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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
IndexIteratorthe type of the iterator to the reads index
ReadStorageIteratorthe type of the iterator to the reads storage
QualStorageIteratorthe type of the iterator to the qualities storage
NameStorageIteratorthe 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 >:
nvbio::io::ReadData nvbio::io::ReadDataDevice nvbio::io::ReadDataRAM

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.


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