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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 {
- 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 

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: