nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator > Struct Template Reference

Detailed description

template< typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>
struct nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >

A storage-less plain-view class to represent the core sequence data iterators. Notice that this class only has runtime knowledge of the underlying alphabet encoding, and as such does provide any direct access to the stored sequences (except for pointers to underlying storage). In order to access the decoded sequences, one needs to provide compile-time knowledge of the alphabet, and create a SequenceDataAccess wrapper.

This class is templated over the iterators pointing to the actual storage, so as to allow them being both raw (const or non-const) pointers or fancier iterators (e.g. cuda::load_pointer or nvbio::vector<system_tag>::iterator's)

Template Parameters

IndexIterator	the type of the iterator to the reads index
ReadStorageIterator	the type of the iterator to the reads storage
QualStorageIterator	the type of the iterator to the qualities storage
NameStorageIterator	the type of the iterator to the names storage

Definition at line 301 of file sequence.h.

#include <sequence.h>

Inheritance diagram for nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >:

Public Types
typedef IndexIterator	index_iterator
	the index iterator More...
typedef SequenceStorageIterator	sequence_storage_iterator
	the read storage iterator More...
typedef QualStorageIterator	qual_storage_iterator
	the qualities iterator More...
typedef NameStorageIterator	name_storage_iterator
	the names string iterator More...
typedef to_const < IndexIterator >::type	const_index_iterator
	the index iterator More...
typedef to_const < SequenceStorageIterator > ::type	const_sequence_storage_iterator
	the read storage iterator More...
typedef to_const < QualStorageIterator >::type	const_qual_storage_iterator
	the qualities iterator More...
typedef to_const < NameStorageIterator >::type	const_name_storage_iterator
	the names string iterator More...

Public Methods
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	SequenceDataViewCore ()
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	SequenceDataViewCore (const SequenceDataInfo &info, const SequenceStorageIterator sequence_stream, const IndexIterator sequence_index, const QualStorageIterator qual_stream, const NameStorageIterator name_stream, const IndexIterator name_index)
template<typename InIndexIterator , typename InSequenceIterator , typename InQualIterator , typename InNameIterator >
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	SequenceDataViewCore (const SequenceDataViewCore< InIndexIterator, InSequenceIterator, InQualIterator, InNameIterator > &in)
template<typename InIndexIterator , typename InSequenceIterator , typename InQualIterator , typename InNameIterator >
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE SequenceDataViewCore &	operator= (const SequenceDataViewCore< InIndexIterator, InSequenceIterator, InQualIterator, InNameIterator > &in)
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE index_iterator	name_index ()
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE index_iterator	sequence_index ()
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE name_storage_iterator	name_stream ()
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE sequence_storage_iterator	sequence_storage ()
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE qual_storage_iterator	qual_stream ()
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_index_iterator	name_index () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_index_iterator	sequence_index () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_name_storage_iterator	name_stream () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_sequence_storage_iterator	sequence_storage () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_qual_storage_iterator	qual_stream () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint2	get_range (const uint32 i) const
Public Methods inherited from nvbio::io::SequenceDataInfo
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
name_storage_iterator	m_name_stream
	a pointer to a buffer containing the names of all the reads in this batch More...
index_iterator	m_name_index
	an array of uint32 with the byte indices of the starting locations of each name in name_stream More...
sequence_storage_iterator	m_sequence_stream
index_iterator	m_sequence_index
	an array of uint32 with the indices of the starting locations of each read in sequence_stream (in base pairs) More...
qual_storage_iterator	m_qual_stream
	a pointer to a buffer containing quality data More...
Public Members inherited from nvbio::io::SequenceDataInfo
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...

Member Typedef Documentation

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

typedef to_const<IndexIterator>::type nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::const_index_iterator

the index iterator

Definition at line 308 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

typedef to_const<NameStorageIterator>::type nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::const_name_storage_iterator

the names string iterator

Definition at line 311 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

typedef to_const<QualStorageIterator>::type nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::const_qual_storage_iterator

the qualities iterator

Definition at line 310 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

typedef to_const<SequenceStorageIterator>::type nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::const_sequence_storage_iterator

the read storage iterator

Definition at line 309 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

typedef IndexIterator nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::index_iterator

the index iterator

Definition at line 303 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

typedef NameStorageIterator nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::name_storage_iterator

the names string iterator

Definition at line 306 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

typedef QualStorageIterator nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::qual_storage_iterator

the qualities iterator

Definition at line 305 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

typedef SequenceStorageIterator nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::sequence_storage_iterator

the read storage iterator

Definition at line 304 of file sequence.h.

Constructor & Destructor Documentation

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::SequenceDataViewCore ( )

inline

empty constructor

Definition at line 316 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::SequenceDataViewCore ( const SequenceDataInfo &  info, const SequenceStorageIterator  sequence_stream, const IndexIterator  sequence_index, const QualStorageIterator  qual_stream, const NameStorageIterator  name_stream, const IndexIterator  name_index  )

inline

constructor

Definition at line 321 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

template<typename InIndexIterator , typename InSequenceIterator , typename InQualIterator , typename InNameIterator >

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::SequenceDataViewCore ( const SequenceDataViewCore< InIndexIterator, InSequenceIterator, InQualIterator, InNameIterator > &  in)

inline

copy constructor

Definition at line 344 of file sequence.h.

Member Function Documentation

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint2 nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::get_range ( const uint32  i) const

inline

get the range of a read in the sequence stream

Definition at line 389 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE index_iterator nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::name_index ( )

inline

Definition at line 375 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_index_iterator nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::name_index ( ) const

inline

Definition at line 381 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE name_storage_iterator nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::name_stream ( )

inline

Definition at line 377 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_name_storage_iterator nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::name_stream ( ) const

inline

Definition at line 383 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

template<typename InIndexIterator , typename InSequenceIterator , typename InQualIterator , typename InNameIterator >

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE SequenceDataViewCore& nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::operator= ( const SequenceDataViewCore< InIndexIterator, InSequenceIterator, InQualIterator, InNameIterator > &  in)

inline

assignment operator

Definition at line 361 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE qual_storage_iterator nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::qual_stream ( )

inline

Definition at line 379 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_qual_storage_iterator nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::qual_stream ( ) const

inline

Definition at line 385 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE index_iterator nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::sequence_index ( )

inline

Definition at line 376 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_index_iterator nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::sequence_index ( ) const

inline

Definition at line 382 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE sequence_storage_iterator nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::sequence_storage ( )

inline

Definition at line 378 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_sequence_storage_iterator nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::sequence_storage ( ) const

inline

Definition at line 384 of file sequence.h.

Member Data Documentation

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

index_iterator nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::m_name_index

an array of uint32 with the byte indices of the starting locations of each name in name_stream

Definition at line 392 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

name_storage_iterator nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::m_name_stream

a pointer to a buffer containing the names of all the reads in this batch

Definition at line 391 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

qual_storage_iterator nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::m_qual_stream

a pointer to a buffer containing quality data

Definition at line 397 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

index_iterator nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::m_sequence_index

an array of uint32 with the indices of the starting locations of each read in sequence_stream (in base pairs)

Definition at line 396 of file sequence.h.

template<typename IndexIterator = uint32*, typename SequenceStorageIterator = uint32*, typename QualStorageIterator = char*, typename NameStorageIterator = char*>

sequence_storage_iterator nvbio::io::SequenceDataViewCore< IndexIterator, SequenceStorageIterator, QualStorageIterator, NameStorageIterator >::m_sequence_stream

a pointer to a buffer containing the read data note that this could point at either host or device memory

Definition at line 393 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