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nvbio::ReadLoader< SequenceDataT, Tag > Struct Template Reference

Detailed description

template< typename SequenceDataT, typename Tag>
struct nvbio::ReadLoader< SequenceDataT, Tag >

Utility class to load a read with a StringLoader. The Tag type allows to specify the caching policy.

Definition at line 277 of file utils.h.

#include <utils.h>

Public Types

typedef
SequenceDataT::sequence_storage_iterator 
read_storage
 
typedef
SequenceDataT::qual_storage_iterator 
qual_iterator
 
typedef PackedStringLoader
< read_storage,
SequenceDataT::SEQUENCE_BITS,
SequenceDataT::SEQUENCE_BIG_ENDIAN,
Tag > 
loader_type
 
typedef loader_type::iterator read_iterator
 
typedef ReadStream
< read_iterator, qual_iterator
string_type
 

Public Methods

NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE string_type 
load (const SequenceDataT &batch, const uint2 range, const DirType dir, const ReadType op)
 
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE string_type 
load (const SequenceDataT &batch, const uint2 range, const DirType dir, const ReadType op, const uint2 subrange)
 

Public Members

loader_type loader
 

Member Typedef Documentation

template<typename SequenceDataT, typename Tag>
typedef PackedStringLoader<read_storage, SequenceDataT::SEQUENCE_BITS, SequenceDataT::SEQUENCE_BIG_ENDIAN,Tag> nvbio::ReadLoader< SequenceDataT, Tag >::loader_type

Definition at line 281 of file utils.h.

template<typename SequenceDataT, typename Tag>
typedef SequenceDataT::qual_storage_iterator nvbio::ReadLoader< SequenceDataT, Tag >::qual_iterator

Definition at line 280 of file utils.h.

template<typename SequenceDataT, typename Tag>
typedef loader_type::iterator nvbio::ReadLoader< SequenceDataT, Tag >::read_iterator

Definition at line 282 of file utils.h.

template<typename SequenceDataT, typename Tag>
typedef SequenceDataT::sequence_storage_iterator nvbio::ReadLoader< SequenceDataT, Tag >::read_storage

Definition at line 279 of file utils.h.

template<typename SequenceDataT, typename Tag>
typedef ReadStream<read_iterator,qual_iterator> nvbio::ReadLoader< SequenceDataT, Tag >::string_type

Definition at line 283 of file utils.h.

Member Function Documentation

template<typename SequenceDataT, typename Tag>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_type nvbio::ReadLoader< SequenceDataT, Tag >::load ( const SequenceDataT &  batch,
const uint2  range,
const DirType  dir,
const ReadType  op 
)
inline

load a read

Definition at line 288 of file utils.h.

template<typename SequenceDataT, typename Tag>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_type nvbio::ReadLoader< SequenceDataT, Tag >::load ( const SequenceDataT &  batch,
const uint2  range,
const DirType  dir,
const ReadType  op,
const uint2  subrange 
)
inline

load a read substring

Definition at line 303 of file utils.h.

Member Data Documentation

template<typename SequenceDataT, typename Tag>
loader_type nvbio::ReadLoader< SequenceDataT, Tag >::loader

Definition at line 316 of file utils.h.


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