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nvbio::io::ReadDataDevice Struct Reference

Detailed description

a read in device memory

Definition at line 465 of file reads.h.

#include <reads.h>

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

Public Types

enum  { READS = 0x01, QUALS = 0x02 }
 
- Public Types inherited from nvbio::io::ReadData
typedef ReadDataView< uint32
*, uint32 *, char *, char * > 
plain_view_type
 
typedef ReadDataView< const
uint32 *, const uint32
*, const char *, const char * > 
const_plain_view_type
 
- Public Types inherited from nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >
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

 ReadDataDevice (const ReadData &host_data, const uint32 flags=READS)
 
 ~ReadDataDevice ()
 
uint64 allocated () const
 
- Public Methods inherited from nvbio::io::ReadData
 ReadData ()
 
virtual ~ReadData ()
 
- Public Methods inherited from nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >
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
 

Additional Inherited Members

- Public Members inherited from nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >
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 inherited from nvbio::io::ReadDataView< IndexIterator, ReadStorageIterator, QualStorageIterator, NameStorageIterator >
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 Enumeration Documentation

anonymous enum
Enumerator
READS 
QUALS 

Definition at line 467 of file reads.h.

Constructor & Destructor Documentation

nvbio::io::ReadDataDevice::ReadDataDevice ( const ReadData host_data,
const uint32  flags = READS 
)

constructor

Definition at line 542 of file reads.cpp.

nvbio::io::ReadDataDevice::~ReadDataDevice ( )

destructor

Definition at line 573 of file reads.cpp.

Member Function Documentation

uint64 nvbio::io::ReadDataDevice::allocated ( ) const
inline

Definition at line 480 of file reads.h.


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