nvbio Namespace Reference

Define a vector_view POD type and plain_view() for std::vector. More...

Namespaces
	aln
	alndiff
	bowtie2
	cuda
	fmindex
	heap
	html
	internals
	io
	mem
	mergesort
	occ
	priqueue
	priv
	qgram
	qgroup
	util

Classes
struct	AtomicInt32
	an atomic integer class More...
struct	AtomicInt64
struct	inplace_or
struct	inplace_or< uint32 >
struct	inplace_or< uint2 >
struct	inplace_or< uint4 >
struct	inplace_or< uint64 >
struct	inplace_or< uint64_2 >
struct	inplace_or< uint64_4 >
struct	bloom_filter
struct	blocked_bloom_filter
struct	BNTAnnData
struct	BNTAnnInfo
struct	BNTAmb
struct	BNTSeq
struct	BNTInfo
struct	BNTSeqLoader
struct	bns_fopen_failure
struct	bns_files_mismatch
struct	cache_overflow
struct	LRU
struct	cached_iterator
struct	const_cached_iterator
struct	deinterleaved_iterator
struct	cuda_error
struct	bad_alloc
struct	runtime_error
struct	logic_error
struct	index_transform_iterator
struct	iterator_category_system
struct	iterator_category_system< input_host_iterator_tag >
struct	iterator_category_system< output_host_iterator_tag >
struct	iterator_category_system< forward_host_iterator_tag >
struct	iterator_category_system< bidirectional_host_iterator_tag >
struct	iterator_category_system< random_access_host_iterator_tag >
struct	iterator_category_system< input_device_iterator_tag >
struct	iterator_category_system< output_device_iterator_tag >
struct	iterator_category_system< forward_device_iterator_tag >
struct	iterator_category_system< bidirectional_device_iterator_tag >
struct	iterator_category_system< random_access_device_iterator_tag >
struct	iterator_category_system< input_universal_iterator_tag >
struct	iterator_category_system< output_universal_iterator_tag >
struct	iterator_category_system< forward_universal_iterator_tag >
struct	iterator_category_system< bidirectional_universal_iterator_tag >
struct	iterator_category_system< random_access_universal_iterator_tag >
struct	iterator_system
struct	iterator_traits
struct	iterator_reference
struct	to_const< iterator_reference< Iterator > >
struct	MappedFile
struct	ServerMappedFile
struct	vector_type
struct	vector_type< char, 1 >
struct	vector_type< char, 2 >
struct	vector_type< char, 3 >
struct	vector_type< char, 4 >
struct	vector_type< unsigned char, 1 >
struct	vector_type< unsigned char, 2 >
struct	vector_type< unsigned char, 3 >
struct	vector_type< unsigned char, 4 >
struct	vector_type< short, 1 >
struct	vector_type< short, 2 >
struct	vector_type< short, 3 >
struct	vector_type< short, 4 >
struct	vector_type< unsigned short, 1 >
struct	vector_type< unsigned short, 2 >
struct	vector_type< unsigned short, 3 >
struct	vector_type< unsigned short, 4 >
struct	vector_type< int, 1 >
struct	vector_type< int, 2 >
struct	vector_type< int, 3 >
struct	vector_type< int, 4 >
struct	vector_type< unsigned int, 1 >
struct	vector_type< unsigned int, 2 >
struct	vector_type< unsigned int, 3 >
struct	vector_type< unsigned int, 4 >
struct	vector_type< int64, 1 >
struct	vector_type< int64, 2 >
struct	vector_type< int64, 3 >
struct	vector_type< int64, 4 >
struct	vector_type< uint64, 1 >
struct	vector_type< uint64, 2 >
struct	vector_type< uint64, 3 >
struct	vector_type< uint64, 4 >
struct	vector_type< float, 1 >
struct	vector_type< float, 2 >
struct	vector_type< float, 3 >
struct	vector_type< float, 4 >
struct	vector_traits
struct	vector_traits< char >
struct	vector_traits< unsigned char >
struct	vector_traits< short >
struct	vector_traits< unsigned short >
struct	vector_traits< int >
struct	vector_traits< unsigned int >
struct	vector_traits< int64 >
struct	vector_traits< uint64 >
struct	vector_traits< float >
struct	vector_traits< double >
struct	vector_traits< char2 >
struct	vector_traits< char3 >
struct	vector_traits< char4 >
struct	vector_traits< uchar2 >
struct	vector_traits< uchar3 >
struct	vector_traits< uchar4 >
struct	vector_traits< short2 >
struct	vector_traits< short3 >
struct	vector_traits< short4 >
struct	vector_traits< ushort2 >
struct	vector_traits< ushort3 >
struct	vector_traits< ushort4 >
struct	vector_traits< int2 >
struct	vector_traits< int3 >
struct	vector_traits< int4 >
struct	vector_traits< uint2 >
struct	vector_traits< uint3 >
struct	vector_traits< uint4 >
struct	vector_traits< float2 >
struct	vector_traits< float3 >
struct	vector_traits< float4 >
struct	vector_traits< uint64_2 >
struct	vector_traits< uint64_3 >
struct	vector_traits< uint64_4 >
struct	vector_traits< int64_2 >
struct	vector_traits< int64_3 >
struct	vector_traits< int64_4 >
struct	LCG_random
struct	Field_traits
struct	Field_traits< int8 >
struct	Field_traits< int16 >
struct	Field_traits< int32 >
struct	Field_traits< int64 >
struct	Constant
struct	Linear
struct	Affine
struct	add_functor
struct	min_functor
struct	max_functor
struct	component_functor
struct	leading_bits
struct	shift_left
struct	shift_right
struct	popc_functor
struct	hi_bits_functor
struct	hi_bits_functor< uint8, uint32 >
struct	hi_bits_functor< uint16, uint32 >
struct	hi_bits_functor< uint32, uint32 >
struct	hi_bits_functor< uint32, uint64 >
struct	get_char_functor
struct	is_true_functor
struct	is_false_functor
struct	equal_to_functor
struct	not_equal_to_functor
struct	equal_functor
struct	not_equal_functor
struct	gather_functor
struct	composition_functor
struct	bind_first_functor
struct	bind_second_functor
struct	reverse_functor
struct	complement_functor
struct	cast_functor
struct	negate_functor
struct	PackedVector
struct	ForwardPackedStream
struct	stream_traits
struct	stream_traits< T * >
struct	stream_traits< const T * >
struct	PackedStreamRef
struct	to_const< PackedStreamRef< Stream > >
struct	PackedStream
struct	stream_traits< PackedStream< InputStream, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > >
struct	iterator_traits< PackedStream< InputStream, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > >
struct	stream_traits< ForwardPackedStream< InputStream, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > >
struct	uint4_as_uint32_iterator
struct	packer
struct	packer< BIG_ENDIAN_T, SYMBOL_SIZE, Symbol, InputStream, IndexType, uint32 >
struct	packer< BIG_ENDIAN_T, SYMBOL_SIZE, Symbol, InputStream, IndexType, uint64 >
struct	packer< BIG_ENDIAN_T, SYMBOL_SIZE, Symbol, InputStream, IndexType, uint8 >
struct	packer< BIG_ENDIAN_T, 2u, Symbol, InputStream, IndexType, uint32 >
struct	packer< BIG_ENDIAN_T, 4u, Symbol, InputStream, IndexType, uint32 >
struct	packer< BIG_ENDIAN_T, 2u, Symbol, InputStream, IndexType, uint4 >
struct	packer< BIG_ENDIAN_T, 4u, Symbol, InputStream, IndexType, uint4 >
struct	packer< BIG_ENDIAN_T, 8u, Symbol, InputStream, IndexType, uint4 >
struct	packer< BIG_ENDIAN_T, 2u, Symbol, InputStream, IndexType, uint64 >
struct	packer< BIG_ENDIAN_T, 4u, Symbol, InputStream, IndexType, uint64 >
struct	forward_packer
struct	forward_packer< BIG_ENDIAN, SYMBOL_SIZE, Symbol, InputStream, IndexType, uint4 >
struct	lmem_cache_tag
struct	uncached_tag
struct	PackedStringLoader
struct	PackedStringLoader< StorageIterator, SYMBOL_SIZE_T, BIG_ENDIAN_T, lmem_cache_tag< CACHE_SIZE > >
struct	PackedStringLoader< StorageIterator, SYMBOL_SIZE_T, BIG_ENDIAN_T, uncached_tag >
struct	Pipeline
struct	PipelineContext
struct	pod_type
struct	pod_writer
struct	pod_reader
struct	for_each_enactor
struct	for_each_enactor< device_tag >
struct	is_sorted_iterator
struct	is_segment_sorted_iterator
class	priority_deque
	Efficient double-ended priority queue. More...
struct	priority_queue
class	WeakPointer
class	SharedPointer
struct	simd4u8
struct	StaticVectorBase
struct	StaticVectorBase< T, 2 >
struct	StaticVectorBase< T, 3 >
struct	StaticVectorBase< T, 4 >
struct	StaticVector
struct	vector_traits< StaticVectorBase< T, DIM_T > >
struct	strided_iterator
struct	block_strided_iterator
struct	SumTree
class	ThreadBase
class	Thread
class	Mutex
class	ScopedLock
class	WorkQueue
	Work queue class. More...
