Detailed description

Base abstract class to encode a host-side read batch. This has no storage, it's meant to be a base for either host or device memory objects

Definition at line 391 of file reads.h.

#include <reads.h>

Inheritance diagram for nvbio::io::ReadData:

Public Types
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
	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 Typedef Documentation

typedef ReadDataView<const uint32*,const uint32*,const char*,const char*> nvbio::io::ReadData::const_plain_view_type

Definition at line 394 of file reads.h.

typedef ReadDataView<uint32*,uint32*,char*,char*> nvbio::io::ReadData::plain_view_type

Definition at line 393 of file reads.h.

Constructor & Destructor Documentation

nvbio::io::ReadData::ReadData ( )

inline

empty constructor

Definition at line 398 of file reads.h.

virtual nvbio::io::ReadData::~ReadData ( )

inlinevirtual

virtual destructor

Definition at line 409 of file reads.h.

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

E:/git/nvbio/nvbio/io/reads/reads.h

Detailed description

Public Types

Public Methods

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation