nvbio::io::SequenceDataInfo Struct Reference

Detailed description

A POD type encapsulating basic sequence information

Definition at line 201 of file sequence.h.

#include <sequence.h>

Inheritance diagram for nvbio::io::SequenceDataInfo:

Public Methods
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	SequenceDataInfo ()
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE Alphabet	alphabet () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	size () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	bps () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	words () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	qs () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	name_stream_len () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool	has_qualities () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	max_sequence_len () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	min_sequence_len () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	avg_sequence_len () const

Public Members
Alphabet	m_alphabet
	the alphabet More...
uint32	m_n_seqs
	number of reads in this struct More...
uint32	m_name_stream_len
	the length (in bytes) of the name_stream buffer More...
uint32	m_sequence_stream_len
	the length of sequence_stream in base pairs More...
uint32	m_sequence_stream_words
	the number of words in sequence_stream More...
uint32	m_has_qualities
	has qualities More...
uint32	m_min_sequence_len
	statistics on the reads More...
uint32	m_max_sequence_len
	statistics on the reads More...
uint32	m_avg_sequence_len
	statistics on the reads More...

Constructor & Destructor Documentation

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::io::SequenceDataInfo::SequenceDataInfo ( )

inline

empty constructor

Definition at line 206 of file sequence.h.

Member Function Documentation

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE Alphabet nvbio::io::SequenceDataInfo::alphabet ( ) const

inline

Definition at line 218 of file sequence.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::SequenceDataInfo::avg_sequence_len ( ) const

inline

Definition at line 227 of file sequence.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::SequenceDataInfo::bps ( ) const

inline

Definition at line 220 of file sequence.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool nvbio::io::SequenceDataInfo::has_qualities ( ) const

inline

Definition at line 224 of file sequence.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::SequenceDataInfo::max_sequence_len ( ) const

inline

Definition at line 225 of file sequence.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::SequenceDataInfo::min_sequence_len ( ) const

inline

Definition at line 226 of file sequence.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::SequenceDataInfo::name_stream_len ( ) const

inline

Definition at line 223 of file sequence.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::SequenceDataInfo::qs ( ) const

inline

Definition at line 222 of file sequence.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::SequenceDataInfo::size ( void  ) const

inline

Definition at line 219 of file sequence.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::SequenceDataInfo::words ( ) const

inline

Definition at line 221 of file sequence.h.

Member Data Documentation

Alphabet nvbio::io::SequenceDataInfo::m_alphabet

the alphabet

Definition at line 229 of file sequence.h.

uint32 nvbio::io::SequenceDataInfo::m_avg_sequence_len

statistics on the reads

Definition at line 238 of file sequence.h.

uint32 nvbio::io::SequenceDataInfo::m_has_qualities

has qualities

Definition at line 234 of file sequence.h.

uint32 nvbio::io::SequenceDataInfo::m_max_sequence_len

statistics on the reads

Definition at line 237 of file sequence.h.

uint32 nvbio::io::SequenceDataInfo::m_min_sequence_len

statistics on the reads

Definition at line 236 of file sequence.h.

uint32 nvbio::io::SequenceDataInfo::m_n_seqs

number of reads in this struct

Definition at line 230 of file sequence.h.

uint32 nvbio::io::SequenceDataInfo::m_name_stream_len

the length (in bytes) of the name_stream buffer

Definition at line 231 of file sequence.h.

uint32 nvbio::io::SequenceDataInfo::m_sequence_stream_len

the length of sequence_stream in base pairs

Definition at line 232 of file sequence.h.

uint32 nvbio::io::SequenceDataInfo::m_sequence_stream_words

the number of words in sequence_stream

Definition at line 233 of file sequence.h.

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

• E:/git/nvbio/nvbio/io/sequence/sequence.h