nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator > Struct Template Reference

Detailed description

template< typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>
struct nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >

Encodes a (storage-less) plain-data view of a read batch. 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 121 of file reads.h.

#include <reads.h>

Inheritance diagram for nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >:

Public Types
typedef IndexIterator	index_iterator
	the index iterator More...
typedef to_const < index_iterator >::type	const_index_iterator
	the const index iterator More...
typedef ReadStorageIterator	read_storage_iterator
	the read storage iterator More...
typedef to_const < read_storage_iterator > ::type	const_read_storage_iterator
	the const read storage iterator More...
typedef QualStorageIterator	qual_storage_iterator
	the qualities iterator More...
typedef to_const < qual_storage_iterator > ::type	const_qual_storage_iterator
	the const qualities iterator More...
typedef NameStorageIterator	name_storage_iterator
	the names string iterator More...
typedef to_const < name_storage_iterator > ::type	const_name_storage_iterator
	the names string iterator More...
typedef PackedStream < read_storage_iterator, uint8, READ_BITS, READ_BIG_ENDIAN >	read_stream_type
	the packed read-stream type More...
typedef PackedStream < const_read_storage_iterator, uint8, READ_BITS, READ_BIG_ENDIAN >	const_read_stream_type
	the const packed read-stream type More...
typedef read_stream_type::iterator	read_stream_iterator
	the read-stream iterator More...
typedef const_read_stream_type::iterator	const_read_stream_iterator
	the const read-stream iterator More...
typedef vector_view < read_stream_iterator >	read_string
	the read string type More...
typedef vector_view < const_read_stream_iterator >	const_read_string
	the const read string type More...
typedef ConcatenatedStringSet < read_stream_iterator, index_iterator >	read_string_set_type
	string-set type More...
typedef ConcatenatedStringSet < const_read_stream_iterator, const_index_iterator >	const_read_string_set_type
	const string-set type More...
typedef ConcatenatedStringSet < qual_storage_iterator, index_iterator >	qual_string_set_type
	quality string-set type More...
typedef ConcatenatedStringSet < const_qual_storage_iterator, const_index_iterator >	const_qual_string_set_type
	const quality string-set type More...
typedef ConcatenatedStringSet < name_storage_iterator, index_iterator >	name_string_set_type
	name string-set type More...
typedef ConcatenatedStringSet < const_name_storage_iterator, const_index_iterator >	const_name_string_set_type
	const name string-set type More...

Public Methods
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	ReadDataView ()
template<typename InIndexIterator , typename InReadIterator , typename InQualIterator , typename InNameIterator >
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	ReadDataView (const ReadDataView< InIndexIterator, InReadIterator, InQualIterator, InNameIterator > &in)
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE index_iterator	name_index ()
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE index_iterator	read_index ()
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE name_storage_iterator	name_stream ()
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE read_storage_iterator	read_stream_storage ()
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE read_stream_type	read_stream ()
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE qual_storage_iterator	qual_stream ()
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_index_iterator	const_name_index () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_index_iterator	const_read_index () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_name_storage_iterator	const_name_stream () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_read_storage_iterator	const_read_stream_storage () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_read_stream_type	const_read_stream () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_qual_storage_iterator	const_qual_stream () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_index_iterator	name_index () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_index_iterator	read_index () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_name_storage_iterator	name_stream () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_read_storage_iterator	read_stream_storage () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_read_stream_type	read_stream () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_qual_storage_iterator	qual_stream () 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	name_stream_len () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	max_read_len () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	min_read_len () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	avg_read_len () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint2	get_range (const uint32 i) const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE read_string_set_type	read_string_set ()
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_read_string_set_type	read_string_set () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_read_string_set_type	const_read_string_set () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE read_string	get_read (const uint32 i)
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE read_string	get_read (const uint32 i) const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE qual_string_set_type	qual_string_set ()
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_qual_string_set_type	qual_string_set () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_qual_string_set_type	const_qual_string_set () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE name_string_set_type	name_string_set ()
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_name_string_set_type	name_string_set () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_name_string_set_type	const_name_string_set () const

