nvbio::io::ReadDataFile Struct Reference

Detailed description

abstract file-backed ReadDataStream

Definition at line 46 of file reads_priv.h.

#include <reads_priv.h>

Inheritance diagram for nvbio::io::ReadDataFile:

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

Public Methods
virtual	~ReadDataFile ()
virtual ReadData *	next (const uint32 batch_size, const uint32 batch_bps)
virtual bool	is_ok (void)
Public Methods inherited from nvbio::io::ReadDataStream
	ReadDataStream (uint32 truncate_read_len=uint32(-1))
virtual	~ReadDataStream ()

Static Public Members
static const uint32	LONG_READ = 32*1024

Proteced Methods
	ReadDataFile (const uint32 max_reads, const uint32 truncate_read_len, const ReadEncoding flags)
virtual int	nextChunk (ReadDataRAM *output, uint32 max_reads, uint32 max_bps)=0

Protected Members
uint32	m_max_reads
ReadEncoding	m_flags
uint32	m_loaded
FileState	m_file_state

Additional Inherited Members
Public Members inherited from nvbio::io::ReadDataStream
uint32	m_truncate_read_len

Member Enumeration Documentation

enum nvbio::io::ReadDataFile::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 52 of file reads_priv.h.

Constructor & Destructor Documentation

nvbio::io::ReadDataFile::ReadDataFile ( const uint32  max_reads, const uint32  truncate_read_len, const ReadEncoding  flags  )

inlineprotected

Definition at line 68 of file reads_priv.h.

virtual nvbio::io::ReadDataFile::~ReadDataFile ( )

inlinevirtual

virtual destructor

Definition at line 81 of file reads_priv.h.

Member Function Documentation

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

inlinevirtual

returns true if the stream is ready to read from

Implements nvbio::io::ReadDataStream.

Definition at line 89 of file reads_priv.h.

ReadData * nvbio::io::ReadDataFile::next ( const uint32  batch_size, const uint32  batch_bps  )

virtual

grab the next batch of reads into a host memory buffer

Implements nvbio::io::ReadDataStream.

Definition at line 586 of file reads.cpp.

virtual int nvbio::io::ReadDataFile::nextChunk ( ReadDataRAM *  output, uint32  max_reads, uint32  max_bps  )

protectedpure virtual

Implemented in nvbio::io::ReadDataFile_SAM, nvbio::io::ReadDataFile_FASTQ_parser, nvbio::io::ReadDataFile_TXT, and nvbio::io::ReadDataFile_BAM.

Member Data Documentation

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

static

Definition at line 48 of file reads_priv.h.

FileState nvbio::io::ReadDataFile::m_file_state

protected

Definition at line 102 of file reads_priv.h.

ReadEncoding nvbio::io::ReadDataFile::m_flags

protected

Definition at line 98 of file reads_priv.h.

uint32 nvbio::io::ReadDataFile::m_loaded

protected

Definition at line 99 of file reads_priv.h.

uint32 nvbio::io::ReadDataFile::m_max_reads

protected

Definition at line 97 of file reads_priv.h.

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

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