NVBIO: nvbio::ReadStream< StreamType, QualType > Struct Template Reference

Detailed description

template< typename StreamType, typename QualType = quality_nop>
struct nvbio::ReadStream< StreamType, QualType >

Helper class to represent a read or its reverse-complement - useful to avoid warp-divergence. This class has a string interface.

Definition at line 169 of file utils.h.

#include <utils.h>

Public Types
typedef StreamType::symbol_type	value_type

typedef StreamType::index_type	index_type

typedef ReadStream< StreamType, QualType >	this_type

typedef ReadStreamQualities < this_type >	qual_string_type

typedef random_access_universal_iterator_tag	iterator_category

typedef value_type	reference

typedef const value_type *	pointer

typedef signed_type < index_type >::type	difference_type

typedef string_iterator < this_type >	iterator

typedef string_iterator < this_type >	const_iterator

typedef string_iterator < this_type >	forward_iterator

Public Methods
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	ReadStream ()

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	ReadStream (const StreamType &s, const uint2 range)

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	ReadStream (const StreamType &s, const QualType q, const uint2 range)

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE void	set_flags (const DirType d, const ReadType t)

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	length () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE value_type	operator[] (uint32 pos) const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint8	quality (const uint32 pos) const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE qual_string_type	qualities () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE iterator	begin ()

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE iterator	end ()

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_iterator	begin () const

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_iterator	end () const

Public Members
uint32	rev
	reverse flag More...

uint32	comp
	complement flag More...

uint32	first

uint32	last
	offset of first and last elements More...

StreamType	stream
	read stream More...

QualType	qual
	quality stream More...

Static Public Members
static const uint32	SYMBOL_SIZE = StreamType::SYMBOL_SIZE

Member Typedef Documentation

template<typename StreamType, typename QualType = quality_nop>

typedef string_iterator<this_type> nvbio::ReadStream< StreamType, QualType >::const_iterator

Definition at line 183 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

typedef signed_type<index_type>::type nvbio::ReadStream< StreamType, QualType >::difference_type

Definition at line 181 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

typedef string_iterator<this_type> nvbio::ReadStream< StreamType, QualType >::forward_iterator

Definition at line 184 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

typedef StreamType::index_type nvbio::ReadStream< StreamType, QualType >::index_type

Definition at line 174 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

typedef string_iterator<this_type> nvbio::ReadStream< StreamType, QualType >::iterator

Definition at line 182 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

typedef random_access_universal_iterator_tag nvbio::ReadStream< StreamType, QualType >::iterator_category

Definition at line 178 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

typedef const value_type* nvbio::ReadStream< StreamType, QualType >::pointer

Definition at line 180 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

typedef ReadStreamQualities<this_type> nvbio::ReadStream< StreamType, QualType >::qual_string_type

Definition at line 176 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

typedef value_type nvbio::ReadStream< StreamType, QualType >::reference

Definition at line 179 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

typedef ReadStream<StreamType,QualType> nvbio::ReadStream< StreamType, QualType >::this_type

Definition at line 175 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

typedef StreamType::symbol_type nvbio::ReadStream< StreamType, QualType >::value_type

Definition at line 173 of file utils.h.

Constructor & Destructor Documentation

template<typename StreamType, typename QualType = quality_nop>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::ReadStream< StreamType, QualType >::ReadStream ( )

inline

default constructor

Definition at line 189 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::ReadStream< StreamType, QualType >::ReadStream	(	const StreamType &	s,
		const uint2	range
	)

inline

constructor

Definition at line 194 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::ReadStream< StreamType, QualType >::ReadStream	(	const StreamType &	s,
		const QualType	q,
		const uint2	range
	)

inline

constructor

Definition at line 200 of file utils.h.

Member Function Documentation

template<typename StreamType, typename QualType = quality_nop>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE iterator nvbio::ReadStream< StreamType, QualType >::begin ( void )

inline

return a begin iterator

Definition at line 241 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_iterator nvbio::ReadStream< StreamType, QualType >::begin ( void ) const

inline

return a begin iterator

Definition at line 251 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE iterator nvbio::ReadStream< StreamType, QualType >::end ( void )

inline

return an end iterator

Definition at line 246 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_iterator nvbio::ReadStream< StreamType, QualType >::end ( void ) const

inline

return an end iterator

Definition at line 256 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::ReadStream< StreamType, QualType >::length ( ) const

inline

return string length

Definition at line 211 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE value_type nvbio::ReadStream< StreamType, QualType >::operator[] ( uint32 pos) const

inline

return a given base

Definition at line 216 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE qual_string_type nvbio::ReadStream< StreamType, QualType >::qualities ( ) const

inline

return qualities

Definition at line 236 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint8 nvbio::ReadStream< StreamType, QualType >::quality ( const uint32 pos) const

inline

return a given base quality

Definition at line 227 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE void nvbio::ReadStream< StreamType, QualType >::set_flags	(	const DirType	d,
		const ReadType	t
	)

inline

set the read flags

Definition at line 206 of file utils.h.

Member Data Documentation

template<typename StreamType, typename QualType = quality_nop>

uint32 nvbio::ReadStream< StreamType, QualType >::comp

complement flag

Definition at line 260 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

uint32 nvbio::ReadStream< StreamType, QualType >::first

Definition at line 261 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

uint32 nvbio::ReadStream< StreamType, QualType >::last

offset of first and last elements

Definition at line 261 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

QualType nvbio::ReadStream< StreamType, QualType >::qual

quality stream

Definition at line 263 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

uint32 nvbio::ReadStream< StreamType, QualType >::rev

reverse flag

Definition at line 259 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

StreamType nvbio::ReadStream< StreamType, QualType >::stream

read stream

Definition at line 262 of file utils.h.

template<typename StreamType, typename QualType = quality_nop>

const uint32 nvbio::ReadStream< StreamType, QualType >::SYMBOL_SIZE = StreamType::SYMBOL_SIZE

static

Definition at line 171 of file utils.h.

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

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