Public Members
uint32	m_n_reads
name_storage_iterator	m_name_stream
uint32	m_name_stream_len
index_iterator	m_name_index
read_storage_iterator	m_read_stream
uint32	m_read_stream_len
uint32	m_read_stream_words
index_iterator	m_read_index
qual_storage_iterator	m_qual_stream
uint32	m_min_read_len
uint32	m_max_read_len
uint32	m_avg_read_len

Static Public Members
static const uint32	READ_BITS = 4
static const bool	HI_BITS = false
static const bool	READ_BIG_ENDIAN = false
static const uint32	READ_SYMBOLS_PER_WORD = (4*sizeof(uint32))/READ_BITS

Member Typedef Documentation

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

typedef to_const<index_iterator>::type nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::const_index_iterator

the const index iterator

Definition at line 124 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

typedef to_const<name_storage_iterator>::type nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::const_name_storage_iterator

the names string iterator

Definition at line 133 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

typedef ConcatenatedStringSet< const_name_storage_iterator, const_index_iterator> nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::const_name_string_set_type

const name string-set type

Definition at line 177 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

typedef to_const<qual_storage_iterator>::type nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::const_qual_storage_iterator

the const qualities iterator

Definition at line 130 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

typedef ConcatenatedStringSet< const_qual_storage_iterator, const_index_iterator> nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::const_qual_string_set_type

const quality string-set type

Definition at line 169 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

typedef to_const<read_storage_iterator>::type nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::const_read_storage_iterator

the const read storage iterator

Definition at line 127 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

typedef const_read_stream_type::iterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::const_read_stream_iterator

the const read-stream iterator

Definition at line 150 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

typedef PackedStream< const_read_storage_iterator,uint8,READ_BITS,READ_BIG_ENDIAN> nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::const_read_stream_type

the const packed read-stream type

Definition at line 147 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

typedef vector_view<const_read_stream_iterator> nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::const_read_string

the const read string type

Definition at line 153 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

typedef ConcatenatedStringSet< const_read_stream_iterator, const_index_iterator> nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::const_read_string_set_type

const string-set type

Definition at line 161 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

typedef IndexIterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::index_iterator

the index iterator

Definition at line 123 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

typedef NameStorageIterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::name_storage_iterator

the names string iterator

Definition at line 132 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

typedef ConcatenatedStringSet< name_storage_iterator, index_iterator> nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::name_string_set_type

name string-set type

Definition at line 173 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

typedef QualStorageIterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::qual_storage_iterator

the qualities iterator

Definition at line 129 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

typedef ConcatenatedStringSet< qual_storage_iterator, index_iterator> nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::qual_string_set_type

quality string-set type

Definition at line 165 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

typedef ReadStorageIterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::read_storage_iterator

the read storage iterator

Definition at line 126 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

typedef read_stream_type::iterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::read_stream_iterator

the read-stream iterator

Definition at line 149 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

typedef PackedStream< read_storage_iterator,uint8,READ_BITS,READ_BIG_ENDIAN> nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::read_stream_type

the packed read-stream type

Definition at line 145 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

typedef vector_view<read_stream_iterator> nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::read_string

the read string type

Definition at line 152 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

typedef ConcatenatedStringSet< read_stream_iterator, index_iterator> nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::read_string_set_type

string-set type

Definition at line 157 of file reads.h.

Constructor & Destructor Documentation

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::ReadDataView ( )

inline

empty constructor

Definition at line 182 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

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

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::ReadDataView ( const ReadDataView< InIndexIterator, InReadIterator, InQualIterator, InNameIterator > &  in)

inline

copy constructor

Definition at line 200 of file reads.h.