struct	device_view_subtype< thrust::device_vector< T > >
struct	plain_view_subtype< thrust::host_vector< T > >
struct	plain_view_subtype< thrust::device_vector< T > >
struct	plain_view_subtype< const thrust::host_vector< T > >
struct	plain_view_subtype< const thrust::device_vector< T > >
struct	Timer
struct	ScopedTimer
struct	FakeTimer
struct	TimeSeries
struct	transform_iterator
struct	binary_transform_iterator
struct	host_tag
struct	device_tag
struct	null_type
struct	to_const
struct	to_const< T & >
struct	to_const< T * >
struct	to_const< const T & >
struct	to_const< const T * >
struct	reference_subtype
struct	reference_subtype< T * >
struct	reference_subtype< const T * >
struct	reference_subtype< null_type >
struct	device_view_subtype
struct	device_view_subtype< null_type >
struct	device_view_subtype< const T * >
struct	device_view_subtype< T * >
struct	plain_view_subtype
struct	plain_view_subtype< const T >
struct	plain_view_subtype< null_type >
struct	plain_view_subtype< const T * >
struct	plain_view_subtype< T * >
struct	signed_type
struct	signed_type< uint32 >
struct	signed_type< uint64 >
struct	signed_type< int32 >
struct	signed_type< int64 >
struct	unsigned_type
struct	unsigned_type< uint32 >
struct	unsigned_type< uint64 >
struct	unsigned_type< int32 >
struct	unsigned_type< int64 >
struct	same_type
struct	same_type< T, T >
struct	if_true
struct	if_true< true, T, F >
struct	if_true< false, T, F >
struct	if_equal
struct	binary_switch
struct	binary_switch< A, B, 0 >
union	BinaryCast
struct	vector
struct	vector< host_tag, T >
struct	vector< device_tag, T >
struct	device_iterator_type
struct	device_iterator_type< T * >
struct	device_iterator_type< const T * >
struct	VectorArrayView
struct	DeviceVectorArray
struct	HostVectorArray
struct	maximum_vector_width
struct	maximum_vector_width< char >
struct	maximum_vector_width< int8 >
struct	maximum_vector_width< uint8 >
struct	maximum_vector_width< int16 >
struct	maximum_vector_width< uint16 >
struct	maximum_vector_width< int32 >
struct	maximum_vector_width< uint32 >
struct	maximum_vector_width< int64 >
struct	maximum_vector_width< uint64 >
struct	vector_loader
struct	vector_loader< 1, T >
struct	vector_loader< 1, char >
struct	vector_loader< 2, char >
struct	vector_loader< 3, char >
struct	vector_loader< 4, char >
struct	vector_loader< 8, char >
struct	vector_loader< 16, char >
struct	vector_loader< 1, int8 >
struct	vector_loader< 2, int8 >
struct	vector_loader< 3, int8 >
struct	vector_loader< 4, int8 >
struct	vector_loader< 8, int8 >
struct	vector_loader< 16, int8 >
struct	vector_loader< 1, uint8 >
struct	vector_loader< 2, uint8 >
struct	vector_loader< 3, uint8 >
struct	vector_loader< 4, uint8 >
struct	vector_loader< 8, uint8 >
struct	vector_loader< 16, uint8 >
struct	vector_loader< 1, int16 >
struct	vector_loader< 2, int16 >
struct	vector_loader< 3, int16 >
struct	vector_loader< 4, int16 >
struct	vector_loader< 1, uint16 >
struct	vector_loader< 2, uint16 >
struct	vector_loader< 3, uint16 >
struct	vector_loader< 4, uint16 >
struct	vector_loader< 1, int32 >
struct	vector_loader< 2, int32 >
struct	vector_loader< 3, int32 >
struct	vector_loader< 4, int32 >
struct	vector_loader< 1, uint32 >
struct	vector_loader< 2, uint32 >
struct	vector_loader< 3, uint32 >
struct	vector_loader< 4, uint32 >
struct	vector_loader< 1, int64 >
struct	vector_loader< 2, int64 >
struct	vector_loader< 1, uint64 >
struct	vector_loader< 2, uint64 >
struct	vector_view
struct	string_traits< vector_view< Iterator, IndexType > >
struct	plain_view_subtype< std::vector< T > >
struct	plain_view_subtype< const std::vector< T > >
struct	FASTA_inc_reader
struct	FASTA_reader
struct	FASTQ_gzfile
struct	FASTQ_file
struct	FASTQ_reader
struct	FASTQ_buffer
struct	FMIndexFilter
struct	FMIndexFilter< host_tag, fm_index_type >
struct	FMIndexFilter< device_tag, fm_index_type >
struct	FMIndexFilterHost
struct	FMIndexFilterDevice
struct	fm_index
struct	fm_index_device_data
struct	MEMFilter
struct	MEMRange
struct	MEMHit
struct	MEMFilter< host_tag, fm_index_type >
struct	MEMFilter< device_tag, fm_index_type >
struct	MEMFilterHost
struct	MEMFilterDevice
struct	PagedText
struct	SparseSymbolSet
struct	divide_ri_functor
struct	copy_insert_pages
struct	copy_merge_pages
struct	rank_dictionary
struct	dispatch_rank
struct	rank_word_traits
struct	rank_word_traits< 2, uint32 >
struct	rank_word_traits< 2, uint64 >
struct	rank_word_traits< 4, uint32 >
struct	rank_word_traits< 4, uint64 >
struct	rank_word_traits< 8, uint32 >
struct	rank_word_traits< 8, uint64 >
struct	dispatch_rank< SYMBOL_SIZE, K, PackedStream< TextStorage, uint8, SYMBOL_SIZE, true, index_type >, OccIterator, CountTable, word_type, index_type >
struct	dispatch_rank< 2, 64, PackedStream< TextStorage, uint8, 2u, true >, OccIterator, CountTable, uint4, uint4 >
struct	SSA_index_multiple_device
struct	SSA_value_multiple_context
struct	SSA_value_multiple
struct	SSA_value_multiple_device
struct	SSA_index_multiple_context
struct	SSA_index_multiple
struct	pod_type< io::Alignment >
struct	pod_type< io::BestAlignments >
struct	OutputStream
struct	GZOutputFile
struct	LZ4OutputFile
struct	ReverseXform
struct	OffsetXform
struct	quality_nop
struct	ReadStreamQualities
struct	ReadStream
struct	ReadLoader
struct	SequenceStreamLoader
struct	QGramFilter
struct	QGramFilter< host_tag, qgram_index_type, query_iterator, index_iterator >
struct	QGramFilter< device_tag, qgram_index_type, query_iterator, index_iterator >
struct	QGramFilterHost
struct	QGramFilterDevice
struct	QGramIndexViewCore
struct	QGramIndexCore
struct	QGramIndexHost
struct	QGramIndexDevice
struct	QGramSetIndexHost
struct	QGramSetIndexDevice
struct	plain_view_subtype< QGramIndexHost >
struct	plain_view_subtype< QGramIndexDevice >
struct	plain_view_subtype< const QGramIndexHost >
struct	plain_view_subtype< const QGramIndexDevice >
struct	plain_view_subtype< QGramSetIndexHost >
struct	plain_view_subtype< QGramSetIndexDevice >
struct	plain_view_subtype< const QGramSetIndexHost >
struct	plain_view_subtype< const QGramSetIndexDevice >
struct	qgram_locate_functor
struct	string_qgram_functor
struct	string_set_qgram_functor
struct	string_qgram_search_functor
struct	localize_functor
struct	QGroupIndexViewCore
struct	QGroupIndexHost
struct	QGroupIndexDevice
struct	plain_view_subtype< QGroupIndexHost >
struct	plain_view_subtype< QGroupIndexDevice >
struct	plain_view_subtype< const QGroupIndexHost >
struct	plain_view_subtype< const QGroupIndexDevice >
struct	AlphabetTraits
struct	AlphabetTraits< DNA >
struct	AlphabetTraits< DNA_N >
struct	AlphabetTraits< DNA_IUPAC >
struct	AlphabetTraits< PROTEIN >
struct	AlphabetTraits< RNA >
struct	AlphabetTraits< RNA_N >
struct	AlphabetTraits< ASCII >
struct	to_char_functor
struct	from_char_functor
struct	InfixCore
struct	InfixCore< StringType, CoordType, 2u >
struct	InfixCore< StringType, CoordType, 4u >
struct	Infix
struct	InfixSetCore
struct	InfixSetCore< SequenceType, InfixIterator, 2u >
struct	InfixSetCore< SequenceType, InfixIterator, 4u >
struct	InfixSet
struct	StringPrefetcher
struct	StringPrefetcher< vector_view< PackedStream< StorageIterator, uint8, SYMBOL_SIZE_T, BIG_ENDIAN_T > >, lmem_cache_tag< CACHE_SIZE > >
struct	StringPrefetcher< Infix< PackedStream< StorageIterator, uint8, SYMBOL_SIZE_T, BIG_ENDIAN_T >, InfixCoordType >, lmem_cache_tag< CACHE_SIZE > >
struct	StringPrefetcher< Infix< vector_view< PackedStream< StorageIterator, uint8, SYMBOL_SIZE_T, BIG_ENDIAN_T > >, InfixCoordType >, lmem_cache_tag< CACHE_SIZE > >
struct	StringPrefetcher< vector_view< const T * >, lmem_cache_tag< CACHE_SIZE > >
struct	StringPrefetcher< vector_view< T * >, lmem_cache_tag< CACHE_SIZE > >
struct	PrefixCore
struct	PrefixCore< StringType, CoordType, 1u >
struct	PrefixCore< StringType, CoordType, 2u >
struct	Prefix
struct	PrefixSetCore
struct	PrefixSetCore< SequenceType, PrefixIterator, 1u >
struct	PrefixSetCore< SequenceType, PrefixIterator, 2u >
struct	PrefixSet
struct	uniform_seeds_functor
struct	project_coords_functor
struct	project_coords_functor< uint32, uint32 >
struct	project_coords_functor< uint64, uint64 >
struct	project_coords_functor< in_coord_type, uint32 >
struct	project_coords_functor< in_coord_type, uint2 >
struct	project_coords_functor< in_coord_type, uint3 >
struct	project_coords_functor< in_coord_type, uint4 >
struct	string_seed_functor
struct	localized_seed_functor
struct	string_iterator
struct	concatenated_string_set_tag
struct	sparse_string_set_tag
struct	strided_string_set_tag
struct	strided_packed_string_set_tag
struct	StringSetIterator
struct	ConcatenatedStringSet
struct	SparseStringSet
struct	StridedPackedStringSet
struct	StridedStringSet
struct	string_set_length_functor
struct	CachedPackedConcatStringSet
struct	CachedPackedConcatStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator, uint4 >
struct	CachedPackedConcatStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator, uint32 >
struct	CachedPackedSparseStringSet
struct	CachedPackedSparseStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator, uint4 >
struct	CachedPackedSparseStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator, uint32 >
struct	copy_dispatch
struct	TransformStringSet
struct	string_traits
struct	string_traits< T * >
struct	string_traits< const T * >
struct	SuffixCore
struct	SuffixCore< StringType, CoordType, 1u >
struct	SuffixCore< StringType, CoordType, 2u >
struct	Suffix
struct	SuffixSetCore
struct	SuffixSetCore< SequenceType, SuffixIterator, 1u >
struct	SuffixSetCore< SequenceType, SuffixIterator, 2u >
struct	SuffixSet
struct	vectorized_string
struct	vectorized_string< const char * >
struct	vectorized_string< vector_view< const T *, IndexType > >
struct	vectorized_string< vector_view< PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > > >
struct	WaveletTree
struct	WaveletTreeStorage
struct	select_bit_functor
struct	wavelet_ranker
struct	BWTEBlock
struct	BWTEContext
struct	DCTable
struct	DCTable< 64 >
struct	DCTable< 128 >
struct	DCTable< 256 >
struct	DCTable< 512 >
struct	DCTable< 1024 >
struct	DCTable< 2048 >
struct	DCSView
struct	DCS
struct	DCSSuffixRanker
struct	BGZFileWriter
struct	BWTBGZWriter
struct	LZ4FileWriter
struct	BWTLZ4Writer
struct	BWTParams
struct	SetBWTHandler
struct	DeviceBWTHandler
struct	HostBWTHandler
struct	HostBWTHandler< PackedStream< word_type *, uint8, SYMBOL_SIZE, BIG_ENDIAN, uint64 > >
struct	DiscardBWTHandler
struct	StringBWTHandler
struct	StringSSAHandler
struct	StringBWTSSAHandler
struct	SortedDictionaryNode
struct	SortedDictionarySuffixTrie
struct	TrieNode
struct	TrieNode5
struct	TrieNode< 2, TYPE_T >
struct	TrieNode< 3, TYPE_T >
struct	TrieNode< 4, TYPE_T >
struct	TrieNode< 5, TYPE_T >
struct	SuffixTrie
struct	Collector
struct	trie_copy
struct	trie_copy< ALPHABET_SIZE_T, CompressedTrie >
struct	lmem_selector
struct	lmem_selector< vector_view< PackedStream< StreamType, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T > > >

Typedefs
typedef std::input_iterator_tag	input_host_iterator_tag
typedef std::output_iterator_tag	output_host_iterator_tag
typedef std::forward_iterator_tag	forward_host_iterator_tag
typedef std::bidirectional_iterator_tag	bidirectional_host_iterator_tag
typedef std::random_access_iterator_tag	random_access_host_iterator_tag
typedef thrust::input_device_iterator_tag	input_device_iterator_tag
typedef thrust::output_device_iterator_tag	output_device_iterator_tag
typedef thrust::forward_device_iterator_tag	forward_device_iterator_tag
typedef thrust::bidirectional_device_iterator_tag	bidirectional_device_iterator_tag
typedef thrust::random_access_device_iterator_tag	random_access_device_iterator_tag
typedef thrust::input_universal_iterator_tag	input_universal_iterator_tag
typedef thrust::output_universal_iterator_tag	output_universal_iterator_tag
typedef thrust::forward_universal_iterator_tag	forward_universal_iterator_tag
typedef thrust::bidirectional_universal_iterator_tag	bidirectional_universal_iterator_tag
typedef thrust::random_access_universal_iterator_tag	random_access_universal_iterator_tag
typedef uchar2	uint8_2
typedef uchar3	uint8_3
typedef uchar4	uint8_4
typedef char2	int8_2
typedef char3	int8_3
typedef char4	int8_4
typedef ushort2	uint16_2
typedef ushort3	uint16_3
typedef ushort4	uint16_4
typedef short2	int16_2
typedef short3	int16_3
typedef short4	int16_4
typedef uint2	uint32_2
typedef uint3	uint32_3
typedef uint4	uint32_4
typedef int2	int32_2
typedef int3	int32_3
typedef int4	int32_4
typedef ulonglong2	uint64_2
typedef ulonglong3	uint64_3
typedef ulonglong4	uint64_4
typedef longlong2	int64_2
