NVBIO: 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:

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