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nvbio::io::SequenceDataFile_FASTQ_gz Struct Reference

Detailed description

loader for gzipped files this also works for plain uncompressed files, as zlib does that transparently

Definition at line 110 of file sequence_fastq.h.

#include <sequence_fastq.h>

Inheritance diagram for nvbio::io::SequenceDataFile_FASTQ_gz:
nvbio::io::SequenceDataFile_FASTQ_parser nvbio::io::SequenceDataFile nvbio::io::SequenceDataInputStream

Public Methods

 SequenceDataFile_FASTQ_gz (const char *read_file_name, const SequenceDataFile::Options &options)
 
 ~SequenceDataFile_FASTQ_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_FASTQ_parser
 SequenceDataFile_FASTQ_parser (const char *read_file_name, const SequenceDataFile::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_FASTQ_parser
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< uint8m_read_bp
 
std::vector< uint8m_read_q
 

Member Function Documentation

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

Implements nvbio::io::SequenceDataFile_FASTQ_parser.

Definition at line 120 of file sequence_fastq.h.


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