typedef longlong3	int64_3
typedef longlong4	int64_4
typedef long	CounterT_default
typedef unsigned long long	uint64
typedef unsigned int	uint32
typedef unsigned short	uint16
typedef unsigned char	uint8
typedef long long	int64
typedef int	int32
typedef short	int16
typedef signed char	int8
typedef QGramIndexViewCore < uint64 *, uint32 *, uint32 * >	QGramIndexView
typedef QGramIndexViewCore < uint64 *, uint32 *, uint2 * >	QGramSetIndexView
typedef QGramIndexViewCore < const uint64 *, const uint32 *, const uint32 * >	ConstQGramIndexView
typedef QGramIndexViewCore < const uint64 *, const uint32 *, const uint2 * >	ConstQGramSetIndexView
typedef QGroupIndexViewCore < uint32 * >	QGroupIndexView
typedef QGroupIndexViewCore < const uint32 * >	ConstQGroupIndexView
typedef uint32_2	string_infix_coord_type
typedef uint64_2	long_string_infix_coord_type
typedef uint32_4	string_set_infix_coord_type
typedef uint64_4	long_string_set_infix_coord_type
typedef uint32	string_prefix_coord_type
typedef uint64	long_string_prefix_coord_type
typedef uint32_2	string_set_prefix_coord_type
typedef uint64_2	long_string_set_prefix_coord_type
typedef uint32	string_suffix_coord_type
typedef uint64	long_string_suffix_coord_type
typedef uint32_2	string_set_suffix_coord_type
typedef uint64_2	long_string_set_suffix_coord_type

Enumerations
enum	block_strided_layout { ROW_MAJOR_LAYOUT = 0u, COLUMN_MAJOR_LAYOUT = 1u }
enum	ReadType { STANDARD = 0u, COMPLEMENT = 1u }
enum	DirType { FORWARD = 0u, REVERSE = 1u }
enum	Alphabet {   DNA = 0u, DNA_N = 1u, DNA_IUPAC = 2u, PROTEIN = 3u,   RNA = 4u, RNA_N = 5u, ASCII = 6u }
enum	TrieType { CompressedTrie, UncompressedTrie }

Functions
template<typename Iterator , typename Predicate >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Iterator	find_pivot (Iterator begin, const uint32 n, const Predicate predicate)
template<typename Iterator , typename Value , typename index_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Iterator	lower_bound (const Value x, Iterator begin, const index_type n)
template<typename Iterator , typename Value , typename index_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Iterator	upper_bound (const Value x, Iterator begin, const index_type n)
template<typename Iterator , typename Value , typename index_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE index_type	lower_bound_index (const Value x, Iterator begin, const index_type n)
template<typename Iterator , typename Value , typename index_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE index_type	upper_bound_index (const Value x, Iterator begin, const index_type n)
template<typename input_iterator1 , typename input_iterator2 , typename output_iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	merge (input_iterator1 first1, input_iterator1 end1, input_iterator2 first2, input_iterator2 end2, output_iterator output)
template<typename key_iterator1 , typename key_iterator2 , typename value_iterator1 , typename value_iterator2 , typename key_iterator , typename value_iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	merge_by_key (key_iterator1 first1, key_iterator1 end1, key_iterator2 first2, key_iterator2 end2, value_iterator1 values1, value_iterator2 values2, key_iterator output_keys, value_iterator output_values)
void	host_release_fence ()
void	host_acquire_fence ()
int32	host_atomic_add (int32 *value, const int32 op)
uint32	host_atomic_add (uint32 *value, const uint32 op)
int64	host_atomic_add (int64 *value, const int64 op)
uint64	host_atomic_add (uint64 *value, const uint64 op)
int32	host_atomic_sub (int32 *value, const int32 op)
uint32	host_atomic_sub (uint32 *value, const uint32 op)
int64	host_atomic_sub (int64 *value, const int64 op)
uint64	host_atomic_sub (uint64 *value, const uint64 op)
uint32	host_atomic_or (uint32 *value, const uint32 op)
uint64	host_atomic_or (uint64 *value, const uint64 op)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	atomic_add (int32 *value, const int32 op)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	atomic_add (uint32 *value, const uint32 op)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	atomic_add (uint64 *value, const uint64 op)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	atomic_sub (int32 *value, const int32 op)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	atomic_sub (uint32 *value, const uint32 op)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	atomic_or (uint32 *value, const uint32 op)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	atomic_or (uint64 *value, const uint64 op)
bool	operator== (const long a, const AtomicInt64 &b)
	comparisons More...
bool	operator!= (const long a, const AtomicInt64 &b)
bool	operator>= (const long a, const AtomicInt64 &b)
bool	operator<= (const long a, const AtomicInt64 &b)
bool	operator> (const long a, const AtomicInt64 &b)
bool	operator< (const long a, const AtomicInt64 &b)
bool	operator== (const int a, const AtomicInt32 &b)
bool	operator!= (const int a, const AtomicInt32 &b)
bool	operator>= (const int a, const AtomicInt32 &b)
bool	operator<= (const int a, const AtomicInt32 &b)
bool	operator> (const int a, const AtomicInt32 &b)
bool	operator< (const int a, const AtomicInt32 &b)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	optimal_bloom_filter_hashes (const float bits_per_key)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE float	optimal_bloom_filter_bits_per_key (const float fp_rate)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE float	optimal_bloom_filter_bits_per_key (const uint32 K)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	optimal_bloom_filter_parameters (const float fp_rate, uint32 *K, float *bits_per_key)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE float	optimal_bloom_filter_fp_rate (const uint32 K, const float bits_per_key)
void	save_bns (const BNTSeq &bns, const char *prefix)
void	load_bns (BNTSeq &bns, const char *prefix)
void	load_bns_info (BNTInfo &bns, const char *prefix)
void	load_bns (BNTSeqLoader *bns, const char *prefix)
template<typename InputStream >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE cached_iterator< InputStream >	make_cached_iterator (InputStream it)
template<typename InputStream >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const_cached_iterator < InputStream >	make_const_cached_iterator (InputStream it)
template<typename Stream >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator< (const const_cached_iterator< Stream > &it1, const const_cached_iterator< Stream > &it2)
template<typename Stream >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator> (const const_cached_iterator< Stream > &it1, const const_cached_iterator< Stream > &it2)
template<typename Stream >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator<= (const const_cached_iterator< Stream > &it1, const const_cached_iterator< Stream > &it2)
template<typename Stream >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator>= (const const_cached_iterator< Stream > &it1, const const_cached_iterator< Stream > &it2)
template<typename Stream >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator== (const const_cached_iterator< Stream > &it1, const const_cached_iterator< Stream > &it2)
template<typename Stream >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator!= (const const_cached_iterator< Stream > &it1, const const_cached_iterator< Stream > &it2)
template<typename Stream >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const_cached_iterator< Stream > &	operator++ (const_cached_iterator< Stream > &it)
template<typename Stream >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const_cached_iterator< Stream >	operator++ (const_cached_iterator< Stream > &it, int dummy)
template<typename Stream >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const_cached_iterator< Stream > &	operator-- (const_cached_iterator< Stream > &it)
template<typename Stream >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const_cached_iterator< Stream >	operator-- (const_cached_iterator< Stream > &it, int dummy)
template<typename Stream >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const_cached_iterator< Stream > &	operator+= (const_cached_iterator< Stream > &it, const typename const_cached_iterator< Stream >::difference_type distance)
template<typename Stream >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const_cached_iterator< Stream > &	operator-= (const_cached_iterator< Stream > &it, const typename const_cached_iterator< Stream >::difference_type distance)
template<typename Stream >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const_cached_iterator< Stream >	operator+ (const const_cached_iterator< Stream > it, const typename const_cached_iterator< Stream >::difference_type distance)
template<typename Stream >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const_cached_iterator< Stream >	operator- (const const_cached_iterator< Stream > it, const typename const_cached_iterator< Stream >::difference_type distance)
template<typename Stream >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE const_cached_iterator< Stream > ::difference_type	operator- (const const_cached_iterator< Stream > it1, const const_cached_iterator< Stream > it2)
template<typename R , typename T >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE transform_iterator< T, cast_functor< typename std::iterator_traits< T > ::value_type, R > >	make_cast_iterator (const T it)
NVBIO_FORCEINLINE NVBIO_DEVICE void	warp_incff (uint32 *count)
NVBIO_FORCEINLINE NVBIO_DEVICE uint32	warp_inc (uint32 *count)
NVBIO_FORCEINLINE NVBIO_DEVICE void	warp_decff (uint32 *count)
NVBIO_FORCEINLINE NVBIO_DEVICE uint32	warp_dec (uint32 *count)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE char	dna_to_char (const uint8 c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8	dna_to_iupac16 (const uint8 c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE char	iupac16_to_char (const uint8 c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8	char_to_dna (const char c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8	char_to_iupac16 (const char c)
template<typename SymbolIterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	dna_to_string (const SymbolIterator begin, const uint32 n, char *string)
template<typename SymbolIterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	dna_to_string (const SymbolIterator begin, const SymbolIterator end, char *string)
template<typename SymbolIterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	iupac16_to_string (const SymbolIterator begin, const uint32 n, char *string)
template<typename SymbolIterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	iupac16_to_string (const SymbolIterator begin, const SymbolIterator end, char *string)
template<typename SymbolIterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	string_to_dna (const char *begin, const char *end, SymbolIterator symbols)
template<typename SymbolIterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	string_to_dna (const char *begin, SymbolIterator symbols)
template<typename SymbolIterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	string_to_iupac16 (const char *begin, const char *end, SymbolIterator symbols)
template<typename SymbolIterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	string_to_iupac16 (const char *begin, SymbolIterator symbols)
template<typename T , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE index_transform_iterator< T, Transform >	make_index_transform_iterator (const T it, const Transform f)
template<typename T , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator== (const index_transform_iterator< T, Transform > it1, const index_transform_iterator< T, Transform > it2)
template<typename T , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator!= (const index_transform_iterator< T, Transform > it1, const index_transform_iterator< T, Transform > it2)
template<typename T , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator< (const index_transform_iterator< T, Transform > it1, const index_transform_iterator< T, Transform > it2)
template<typename T , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator<= (const index_transform_iterator< T, Transform > it1, const index_transform_iterator< T, Transform > it2)
template<typename T , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator> (const index_transform_iterator< T, Transform > it1, const index_transform_iterator< T, Transform > it2)
