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nvbio::io::ReadDataFile Struct Referenceabstract

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:
nvbio::io::ReadDataStream nvbio::io::ReadDataFile_BAM nvbio::io::ReadDataFile_FASTQ_parser nvbio::io::ReadDataFile_SAM nvbio::io::ReadDataFile_TXT nvbio::io::ReadDataFile_FASTQ_gz nvbio::io::ReadDataFile_TXT_gz

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 ReadDatanext (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 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

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.


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