio::io::SequenceDataFile_BAM, and nvbio::io::SequenceDataFile_FASTA_gz.

Member Data Documentation

const uint32 nvbio::io::SequenceDataFile::LONG_READ = 32*1024

static

Definition at line 68 of file sequence_priv.h.

FileState nvbio::io::SequenceDataFile::m_file_state

protected

Definition at line 119 of file sequence_priv.h.

uint32 nvbio::io::SequenceDataFile::m_loaded

protected

Definition at line 116 of file sequence_priv.h.

Options nvbio::io::SequenceDataFile::m_options

protected

Definition at line 115 of file sequence_priv.h.

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

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