template<typename T , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator>= (const index_transform_iterator< T, Transform > it1, const index_transform_iterator< T, Transform > it2)
template<typename Iterator , typename Compare >
NVBIO_HOST_DEVICE bool	merge_sort (uint32 n, Iterator A, Iterator B, const Compare cmp)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8	comp (const uchar2 a, const char c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE char	comp (const char2 a, const char c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8	comp (const uchar4 a, const char c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE char	comp (const char4 a, const char c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE signed char &	select (char4 &a, const char c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	comp (const uint2 a, const uint32 c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	set (uint2 &a, const uint32 c, const uint32 v)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	comp (const ulonglong2 a, const uint32 c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	set (ulonglong2 &a, const uint32 c, const uint64 v)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	comp (const int2 a, const uint32 c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	comp (const uint4 a, const uint32 c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	set (uint4 &a, const uint32 c, const uint32 v)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	comp (const int4 a, const uint32 c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 &	select (uint4 &a, const uint32 c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint16	comp (const ushort4 a, const uint32 c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	comp (const ulonglong4 a, const uint32 c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	set (ulonglong4 &a, const uint32 c, const uint64 v)
template<typename T >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE vector_type < T, 1 >::type	make_vector (const T i1)
template<typename T >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE vector_type < T, 2 >::type	make_vector (const T i1, const T i2)
template<typename T >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE vector_type < T, 3 >::type	make_vector (const T i1, const T i2, const T i3)
template<typename T >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE vector_type < T, 4 >::type	make_vector (const T i1, const T i2, const T i3, const T i4)
template<typename T >
NVBIO_HOST_DEVICE T	sgn (const T x)
NVBIO_HOST_DEVICE float	round (const float x)
NVBIO_HOST_DEVICE float	min (const float a, const float b)
NVBIO_HOST_DEVICE float	max (const float a, const float b)
NVBIO_HOST_DEVICE int8	min (const int8 a, const int8 b)
NVBIO_HOST_DEVICE int8	max (const int8 a, const int8 b)
NVBIO_HOST_DEVICE uint8	min (const uint8 a, const uint8 b)
NVBIO_HOST_DEVICE uint8	max (const uint8 a, const uint8 b)
NVBIO_HOST_DEVICE uint16	min (const uint16 a, const uint16 b)
NVBIO_HOST_DEVICE uint16	max (const uint16 a, const uint16 b)
NVBIO_HOST_DEVICE int32	min (const int32 a, const int32 b)
NVBIO_HOST_DEVICE int32	max (const int32 a, const int32 b)
NVBIO_HOST_DEVICE uint32	min (const uint32 a, const uint32 b)
NVBIO_HOST_DEVICE uint32	max (const uint32 a, const uint32 b)
NVBIO_HOST_DEVICE int64	min (const int64 a, const int64 b)
NVBIO_HOST_DEVICE int64	max (const int64 a, const int64 b)
NVBIO_HOST_DEVICE uint64	min (const uint64 a, const uint64 b)
NVBIO_HOST_DEVICE uint64	max (const uint64 a, const uint64 b)
NVBIO_HOST_DEVICE uint32	quantize (const float x, const uint32 n)
float NVBIO_HOST_DEVICE	mod (const float x, const float m)
NVBIO_HOST_DEVICE uint32	log2 (uint32 n)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	hash (uint32 a)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	hash2 (uint32 key)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	hash (uint64 key)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	hash2 (uint64 key)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	hash3 (uint64 key)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE float	radical_inverse (unsigned int n)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8	min3 (const uint8 op1, const uint8 op2, const uint8 op3)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	min3 (const uint32 op1, const uint32 op2, const uint32 op3)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	max3 (const uint32 op1, const uint32 op2, const uint32 op3)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	min3 (const int32 op1, const int32 op2, const int32 op3)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	max3 (const int32 op1, const int32 op2, const int32 op3)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE float	min3 (const float op1, const float op2, const float op3)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE float	max3 (const float op1, const float op2, const float op3)
NVBIO_HOST_DEVICE float	fast_pow (const float a, const float b)
NVBIO_HOST_DEVICE float	fast_sin (const float x)
NVBIO_HOST_DEVICE float	fast_cos (const float x)
NVBIO_HOST_DEVICE float	fast_sqrt (const float x)
template<typename Iterator >
gather_functor< Iterator >	make_gather_functor (const Iterator perm)
template<typename Functor2 , typename Functor1 >
composition_functor< Functor2, Functor1 >	make_composition_functor (const Functor2 fun2, const Functor1 fun1)
template<typename options_type >
bool	bool_option (const options_type &options, const char *name, const bool val)
template<typename options_type >
bool	bool_option (const options_type &options, const char *name1, const char *name2, const bool val)
template<typename options_type >
uint32	uint_option (const options_type &options, const char *name, const uint32 val)
template<typename options_type >
uint32	uint_option (const options_type &options, const char *name1, const char *name2, const uint32 val)
template<typename options_type >
int32	int_option (const options_type &options, const char *name, const int32 val)
template<typename options_type >
int32	int_option (const options_type &options, const char *name1, const char *name2, const uint32 val)
template<typename options_type >
int64	int64_option (const options_type &options, const char *name, const int64 val)
template<typename options_type >
int64	int64_option (const options_type &options, const char *name1, const char *name2, const uint32 val)
template<typename options_type >
float	float_option (const options_type &options, const char *name, const float val)
template<typename options_type >
float	float_option (const options_type &options, const char *name1, const char *name2, const uint32 val)
template<typename options_type >
std::string	string_option (const options_type &options, const char *name, const char *val)
template<typename options_type >
std::string	string_option (const options_type &options, const char *name1, const char *name2, const char *val)
template<typename options_type >
int2	int2_option (const options_type &options, const char *name, const int2 val)
template<typename SystemTag , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >
PackedVector< SystemTag, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType >::plain_view_type	plain_view (PackedVector< SystemTag, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &vec)
template<typename SystemTag , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >
PackedVector< SystemTag, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > ::const_plain_view_type	plain_view (const PackedVector< SystemTag, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &vec)
template<uint32 BLOCKDIM, uint32 BITS, bool BIG_ENDIAN, typename InStreamIterator , typename OutStreamIterator >
NVBIO_HOST_DEVICE void	transpose_packed_streams (const uint32 stride, const uint32 N, const uint32 in_offset, const InStreamIterator in_stream, OutStreamIterator out_stream)
template<typename InputStream , typename Symbol , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator< (const PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &it1, const PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &it2)
template<typename InputStream , typename Symbol , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator> (const PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &it1, const PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &it2)
template<typename InputStream , typename Symbol , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator== (const PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &it1, const PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &it2)
template<typename InputStream , typename Symbol , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator!= (const PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &it1, const PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &it2)
template<typename InputStream , typename Symbol , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator< (const ForwardPackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &it1, const ForwardPackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &it2)
template<typename InputStream , typename Symbol , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator> (const ForwardPackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &it1, const ForwardPackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &it2)
template<typename InputStream , typename Symbol , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator== (const ForwardPackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &it1, const ForwardPackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &it2)
template<typename InputStream , typename Symbol , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator!= (const ForwardPackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &it1, const ForwardPackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &it2)
template<typename InputIterator , typename InputStream , typename Symbol , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >
NVBIO_HOST_DEVICE void	assign (const host_tag tag, const IndexType input_len, const InputIterator input_string, PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > packed_string)
template<typename InputIterator , typename InputStream , typename Symbol , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >
NVBIO_HOST_DEVICE void	assign (const IndexType input_len, const InputIterator input_string, PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > packed_string)
template<typename T >
NVBIO_FORCEINLINE NVBIO_DEVICE void	write (T *ptr, const T &e)
template<typename T >
NVBIO_FORCEINLINE NVBIO_DEVICE T	read (const T *ptr)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	popc (const int32 i)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	popc (const uint32 i)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	popc (const uint8 i)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	find_nthbit4 (const uint32 mask, const uint32 n)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	popc4 (const uint32 mask)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	find_nthbit8 (const uint32 mask, const uint32 n)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	ffs (const int32 x)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	lzc (const uint32 x)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	popc_2bit (const uint32 x, int c)
template<typename CountTable >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	popc_2bit_all (const uint32 b, const CountTable count_table)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	hibits_2bit (const uint32 mask, const uint32 i)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	popc_2bit (const uint32 mask, int c, const uint32 i)
template<uint32 N>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	popc_nbit (const uint32 x, int c)
template<uint32 N>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	hibits_nbit (const uint32 mask, const uint32 i)
template<uint32 N>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	popc_nbit (const uint32 mask, int c, const uint32 i)
template<typename CountTable >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	popc_2bit_all (const uint32 mask, const CountTable count_table, const uint32 i)
