nvbio::ReadStreamQualities< ReadStreamType > Struct Template Reference

Detailed description

template< typename ReadStreamType>
struct nvbio::ReadStreamQualities< ReadStreamType >

Helper class to extract qualities from a read. This class has a string interface.

Definition at line 111 of file utils.h.

#include <utils.h>

Public Types
typedef ReadStreamQualities < ReadStreamType >	this_type
typedef random_access_universal_iterator_tag	iterator_category
typedef uint8	value_type
typedef value_type	reference
typedef const value_type *	pointer
typedef ReadStreamType::difference_type	difference_type
typedef ReadStreamType::index_type	index_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	ReadStreamQualities ()
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	ReadStreamQualities (const ReadStreamType &read)
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint8	operator[] (const uint32 pos) 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
const ReadStreamType *	m_read

Static Public Members
static const uint32	SYMBOL_SIZE = 8u

Member Typedef Documentation

template<typename ReadStreamType >

typedef string_iterator<this_type> nvbio::ReadStreamQualities< ReadStreamType >::const_iterator

Definition at line 123 of file utils.h.

template<typename ReadStreamType >

typedef ReadStreamType::difference_type nvbio::ReadStreamQualities< ReadStreamType >::difference_type

Definition at line 120 of file utils.h.

template<typename ReadStreamType >

typedef string_iterator<this_type> nvbio::ReadStreamQualities< ReadStreamType >::forward_iterator

Definition at line 124 of file utils.h.

template<typename ReadStreamType >

typedef ReadStreamType::index_type nvbio::ReadStreamQualities< ReadStreamType >::index_type

Definition at line 121 of file utils.h.

template<typename ReadStreamType >

typedef string_iterator<this_type> nvbio::ReadStreamQualities< ReadStreamType >::iterator

Definition at line 122 of file utils.h.

template<typename ReadStreamType >

typedef random_access_universal_iterator_tag nvbio::ReadStreamQualities< ReadStreamType >::iterator_category

Definition at line 116 of file utils.h.

template<typename ReadStreamType >

typedef const value_type* nvbio::ReadStreamQualities< ReadStreamType >::pointer

Definition at line 119 of file utils.h.

template<typename ReadStreamType >

typedef value_type nvbio::ReadStreamQualities< ReadStreamType >::reference

Definition at line 118 of file utils.h.

template<typename ReadStreamType >

typedef ReadStreamQualities<ReadStreamType> nvbio::ReadStreamQualities< ReadStreamType >::this_type

Definition at line 115 of file utils.h.

template<typename ReadStreamType >

typedef uint8 nvbio::ReadStreamQualities< ReadStreamType >::value_type

Definition at line 117 of file utils.h.

Constructor & Destructor Documentation

template<typename ReadStreamType >

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::ReadStreamQualities< ReadStreamType >::ReadStreamQualities ( )

inline

default constructor

Definition at line 129 of file utils.h.

template<typename ReadStreamType >

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::ReadStreamQualities< ReadStreamType >::ReadStreamQualities ( const ReadStreamType &  read)

inline

constructor

Definition at line 134 of file utils.h.

Member Function Documentation

template<typename ReadStreamType >

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE iterator nvbio::ReadStreamQualities< ReadStreamType >::begin ( void  )

inline

return a begin iterator

Definition at line 144 of file utils.h.

template<typename ReadStreamType >

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_iterator nvbio::ReadStreamQualities< ReadStreamType >::begin ( void  ) const

inline

return a begin iterator

Definition at line 154 of file utils.h.

template<typename ReadStreamType >

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE iterator nvbio::ReadStreamQualities< ReadStreamType >::end ( void  )

inline

return an end iterator

Definition at line 149 of file utils.h.

template<typename ReadStreamType >

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const_iterator nvbio::ReadStreamQualities< ReadStreamType >::end ( void  ) const

inline

return an end iterator

Definition at line 159 of file utils.h.

template<typename ReadStreamType >

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint8 nvbio::ReadStreamQualities< ReadStreamType >::operator[] ( const uint32  pos) const

inline

indexing operator

Definition at line 139 of file utils.h.

Member Data Documentation

template<typename ReadStreamType >

const ReadStreamType* nvbio::ReadStreamQualities< ReadStreamType >::m_read

Definition at line 161 of file utils.h.

template<typename ReadStreamType >

const uint32 nvbio::ReadStreamQualities< ReadStreamType >::SYMBOL_SIZE = 8u

static

Definition at line 113 of file utils.h.

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

• E:/git/nvbio/nvbio/io/utils.h