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nvbio::io::SequenceDataInputStream Struct Referenceabstract
Sequence Data Input

Detailed description

A stream of SequenceData, allowing to process the associated reads in batches.

Definition at line 598 of file sequence.h.

#include <sequence.h>

Inheritance diagram for nvbio::io::SequenceDataInputStream:
nvbio::io::SequenceDataFile nvbio::io::SequenceDataFile_BAM nvbio::io::SequenceDataFile_FASTA_gz nvbio::io::SequenceDataFile_FASTQ_parser nvbio::io::SequenceDataFile_SAM nvbio::io::SequenceDataFile_TXT nvbio::io::SequenceDataFile_FASTQ_gz nvbio::io::SequenceDataFile_TXT_gz

Public Methods

virtual ~SequenceDataInputStream ()
 
virtual int next (struct SequenceDataEncoder *encoder, const uint32 batch_size, const uint32 batch_bps=uint32(-1))=0
 
virtual bool is_ok ()=0
 
virtual bool rewind ()=0
 

Related Functions

(Note that these are not member functions.)

int next (const Alphabet alphabet, SequenceDataHost *data, SequenceDataInputStream *stream, const uint32 batch_size, const uint32 batch_bps=uint32(-1))
 
int append (const Alphabet alphabet, SequenceDataHost *data, SequenceDataInputStream *stream, const uint32 batch_size, const uint32 batch_bps=uint32(-1))
 
int skip (SequenceDataInputStream *stream, const uint32 batch_size)
 
SequenceDataInputStream * open_sequence_file (const char *sequence_file_name, const QualityEncoding qualities=Phred33, const uint32 max_seqs=uint32(-1), const uint32 max_sequence_len=uint32(-1), const SequenceEncoding flags=FORWARD, const uint32 trim3=0, const uint32 trim5=0)
 

Constructor & Destructor Documentation

virtual nvbio::io::SequenceDataInputStream::~SequenceDataInputStream ( )
inlinevirtual

virtual destructor

Definition at line 602 of file sequence.h.

Member Function Documentation

virtual bool nvbio::io::SequenceDataInputStream::is_ok ( )
pure virtual

is the stream ok?

Implemented in nvbio::io::SequenceDataFile.

virtual int nvbio::io::SequenceDataInputStream::next ( struct SequenceDataEncoder *  encoder,
const uint32  batch_size,
const uint32  batch_bps = uint32(-1) 
)
pure virtual

next batch

Implemented in nvbio::io::SequenceDataFile.

virtual bool nvbio::io::SequenceDataInputStream::rewind ( )
pure virtual

rewind

Implemented in nvbio::io::SequenceDataFile_FASTQ_gz, nvbio::io::SequenceDataFile_TXT_gz, nvbio::io::SequenceDataFile_SAM, nvbio::io::SequenceDataFile_BAM, and nvbio::io::SequenceDataFile_FASTA_gz.

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