void	gen_2bit_count_table (uint32 *count_table)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	popc (const uint64 i)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	find_nthbit16 (const uint32 mask, const uint32 n)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	find_nthbit (const uint32 mask, const uint32 n)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	find_nthbit (const uint8 mask, const uint32 n)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	find_nthbit (const uint16 mask, const uint32 n)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	popc_2bit (const uint64 x, int c)
template<typename CountTable >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	popc_2bit_all (const uint64 b, const CountTable count_table)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	hibits_2bit (const uint64 mask, const uint32 i)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	popc_2bit (const uint64 mask, int c, const uint32 i)
template<uint32 N>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	popc_nbit (const uint64 x, int c)
template<uint32 N>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	hibits_nbit (const uint64 mask, const uint32 i)
template<uint32 N>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	popc_nbit (const uint64 mask, int c, const uint32 i)
template<typename CountTable >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	popc_2bit_all (const uint64 mask, const CountTable count_table, const uint32 i)
template<typename system_tag , typename PredicateIterator >
bool	any (const uint32 n, const PredicateIterator pred)
template<typename system_tag , typename PredicateIterator >
bool	all (const uint32 n, const PredicateIterator pred)
template<typename system_tag , typename Iterator >
bool	is_sorted (const uint32 n, const Iterator values)
template<typename system_tag , typename Iterator , typename Headflags >
bool	is_segment_sorted (const uint32 n, const Iterator values, const Headflags flags)
template<typename system_tag , typename Iterator , typename Functor >
void	for_each (const uint64 n, const Iterator in, Functor functor)
template<typename system_tag , typename Iterator , typename Output , typename Functor >
void	transform (const uint32 n, const Iterator in, const Output out, const Functor functor)
template<typename system_tag , typename Iterator1 , typename Iterator2 , typename Output , typename Functor >
void	transform (const uint32 n, const Iterator1 in1, const Iterator2 in2, const Output out, const Functor functor)
template<typename system_tag , typename InputIterator , typename BinaryOp >
std::iterator_traits < InputIterator >::value_type	reduce (const uint32 n, InputIterator in, BinaryOp op, nvbio::vector< system_tag, uint8 > &temp_storage)
template<typename system_tag , typename InputIterator , typename OutputIterator , typename BinaryOp >
void	inclusive_scan (const uint32 n, InputIterator in, OutputIterator out, BinaryOp op, nvbio::vector< system_tag, uint8 > &temp_storage)
template<typename system_tag , typename InputIterator , typename OutputIterator , typename BinaryOp , typename Identity >
void	exclusive_scan (const uint32 n, InputIterator in, OutputIterator out, BinaryOp op, Identity identity, nvbio::vector< system_tag, uint8 > &temp_storage)
template<typename system_tag , typename InputIterator , typename FlagsIterator , typename OutputIterator >
uint32	copy_flagged (const uint32 n, InputIterator in, FlagsIterator flags, OutputIterator out, nvbio::vector< system_tag, uint8 > &temp_storage)
template<typename system_tag , typename InputIterator , typename OutputIterator , typename Predicate >
uint32	copy_if (const uint32 n, InputIterator in, OutputIterator out, const Predicate pred, nvbio::vector< system_tag, uint8 > &temp_storage)
template<typename system_tag , typename InputIterator , typename OutputIterator , typename CountIterator >
uint32	runlength_encode (const uint32 n, InputIterator in, OutputIterator out, CountIterator counts, nvbio::vector< system_tag, uint8 > &temp_storage)
template<typename system_tag , typename KeyIterator , typename ValueIterator , typename OutputKeyIterator , typename OutputValueIterator , typename ReductionOp >
uint32	reduce_by_key (const uint32 n, KeyIterator keys_in, ValueIterator values_in, OutputKeyIterator keys_out, OutputValueIterator values_out, ReductionOp reduction_op, nvbio::vector< system_tag, uint8 > &temp_storage)
template<typename system_tag , typename KeyIterator , typename ValueIterator , typename OutputIterator >
void	lower_bound (const uint32 n, ValueIterator values, const uint32 n_keys, KeyIterator keys, OutputIterator indices)
template<typename system_tag , typename KeyIterator , typename ValueIterator , typename OutputIterator >
void	upper_bound (const uint32 n, ValueIterator values, const uint32 n_keys, KeyIterator keys, OutputIterator indices)
template<typename system_tag , typename KeyIterator >
void	radix_sort (const uint32 n, KeyIterator keys, nvbio::vector< system_tag, uint8 > &temp_storage)
template<typename system_tag , typename KeyIterator , typename ValueIterator >
void	radix_sort (const uint32 n, KeyIterator keys, ValueIterator values, nvbio::vector< system_tag, uint8 > &temp_storage)
template<typename system_tag , typename key_iterator1 , typename key_iterator2 , typename value_iterator1 , typename value_iterator2 , typename key_output , typename value_output >
void	merge_by_key (const uint32 A_len, const uint32 B_len, const key_iterator1 A_keys, const key_iterator2 B_keys, const value_iterator1 A_values, const value_iterator2 B_values, key_output C_keys, value_output C_values, nvbio::vector< system_tag, uint8 > &temp_storage)
template<typename PredicateIterator >
bool	any (const host_tag tag, const uint32 n, const PredicateIterator pred)
template<typename PredicateIterator >
bool	all (const host_tag tag, const uint32 n, const PredicateIterator pred)
template<typename T1 , typename T2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE is_sorted_iterator< T1, T2 >	operator+ (const is_sorted_iterator< T1, T2 > it, const int64 i)
template<typename T1 , typename T2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int64	operator- (const is_sorted_iterator< T1, T2 > it1, const is_sorted_iterator< T1, T2 > it2)
template<typename T1 , typename T2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator!= (const is_sorted_iterator< T1, T2 > it1, const is_sorted_iterator< T1, T2 > it2)
template<typename T1 , typename T2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator== (const is_sorted_iterator< T1, T2 > it1, const is_sorted_iterator< T1, T2 > it2)
template<typename T1 , typename T2 , typename H >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE is_segment_sorted_iterator< T1, T2, H >	operator+ (const is_segment_sorted_iterator< T1, T2, H > it, const int64 i)
template<typename T1 , typename T2 , typename H >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int64	operator- (const is_segment_sorted_iterator< T1, T2, H > it1, const is_segment_sorted_iterator< T1, T2, H > it2)
template<typename T1 , typename T2 , typename H >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator!= (const is_segment_sorted_iterator< T1, T2, H > it1, const is_segment_sorted_iterator< T1, T2, H > it2)
template<typename T1 , typename T2 , typename H >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator== (const is_segment_sorted_iterator< T1, T2, H > it1, const is_segment_sorted_iterator< T1, T2, H > it2)
template<typename Iterator , typename Functor >
void	for_each (const host_tag tag, const uint64 n, const Iterator in, Functor functor)
template<typename Iterator , typename Functor >
void	for_each (const device_tag tag, const uint64 n, const Iterator in, Functor functor)
template<typename Iterator , typename Output , typename Functor >
void	transform (const device_tag tag, const uint64 n, const Iterator in, const Output out, const Functor functor)
template<typename Iterator , typename Output , typename Functor >
void	transform (const host_tag tag, const uint32 n, const Iterator in, const Output out, const Functor functor)
template<typename Iterator1 , typename Iterator2 , typename Output , typename Functor >
void	transform (const device_tag tag, const uint32 n, const Iterator1 in1, const Iterator2 in2, const Output out, const Functor functor)
template<typename Iterator1 , typename Iterator2 , typename Output , typename Functor >
void	transform (const host_tag tag, const uint32 n, const Iterator1 in1, const Iterator2 in2, const Output out, const Functor functor)
template<typename InputIterator , typename BinaryOp >
std::iterator_traits < InputIterator >::value_type	reduce (host_tag tag, const uint32 n, InputIterator in, BinaryOp op, nvbio::vector< host_tag, uint8 > &temp_storage)
template<typename InputIterator , typename OutputIterator , typename BinaryOp >
void	inclusive_scan (host_tag tag, const uint32 n, InputIterator in, OutputIterator out, BinaryOp op, nvbio::vector< host_tag, uint8 > &temp_storage)
template<typename InputIterator , typename OutputIterator , typename BinaryOp , typename Identity >
void	exclusive_scan (host_tag tag, const uint32 n, InputIterator in, OutputIterator out, BinaryOp op, Identity identity, nvbio::vector< host_tag, uint8 > &temp_storage)
template<typename InputIterator , typename FlagsIterator , typename OutputIterator >
uint32	copy_flagged (const host_tag tag, const uint32 n, InputIterator in, FlagsIterator flags, OutputIterator out, nvbio::vector< host_tag, uint8 > &temp_storage)
template<typename InputIterator , typename OutputIterator , typename Predicate >
uint32	copy_if (const host_tag tag, const uint32 n, InputIterator in, OutputIterator out, const Predicate pred, nvbio::vector< host_tag, uint8 > &temp_storage)
template<typename InputIterator , typename OutputIterator , typename CountIterator >
uint32	runlength_encode (const host_tag tag, const uint32 n, InputIterator in, OutputIterator out, CountIterator counts, nvbio::vector< host_tag, uint8 > &temp_storage)
template<typename KeyIterator , typename ValueIterator , typename OutputKeyIterator , typename OutputValueIterator , typename ReductionOp >
uint32	reduce_by_key (const host_tag tag, const uint32 n, KeyIterator keys_in, ValueIterator values_in, OutputKeyIterator keys_out, OutputValueIterator values_out, ReductionOp reduction_op, nvbio::vector< host_tag, uint8 > &temp_storage)
template<typename KeyIterator , typename ValueIterator , typename OutputIterator >
void	lower_bound (const device_tag tag, const uint32 n, ValueIterator values, const uint32 n_keys, KeyIterator keys, OutputIterator indices)
template<typename KeyIterator , typename ValueIterator , typename OutputIterator >
void	lower_bound (const host_tag tag, const uint32 n, ValueIterator values, const uint32 n_keys, KeyIterator keys, OutputIterator indices)
template<typename KeyIterator , typename ValueIterator , typename OutputIterator >
void	upper_bound (const device_tag tag, const uint32 n, ValueIterator values, const uint32 n_keys, KeyIterator keys, OutputIterator indices)
template<typename KeyIterator , typename ValueIterator , typename OutputIterator >
void	upper_bound (const host_tag tag, const uint32 n, ValueIterator values, const uint32 n_keys, KeyIterator keys, OutputIterator indices)
template<typename KeyIterator >
void	radix_sort (const host_tag tag, const uint32 n, KeyIterator keys, nvbio::vector< host_tag, uint8 > &temp_storage)
template<typename KeyIterator , typename ValueIterator >
void	radix_sort (const host_tag tag, const uint32 n, KeyIterator keys, ValueIterator values, nvbio::vector< host_tag, uint8 > &temp_storage)
template<typename key_iterator1 , typename key_iterator2 >
uint2	corank (const int32 i, const key_iterator1 A, const int32 m, const key_iterator2 B, const int32 n)
template<typename key_iterator1 , typename key_iterator2 , typename value_iterator1 , typename value_iterator2 , typename key_output , typename value_output >
void	merge_by_key (const host_tag tag, const uint32 A_len, const uint32 B_len, const key_iterator1 A_keys, const key_iterator2 B_keys, const value_iterator1 A_values, const value_iterator2 B_values, key_output C_keys, value_output C_values)
template<typename key_iterator1 , typename key_iterator2 , typename value_iterator1 , typename value_iterator2 , typename key_output , typename value_output >
void	merge_by_key (const device_tag tag, const uint32 A_len, const uint32 B_len, const key_iterator1 A_keys, const key_iterator2 B_keys, const value_iterator1 A_values, const value_iterator2 B_values, key_output C_keys, value_output C_values)
template<typename Type , typename Sequence , typename Compare >
void	swap (priority_deque< Type, Sequence, Compare > &deque1, priority_deque< Type, Sequence, Compare > &deque2)
	Swaps the elements of two priority deques. More...