Member Function Documentation

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::avg_read_len ( ) const

inline

Definition at line 242 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::bps ( ) const

inline

Definition at line 237 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_index_iterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::const_name_index ( ) const

inline

Definition at line 222 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_name_storage_iterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::const_name_stream ( ) const

inline

Definition at line 224 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_name_string_set_type nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::const_name_string_set ( ) const

inline

return the a string-set view of this set of reads

Definition at line 343 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_qual_storage_iterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::const_qual_stream ( ) const

inline

Definition at line 227 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_qual_string_set_type nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::const_qual_string_set ( ) const

inline

return the a string-set view of this set of reads

Definition at line 313 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_index_iterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::const_read_index ( ) const

inline

Definition at line 223 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_read_stream_type nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::const_read_stream ( ) const

inline

Definition at line 226 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_read_storage_iterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::const_read_stream_storage ( ) const

inline

Definition at line 225 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_read_string_set_type nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::const_read_string_set ( ) const

inline

return the a string-set view of this set of reads

Definition at line 267 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

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

inline

Definition at line 243 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE read_string nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::get_read ( const uint32  i)

inline

return the i-th read as a string

Definition at line 277 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE read_string nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::get_read ( const uint32  i) const

inline

return the i-th read as a string

Definition at line 285 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::max_read_len ( ) const

inline

Definition at line 240 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::min_read_len ( ) const

inline

Definition at line 241 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE index_iterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::name_index ( )

inline

Definition at line 215 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

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

inline

Definition at line 229 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE name_storage_iterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::name_stream ( )

inline

Definition at line 217 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

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

inline

Definition at line 231 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::name_stream_len ( ) const

inline

Definition at line 239 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE name_string_set_type nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::name_string_set ( )

inline

return the a string-set view of this set of reads

Definition at line 323 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_name_string_set_type nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::name_string_set ( ) const

inline

return the a string-set view of this set of reads

Definition at line 333 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE qual_storage_iterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::qual_stream ( )

inline

Definition at line 220 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

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

inline

Definition at line 234 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE qual_string_set_type nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::qual_string_set ( )

inline

return the a string-set view of this set of reads

Definition at line 293 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_qual_string_set_type nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::qual_string_set ( ) const

inline

return the a string-set view of this set of reads

Definition at line 303 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE index_iterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::read_index ( )

inline

Definition at line 216 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_index_iterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::read_index ( ) const

inline

Definition at line 230 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE read_stream_type nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::read_stream ( )

inline

Definition at line 219 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_read_stream_type nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::read_stream ( ) const

inline

Definition at line 233 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE read_storage_iterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::read_stream_storage ( )

inline

Definition at line 218 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_read_storage_iterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::read_stream_storage ( ) const

inline

Definition at line 232 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE read_string_set_type nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::read_string_set ( )

inline

return the a string-set view of this set of reads

Definition at line 247 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_read_string_set_type nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::read_string_set ( ) const

inline

return the a string-set view of this set of reads

Definition at line 257 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::size ( void  ) const

inline

Definition at line 236 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::words ( ) const

inline

Definition at line 238 of file reads.h.

Member Data Documentation

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

const bool nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::HI_BITS = false

static

Definition at line 138 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

uint32 nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::m_avg_read_len

Definition at line 379 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

uint32 nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::m_max_read_len

Definition at line 378 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

uint32 nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::m_min_read_len

Definition at line 377 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

uint32 nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::m_n_reads

Definition at line 353 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

index_iterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::m_name_index

Definition at line 360 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

name_storage_iterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::m_name_stream

Definition at line 356 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

uint32 nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::m_name_stream_len

Definition at line 358 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

qual_storage_iterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::m_qual_stream

Definition at line 374 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

index_iterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::m_read_index

Definition at line 370 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

read_storage_iterator nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::m_read_stream

Definition at line 364 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

uint32 nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::m_read_stream_len

Definition at line 366 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

uint32 nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::m_read_stream_words

Definition at line 368 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

const bool nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::READ_BIG_ENDIAN = false

static

Definition at line 140 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

const uint32 nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::READ_BITS = 4

static

Definition at line 136 of file reads.h.

template<typename IndexIterator, typename ReadStorageIterator, typename QualStorageIterator, typename NameStorageIterator>

const uint32 nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >::READ_SYMBOLS_PER_WORD = (4*sizeof(uint32))/READ_BITS

static

Definition at line 142 of file reads.h.

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

• E:/git/nvbio/nvbio/io/reads/reads.h