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Proteced Methods | Protected Members | List of all members
nvbio::io::ReadDataFile_TXT Struct Referenceabstract

Detailed description

Definition at line 51 of file reads_txt.h.

#include <reads_txt.h>

Inheritance diagram for nvbio::io::ReadDataFile_TXT:
nvbio::io::ReadDataFile nvbio::io::ReadDataStream nvbio::io::ReadDataFile_TXT_gz

Proteced Methods

 ReadDataFile_TXT (const char *read_file_name, const QualityEncoding quality_encoding, const uint32 max_reads, const uint32 max_read_len, const ReadEncoding flags, const uint32 buffer_size=64536u)
 
virtual int nextChunk (ReadDataRAM *output, uint32 max_reads, uint32 max_bps)
 
virtual FileState fillBuffer (void)=0
 
- Proteced Methods inherited from nvbio::io::ReadDataFile
 ReadDataFile (const uint32 max_reads, const uint32 truncate_read_len, const ReadEncoding flags)
 

Protected Members

const char * m_file_name
 
QualityEncoding m_quality_encoding
 
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< uint8m_read_bp
 
std::vector< uint8m_read_q
 
- Protected Members inherited from nvbio::io::ReadDataFile
uint32 m_max_reads
 
ReadEncoding m_flags
 
uint32 m_loaded
 
FileState m_file_state
 

Additional Inherited Members

- Public Types inherited from nvbio::io::ReadDataFile
enum  FileState {
  FILE_NOT_READY, FILE_OPEN_FAILED, FILE_OK, FILE_EOF,
  FILE_STREAM_ERROR, FILE_PARSE_ERROR
}
 
- Public Methods inherited from nvbio::io::ReadDataFile
virtual ~ReadDataFile ()
 
virtual ReadDatanext (const uint32 batch_size, const uint32 batch_bps)
 
virtual bool is_ok (void)
 
- Public Members inherited from nvbio::io::ReadDataStream
uint32 m_truncate_read_len
 
- Static Public Members inherited from nvbio::io::ReadDataFile
static const uint32 LONG_READ = 32*1024
 

Constructor & Destructor Documentation

nvbio::io::ReadDataFile_TXT::ReadDataFile_TXT ( const char *  read_file_name,
const QualityEncoding  quality_encoding,
const uint32  max_reads,
const uint32  max_read_len,
const ReadEncoding  flags,
const uint32  buffer_size = 64536u 
)
inlineprotected

Definition at line 54 of file reads_txt.h.

Member Function Documentation

virtual FileState nvbio::io::ReadDataFile_TXT::fillBuffer ( void  )
protectedpure virtual

Member Data Documentation

std::vector<char> nvbio::io::ReadDataFile_TXT::m_buffer
protected

Definition at line 89 of file reads_txt.h.

uint32 nvbio::io::ReadDataFile_TXT::m_buffer_pos
protected

Definition at line 91 of file reads_txt.h.

uint32 nvbio::io::ReadDataFile_TXT::m_buffer_size
protected

Definition at line 90 of file reads_txt.h.

uint8 nvbio::io::ReadDataFile_TXT::m_error_char
protected

Definition at line 97 of file reads_txt.h.

const char* nvbio::io::ReadDataFile_TXT::m_file_name
protected

Definition at line 84 of file reads_txt.h.

uint32 nvbio::io::ReadDataFile_TXT::m_line
protected

Definition at line 94 of file reads_txt.h.

std::vector<char> nvbio::io::ReadDataFile_TXT::m_name
protected

Definition at line 100 of file reads_txt.h.

QualityEncoding nvbio::io::ReadDataFile_TXT::m_quality_encoding
protected

Definition at line 86 of file reads_txt.h.

std::vector<uint8> nvbio::io::ReadDataFile_TXT::m_read_bp
protected

Definition at line 101 of file reads_txt.h.

std::vector<uint8> nvbio::io::ReadDataFile_TXT::m_read_q
protected

Definition at line 102 of file reads_txt.h.


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