template<typename T , typename CounterT >
void	swap (SharedPointer< T, CounterT > &a, SharedPointer< T, CounterT > &b)
template<typename T , typename U , typename CounterT >
SharedPointer< T, CounterT >	static_pointer_cast (const SharedPointer< U, CounterT > &r)
template<typename T , typename U , typename CounterT >
SharedPointer< T, CounterT >	const_pointer_cast (const SharedPointer< U, CounterT > &r)
template<typename T , typename U , typename CounterT >
SharedPointer< T, CounterT >	dynamic_pointer_cast (const SharedPointer< U, CounterT > &r)
template<typename CharT , typename TraitsT , typename T , typename CounterT >
std::basic_ostream< CharT, TraitsT > &	operator<< (std::basic_ostream< CharT, TraitsT > &os, const SharedPointer< T, CounterT > &p)
template<typename DeleterT , typename T , typename CounterT >
DeleterT *	get_deleter (const SharedPointer< T, CounterT > &p)
template<typename T , typename CounterT >
void	swap (WeakPointer< T, CounterT > &a, WeakPointer< T, CounterT > &b)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	any (const simd4u8 op)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8	operator~ (const simd4u8 op)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8	operator== (const simd4u8 op1, const simd4u8 op2)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8	operator!= (const simd4u8 op1, const simd4u8 op2)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8	operator>= (const simd4u8 op1, const simd4u8 op2)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8	operator> (const simd4u8 op1, const simd4u8 op2)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8	operator<= (const simd4u8 op1, const simd4u8 op2)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8	operator< (const simd4u8 op1, const simd4u8 op2)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8	operator+ (const simd4u8 op1, const simd4u8 op2)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8 &	operator+= (simd4u8 &op1, const simd4u8 op2)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8	operator- (const simd4u8 op1, const simd4u8 op2)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8 &	operator-= (simd4u8 &op1, const simd4u8 op2)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8	max (const simd4u8 op1, const simd4u8 op2)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8	min (const simd4u8 op1, const simd4u8 op2)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8	and_op (const simd4u8 op1, const simd4u8 op2)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8	or_op (const simd4u8 op1, const simd4u8 op2)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8	ternary_op (const simd4u8 mask, const simd4u8 op1, const simd4u8 op2)
template<uint32 I>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8	get (const simd4u8 op)
template<uint32 I>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	set (simd4u8 op, const uint8 v)
template<typename T , uint32 DIM>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StaticVector < T, DIM >	operator+ (const StaticVector< T, DIM > &op1, const StaticVector< T, DIM > &op2)
template<typename T , uint32 DIM>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StaticVector < T, DIM > &	operator+= (StaticVector< T, DIM > &op1, const StaticVector< T, DIM > &op2)
template<typename T , uint32 DIM>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StaticVector < T, DIM >	operator- (const StaticVector< T, DIM > &op1, const StaticVector< T, DIM > &op2)
template<typename T , uint32 DIM>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StaticVector < T, DIM > &	operator-= (StaticVector< T, DIM > &op1, const StaticVector< T, DIM > &op2)
template<typename T , uint32 DIM>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StaticVector < T, DIM >	operator* (const StaticVector< T, DIM > &op1, const StaticVector< T, DIM > &op2)
template<typename T , uint32 DIM>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StaticVector < T, DIM > &	operator*= (StaticVector< T, DIM > &op1, const StaticVector< T, DIM > &op2)
template<typename T , uint32 DIM>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StaticVector < T, DIM >	operator/ (const StaticVector< T, DIM > &op1, const StaticVector< T, DIM > &op2)
template<typename T , uint32 DIM>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StaticVector < T, DIM > &	operator/= (StaticVector< T, DIM > &op1, const StaticVector< T, DIM > &op2)
template<typename T , uint32 DIM>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StaticVector < T, DIM >	min (const StaticVector< T, DIM > &op1, const StaticVector< T, DIM > &op2)
template<typename T , uint32 DIM>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StaticVector < T, DIM >	max (const StaticVector< T, DIM > &op1, const StaticVector< T, DIM > &op2)
template<typename T , uint32 DIM>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	any (const StaticVector< T, DIM > &op)
template<typename T , uint32 DIM>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	all (const StaticVector< T, DIM > &op)
template<typename T , uint32 DIM>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator== (const StaticVector< T, DIM > &op1, const StaticVector< T, DIM > &op2)
template<typename T , uint32 DIM>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator!= (const StaticVector< T, DIM > &op1, const StaticVector< T, DIM > &op2)
template<typename T >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE strided_iterator< T >	make_strided_iterator (T it, const uint32 stride)
template<typename T >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator== (const strided_iterator< T > it1, const strided_iterator< T > it2)
template<typename T >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator!= (const strided_iterator< T > it1, const strided_iterator< T > it2)
template<typename T >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator< (const strided_iterator< T > it1, const strided_iterator< T > it2)
template<typename T >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator<= (const strided_iterator< T > it1, const strided_iterator< T > it2)
template<typename T >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator> (const strided_iterator< T > it1, const strided_iterator< T > it2)
template<typename T >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator>= (const strided_iterator< T > it1, const strided_iterator< T > it2)
template<uint32 BLOCKSIZE, typename T , block_strided_layout LAYOUT>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator== (const block_strided_iterator< BLOCKSIZE, T, LAYOUT > it1, const block_strided_iterator< BLOCKSIZE, T, LAYOUT > it2)
template<uint32 BLOCKSIZE, typename T , block_strided_layout LAYOUT>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator!= (const block_strided_iterator< BLOCKSIZE, T, LAYOUT > it1, const block_strided_iterator< BLOCKSIZE, T, LAYOUT > it2)
template<typename Iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	sample (const SumTree< Iterator > &tree, const float value)
uint64	peak_resident_memory ()
uint32	num_physical_cores ()
uint32	num_logical_cores ()
void	yield ()
uint32	balance_batch_size (uint32 batch_size, uint32 total_count, uint32 thread_count)
	return a number close to batch_size that achieves best threading balance More...
template<typename T >
vector_view< T *, uint64 >	device_view (thrust::device_vector< T > &vec)
template<typename T >
vector_view< const T *, uint64 >	device_view (const thrust::device_vector< T > &vec)
template<typename T >
vector_view< T *, uint64 >	plain_view (thrust::device_vector< T > &vec)
template<typename T >
vector_view< const T *, uint64 >	plain_view (const thrust::device_vector< T > &vec)
template<typename T >
vector_view< T *, uint64 >	plain_view (thrust::host_vector< T > &vec)
template<typename T >
vector_view< const T *, uint64 >	plain_view (const thrust::host_vector< T > &vec)
template<typename T >
T *	raw_pointer (thrust::device_vector< T > &vec)
template<typename T >
const T *	raw_pointer (const thrust::device_vector< T > &vec)
template<typename T >
T *	raw_pointer (thrust::host_vector< T > &vec)
template<typename T >
const T *	raw_pointer (const thrust::host_vector< T > &vec)
template<typename T >
thrust::device_vector< T > ::iterator	begin (thrust::device_vector< T > &vec)
template<typename T >
thrust::device_vector< T > ::const_iterator	begin (const thrust::device_vector< T > &vec)
template<typename T >
thrust::host_vector< T >::iterator	begin (thrust::host_vector< T > &vec)
template<typename T >
thrust::host_vector< T > ::const_iterator	begin (const thrust::host_vector< T > &vec)
template<typename T , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE transform_iterator< T, Transform >	make_transform_iterator (const T it, const Transform f)
template<typename T , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator== (const transform_iterator< T, Transform > it1, const transform_iterator< T, Transform > it2)
template<typename T , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator!= (const transform_iterator< T, Transform > it1, const transform_iterator< T, Transform > it2)
template<typename T , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator< (const transform_iterator< T, Transform > it1, const transform_iterator< T, Transform > it2)
template<typename T , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator<= (const transform_iterator< T, Transform > it1, const transform_iterator< T, Transform > it2)
template<typename T , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator> (const transform_iterator< T, Transform > it1, const transform_iterator< T, Transform > it2)
template<typename T , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator>= (const transform_iterator< T, Transform > it1, const transform_iterator< T, Transform > it2)
template<typename T1 , typename T2 , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE binary_transform_iterator< T1, T2, Transform >	make_binary_transform_iterator (const T1 it1, const T2 it2, const Transform f)
template<typename T1 , typename T2 , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator== (const binary_transform_iterator< T1, T2, Transform > it1, const binary_transform_iterator< T1, T2, Transform > it2)
template<typename T1 , typename T2 , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator!= (const binary_transform_iterator< T1, T2, Transform > it1, const binary_transform_iterator< T1, T2, Transform > it2)
template<typename T1 , typename T2 , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator< (const binary_transform_iterator< T1, T2, Transform > it1, const binary_transform_iterator< T1, T2, Transform > it2)
template<typename T1 , typename T2 , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator<= (const binary_transform_iterator< T1, T2, Transform > it1, const binary_transform_iterator< T1, T2, Transform > it2)
template<typename T1 , typename T2 , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator> (const binary_transform_iterator< T1, T2, Transform > it1, const binary_transform_iterator< T1, T2, Transform > it2)
template<typename T1 , typename T2 , typename Transform >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator>= (const binary_transform_iterator< T1, T2, Transform > it1, const binary_transform_iterator< T1, T2, Transform > it2)
template<typename A , typename B >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	equal ()
template<typename Out , typename In >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Out	binary_cast (const In in)
template<uint32 C>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	is_pow2 ()
template<uint32 N, typename I >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE I	align (const I a)
template<uint32 N, typename I >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE I	align_down (const I a)
template<typename T >
device_iterator_type< T >::type	device_iterator (const T it)
template<uint32 VECTOR_WIDTH, typename T >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	vector_load (const T *ptr, T *vec)
template<typename Iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	length (const vector_view< Iterator > &vec)
template<typename T >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE T	raw_pointer (const vector_view< T > &vec)
template<typename T , typename I >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE T	begin (vector_view< T, I > &vec)
template<typename T , typename I >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE T	begin (const vector_view< T, I > &vec)
template<typename T >
vector_view< T *, uint64 >	plain_view (std::vector< T > &vec)
template<typename T >
vector_view< const T *, uint64 >	plain_view (const std::vector< T > &vec)
template<typename T >
T *	raw_pointer (std::vector< T > &vec)
template<typename T >
const T *	raw_pointer (const std::vector< T > &vec)
template<typename T >
T *	begin (T *vec)
template<typename T >
const T *	begin (const T *vec)
template<typename FMIndex , typename String , typename Stack , typename Delegate >
NVBIO_HOST_DEVICE void	hamming_backtrack (const FMIndex fmi, const String pattern, const uint32 len, const uint32 seed, const uint32 mismatches, Stack stack, Delegate &delegate)
template<typename TRankDictionary1 , typename TSuffixArray1 , typename TRankDictionary2 , typename TSuffixArray2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	extend_forward (const fm_index< TRankDictionary1, TSuffixArray1 > &f_fmi, const fm_index< TRankDictionary2, TSuffixArray2 > &r_fmi, typename fm_index< TRankDictionary1, TSuffixArray1 >::range_type &f_range, typename fm_index< TRankDictionary2, TSuffixArray2 >::range_type &r_range, uint8 c)
template<typename TRankDictionary1 , typename TSuffixArray1 , typename TRankDictionary2 , typename TSuffixArray2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	extend_backwards (const fm_index< TRankDictionary1, TSuffixArray1 > &f_fmi, const fm_index< TRankDictionary2, TSuffixArray2 > &r_fmi, typename fm_index< TRankDictionary1, TSuffixArray1 >::range_type &f_range, typename fm_index< TRankDictionary2, TSuffixArray2 >::range_type &r_range, uint8 c)
template<typename StreamIterator >
uint32	gen_sa (const uint32 n, const StreamIterator T, int32 *SA)
template<typename StreamIterator >
uint32	gen_bwt_from_sa (const uint32 n, const StreamIterator T, const int32 *SA, StreamIterator bwt)
template<typename StreamIterator >
int32	gen_bwt (const uint32 n, const StreamIterator T, int32 *buffer, StreamIterator bwt)
template<typename StreamIterator >
int64	gen_bwt (const uint32 n, const StreamIterator T, int64 *buffer, StreamIterator bwt)
void	gen_bwt_count_table (uint32 *count_table)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	rank_all (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type k, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::vector_type *out)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	rank_all (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::range_type range, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::vector_type *outl, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::vector_type *outh)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::index_type	basic_inv_psi (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::range_type i)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::index_type	rank (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type k, uint8 c)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::range_type	rank (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::range_type range, uint8 c)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE TRankDictionary::vec4_type	rank4 (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type k)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	rank4 (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, typename fm_index< TRankDictionary, TSuffixArray, TL2 >::range_type range, typename TRankDictionary::vec4_type *outl, typename TRankDictionary::vec4_type *outh)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 , typename Iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::range_type	match (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const Iterator pattern, const uint32 pattern_len)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 , typename Iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::range_type	match (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const Iterator pattern, const uint32 pattern_len, const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::range_type in_range)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 , typename Iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::range_type	match_reverse (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const Iterator pattern, const uint32 pattern_len)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::index_type	basic_inv_psi (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type i)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::range_type	inv_psi (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type i)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::index_type	locate (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type i)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::range_type	locate_ssa_iterator (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type i)
template<typename TRankDictionary , typename TSuffixArray , typename TL2 >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index < TRankDictionary, TSuffixArray, TL2 > ::index_type	lookup_ssa_iterator (const fm_index< TRankDictionary, TSuffixArray, TL2 > &fmi, const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::range_type it)
template<typename pattern_type , typename fm_index_type , typename delegate_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	find_kmems (const uint32 pattern_len, const pattern_type pattern, const uint32 x, const fm_index_type f_index, const fm_index_type r_index, delegate_type &handler, const uint32 min_intv=1u, const uint32 min_span=1u)
template<typename pattern_type , typename fm_index_type , typename delegate_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	find_threshold_kmems (const uint32 pattern_len, const pattern_type pattern, const uint32 x, const fm_index_type f_index, const fm_index_type r_index, delegate_type &handler, const uint32 min_intv=1u, const uint32 min_span=1u)
template<typename system_tag , typename fm_index_type >
uint32	string_batch_bound (const MEMFilter< system_tag, fm_index_type > &filter, const uint32 mem_count)
void	build_buckets (const uint64 key_range, const uint32 n_keys, const uint64 *keys, const uint32 bucket_size, nvbio::vector< host_tag, uint32 > &buckets, const bool upper)
template<uint8 c>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	popc_2bit (const uint64 x)
template<uint8 c>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	popc_2bit (const uint64 mask, const uint32 i)
uint32	popc_2bit (const uint64 *page, const uint32 n, const uint32 mod, const uint32 c)
template<typename input_storage , typename output_storage , uint32 SYMBOL_SIZE, typename index_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	copy (const uint32 len, const PackedStream< input_storage, uint8, SYMBOL_SIZE, true, index_type > in, PackedStream< output_storage, uint8, SYMBOL_SIZE, true, index_type > out)
template<uint32 SYMBOL_COUNT>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	save_occurrences (const uint32 k, const uint32 occ_intv_log, const uint32 occ_intv, const uint32 *partials, uint32 *occ)
template<typename input_storage , typename output_storage , uint32 SYMBOL_SIZE, typename index_type >
NVBIO_FORCEINLINE NVBIO_HOST void	copy (const uint32 len, const PackedStream< input_storage, uint8, SYMBOL_SIZE, true, index_type > in, PackedStream< output_storage, uint8, SYMBOL_SIZE, true, index_type > out, const uint32 occ_intv_log, const uint32 occ_intv, uint32 *partials, uint32 *occ, const uint32 *count_table)
template<uint32 SYMBOL_SIZE, uint32 K, typename SymbolIterator , typename IndexType >
void	build_occurrence_table (SymbolIterator begin, SymbolIterator end, IndexType *occ, IndexType *cnt)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	unpack_add (uint4 *op1, const uint32 op2)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	unpack_add (uint64_4 *op1, const uint32 op2)
template<uint32 SYMBOL_SIZE_T, uint32 K, typename TextString , typename OccIterator , typename CountTable >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8	text (const rank_dictionary< SYMBOL_SIZE_T, K, TextString, OccIterator, CountTable > &dict, const uint32 i)
template<uint32 SYMBOL_SIZE_T, uint32 K, typename TextString , typename OccIterator , typename CountTable >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8	text (const rank_dictionary< SYMBOL_SIZE_T, K, TextString, OccIterator, CountTable > &dict, const uint64 i)
template<uint32 SYMBOL_SIZE_T, uint32 K, typename TextString , typename OccIterator , typename CountTable , typename IndexType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE IndexType	rank (const rank_dictionary< SYMBOL_SIZE_T, K, TextString, OccIterator, CountTable > &dict, const IndexType i, const uint32 c)
template<uint32 SYMBOL_SIZE_T, uint32 K, typename TextString , typename OccIterator , typename CountTable , typename IndexType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE vector_type < IndexType, 2 >::type	rank (const rank_dictionary< SYMBOL_SIZE_T, K, TextString, OccIterator, CountTable > &dict, const typename vector_type< IndexType, 2 >::type range, const uint32 c)
template<uint32 K, typename TextString , typename OccIterator , typename CountTable , typename IndexType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE vector_type < IndexType, 4 >::type	rank4 (const rank_dictionary< 2, K, TextString, OccIterator, CountTable > &dict, const IndexType i)
template<uint32 K, typename TextString , typename OccIterator , typename CountTable >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	rank4 (const rank_dictionary< 2, K, TextString, OccIterator, CountTable > &dict, const uint2 range, uint4 *outl, uint4 *outh)
template<uint32 K, typename TextString , typename OccIterator , typename CountTable >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	rank4 (const rank_dictionary< 2, K, TextString, OccIterator, CountTable > &dict, const uint64_2 range, uint64_4 *outl, uint64_4 *outh)
template<uint32 SYMBOL_SIZE, uint32 K, typename TextString , typename OccIterator , typename CountTable >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE rank_dictionary< SYMBOL_SIZE, K, TextString, OccIterator, CountTable >::vector_type	rank_all (const rank_dictionary< SYMBOL_SIZE, K, TextString, OccIterator, CountTable > &dict, const typename rank_dictionary< SYMBOL_SIZE, K, TextString, OccIterator, CountTable >::index_type i)
template<uint32 SYMBOL_SIZE, uint32 K, typename TextString , typename OccIterator , typename CountTable >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	rank_all (const rank_dictionary< SYMBOL_SIZE, K, TextString, OccIterator, CountTable > &dict, const typename rank_dictionary< SYMBOL_SIZE, K, TextString, OccIterator, CountTable >::index_type i, typename rank_dictionary< SYMBOL_SIZE, K, TextString, OccIterator, CountTable >::vector_type *out)
template<uint32 SYMBOL_SIZE, uint32 K, typename TextString , typename OccIterator , typename CountTable >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	rank_all (const rank_dictionary< SYMBOL_SIZE, K, TextString, OccIterator, CountTable > &dict, const typename rank_dictionary< SYMBOL_SIZE, K, TextString, OccIterator, CountTable >::range_type range, typename rank_dictionary< SYMBOL_SIZE, K, TextString, OccIterator, CountTable >::vector_type *outl, typename rank_dictionary< SYMBOL_SIZE, K, TextString, OccIterator, CountTable >::vector_type *outh)
SSA_value_multiple::plain_view_type	plain_view (const SSA_value_multiple &vec)
SSA_value_multiple_device::plain_view_type	plain_view (const SSA_value_multiple_device &vec)
template<uint32 K, typename index_type >
SSA_index_multiple< K, index_type >::plain_view_type	plain_view (const SSA_index_multiple< K, index_type > &vec)
OutputStream *	open_output_file (const char *file_name, const char *compressor, const char *options)
io::ReadData::plain_view_type	plain_view (io::ReadData &read_data)
io::ReadData::const_plain_view_type	plain_view (const io::ReadData &read_data)
io::SequenceData::plain_view_type	plain_view (io::SequenceData &sequence_data)
io::SequenceData::const_plain_view_type	plain_view (const io::SequenceData &sequence_data)
template<typename system_tag >
io::SequenceDataStorage < system_tag > ::plain_view_type	plain_view (io::SequenceDataStorage< system_tag > &sequence_data)
template<typename system_tag >
io::SequenceDataStorage < system_tag > ::const_plain_view_type	plain_view (const io::SequenceDataStorage< system_tag > &sequence_data)
template<typename StreamType , typename QualType >
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	length (const ReadStream< StreamType, QualType > &read)
template<typename string_type , typename index_iterator , typename qgram_iterator >
void	generate_qgrams (const uint32 q, const uint32 symbol_size, const uint32 string_len, const string_type string, const uint32 n_qgrams, const index_iterator indices, qgram_iterator qgrams)
template<typename string_set_type , typename index_iterator , typename qgram_iterator >
void	generate_qgrams (const uint32 q, const uint32 symbol_size, const string_set_type string_set, const uint32 n_qgrams, const index_iterator indices, qgram_iterator qgrams)
template<typename SystemTag , typename QT , typename IT , typename CT >
QGramIndexViewCore< QT, IT, CT >	plain_view (const QGramIndexViewCore< QT, IT, CT > qgram)
template<typename SystemTag , typename QT , typename IT , typename CT >
QGramIndexViewCore< QT *, IT *, CT * >	plain_view (QGramIndexCore< SystemTag, QT, IT, CT > &qgram)
template<typename SystemTag , typename QT , typename IT , typename CT >
QGramIndexViewCore< const QT *, const IT *, const CT * >	plain_view (const QGramIndexCore< SystemTag, QT, IT, CT > &qgram)
QGroupIndexView	plain_view (const QGroupIndexView qgram)
ConstQGroupIndexView	plain_view (const ConstQGroupIndexView qgram)
QGroupIndexView	plain_view (QGroupIndexDevice &qgroup)
ConstQGroupIndexView	plain_view (const QGroupIndexDevice &qgroup)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	bits_per_symbol (const Alphabet alphabet)
template<Alphabet ALPHABET>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE char	to_char (const uint8 c)
template<Alphabet ALPHABET>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8	from_char (const char c)
template<Alphabet ALPHABET, typename SymbolIterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	to_string (const SymbolIterator begin, const uint32 n, char *string)
template<Alphabet ALPHABET, typename SymbolIterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	to_string (const SymbolIterator begin, const SymbolIterator end, char *string)
template<Alphabet ALPHABET, typename SymbolIterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	from_string (const char *begin, const char *end, SymbolIterator symbols)
template<Alphabet ALPHABET, typename SymbolIterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	from_string (const char *begin, SymbolIterator symbols)
template<Alphabet ALPHABET, typename Iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE transform_iterator< Iterator, to_char_functor< ALPHABET > >	to_string (Iterator it)
template<Alphabet ALPHABET, typename Iterator >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE transform_iterator< Iterator, from_char_functor< ALPHABET > >	from_string (Iterator it)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE char	rna_to_char (const uint8 c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8	char_to_rna (const char c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE char	protein_to_char (const uint8 c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8	char_to_protein (const char c)
template<typename StringType , typename CoordType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Infix < StringType, CoordType >	make_infix (const StringType string, const CoordType coords)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	infix_begin (const uint32_2 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	infix_end (const uint32_2 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	length (const uint32_2 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	infix_begin (const uint64_2 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	infix_end (const uint64_2 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	length (const uint64_2 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	infix_begin (const uint32_4 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	infix_end (const uint32_4 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	length (const uint32_4 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	infix_begin (const uint64_4 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	infix_end (const uint64_4 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	length (const uint64_4 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	string_id (const uint32_4 &infix)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	string_id (const uint64_4 &infix)
template<typename StringType , typename CoordType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Infix < StringType, CoordType > ::index_type	infix_begin (const Infix< StringType, CoordType > &infix)
template<typename StringType , typename CoordType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Infix < StringType, CoordType > ::index_type	infix_end (const Infix< StringType, CoordType > &infix)
template<typename StringType , typename CoordType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	string_id (const InfixCore< StringType, CoordType, 4u > &infix)
template<typename StringType , typename CoordType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	length (const Infix< StringType, CoordType > &infix)
template<typename StringType , typename CoordType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Prefix < StringType, CoordType >	make_prefix (const StringType string, const CoordType coords)
template<typename StringType , typename CoordType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	string_id (const PrefixCore< StringType, CoordType, 2u > &prefix)
template<typename StringType , typename CoordType , uint32 CoordDim>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	length (const PrefixCore< StringType, CoordType, CoordDim > &prefix)
template<typename index_type , typename seed_functor , typename index_vector_type >
index_type	enumerate_string_seeds (const index_type string_len, const seed_functor seeder, index_vector_type &indices)
template<typename string_set_type , typename seed_functor , typename index_vector_type >
uint64	enumerate_string_set_seeds (const string_set_type string_set, const seed_functor seeder, index_vector_type &indices)
template<typename out_coord_type , typename in_coord_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE out_coord_type	project_coords (const in_coord_type i)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64	length (const char *str)
template<typename StringType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator< (const string_iterator< StringType > &it1, const string_iterator< StringType > &it2)
template<typename StringType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator<= (const string_iterator< StringType > &it1, const string_iterator< StringType > &it2)
template<typename StringType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator> (const string_iterator< StringType > &it1, const string_iterator< StringType > &it2)
template<typename StringType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator>= (const string_iterator< StringType > &it1, const string_iterator< StringType > &it2)
template<typename StringType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator== (const string_iterator< StringType > &it1, const string_iterator< StringType > &it2)
template<typename StringType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator!= (const string_iterator< StringType > &it1, const string_iterator< StringType > &it2)
template<typename StringType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_iterator< StringType > &	operator++ (string_iterator< StringType > &it)
template<typename StringType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_iterator< StringType >	operator++ (string_iterator< StringType > &it, int dummy)
template<typename StringType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_iterator< StringType > &	operator-- (string_iterator< StringType > &it)
template<typename StringType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_iterator< StringType >	operator-- (string_iterator< StringType > &it, int dummy)
template<typename StringType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_iterator< StringType > &	operator+= (string_iterator< StringType > &it, const typename string_iterator< StringType >::difference_type distance)
template<typename StringType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_iterator< StringType > &	operator-= (string_iterator< StringType > &it, const typename string_iterator< StringType >::difference_type distance)
template<typename StringType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_iterator< StringType >	operator+ (const string_iterator< StringType > it, const typename string_iterator< StringType >::difference_type distance)
template<typename StringType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_iterator< StringType >	operator- (const string_iterator< StringType > it, const typename string_iterator< StringType >::difference_type distance)
template<typename StringType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_iterator< StringType > ::difference_type	operator- (const string_iterator< StringType > it1, const string_iterator< StringType > it2)
template<typename StringSet >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StringSetIterator< StringSet > ::difference_type	operator- (const StringSetIterator< StringSet > &it1, const StringSetIterator< StringSet > &it2)
template<typename StringSet >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StringSetIterator< StringSet >	operator+ (const StringSetIterator< StringSet > &it, const int32 d)
template<typename StringSet >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StringSetIterator< StringSet >	operator- (const StringSetIterator< StringSet > &it, const int32 d)
template<typename StringSet >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StringSetIterator< StringSet > &	operator+= (StringSetIterator< StringSet > &it, const int32 d)
template<typename StringSet >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StringSetIterator< StringSet > &	operator-= (StringSetIterator< StringSet > &it, const int32 d)
template<typename StringSet >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator< (const StringSetIterator< StringSet > &it1, const StringSetIterator< StringSet > &it2)
template<typename StringSet >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator> (const StringSetIterator< StringSet > &it1, const StringSetIterator< StringSet > &it2)
template<typename StringSet >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator<= (const StringSetIterator< StringSet > &it1, const StringSetIterator< StringSet > &it2)
template<typename StringSet >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator>= (const StringSetIterator< StringSet > &it1, const StringSetIterator< StringSet > &it2)
template<typename StringSet >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator== (const StringSetIterator< StringSet > &it1, const StringSetIterator< StringSet > &it2)
template<typename StringSet >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	operator!= (const StringSetIterator< StringSet > &it1, const StringSetIterator< StringSet > &it2)
template<typename InStringSet , typename StringIterator , typename OffsetIterator >
void	copy (const InStringSet &in_string_set, ConcatenatedStringSet< StringIterator, OffsetIterator > &out_string_set)
template<typename InStringSet , typename StringIterator , typename LengthIterator >
void	copy (const InStringSet &in_string_set, StridedStringSet< StringIterator, LengthIterator > &out_string_set)
template<typename InStringSet , typename StreamIterator , typename SymbolType , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator >
void	copy (const InStringSet &in_string_set, StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator > &out_string_set)
template<typename StreamIterator , typename SymbolType , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator >
CachedPackedSparseStringSet < StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator, typename std::iterator_traits < StreamIterator >::value_type > ::cached_string_set	make_cached_string_set (const SparseStringSet< PackedStream< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T >, LengthIterator > string_set)
template<typename StreamIterator , typename SymbolType , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator >
CachedPackedConcatStringSet < StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator, typename std::iterator_traits < StreamIterator >::value_type > ::cached_string_set	make_cached_string_set (const ConcatenatedStringSet< PackedStream< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T >, LengthIterator > string_set)
template<typename StringType , typename CoordType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Suffix < StringType, CoordType >	make_suffix (const StringType string, const CoordType coords)
template<typename StringType , typename CoordType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	string_id (const SuffixCore< StringType, CoordType, 2u > &suffix)
template<typename StringType , typename CoordType , uint32 CoordDim>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	length (const SuffixCore< StringType, CoordType, CoordDim > &suffix)
template<typename string_set_type >
int32	compare_suffixes (const string_set_type string_set, const uint2 suffix1, const uint2 suffix2)
template<typename string_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint2	vectorized_string_range (const string_type &string)
template<typename string_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	vectorized_string_load (const string_type &string, const uint32 i, typename string_traits< string_type >::value_type *vector)
template<typename system_tag , typename string_iterator , typename index_type , typename symbol_type >
void	setup (const index_type string_len, const string_iterator &string, WaveletTreeStorage< system_tag, index_type, symbol_type > &out_tree)
template<typename BitStreamIterator , typename IndexIterator , typename SymbolType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE WaveletTree < BitStreamIterator, IndexIterator, SymbolType > ::index_type	rank (const WaveletTree< BitStreamIterator, IndexIterator, SymbolType > &tree, const typename WaveletTree< BitStreamIterator, IndexIterator, SymbolType >::index_type i, const uint32 c)
template<typename BitStreamIterator , typename IndexIterator , typename SymbolType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE WaveletTree < BitStreamIterator, IndexIterator, SymbolType > ::range_type	rank (const WaveletTree< BitStreamIterator, IndexIterator, SymbolType > &tree, const typename WaveletTree< BitStreamIterator, IndexIterator, SymbolType >::range_type range, const uint32 c)
template<typename BitStreamIterator , typename IndexIterator , typename IndexType , typename SymbolType >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE SymbolType	text (const WaveletTree< BitStreamIterator, IndexIterator, SymbolType > &tree, const IndexType i)
template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type , typename offsets_iterator >
void	bwte (const ConcatenatedStringSet< PackedStream< storage_type, uint8, SYMBOL_SIZE, BIG_ENDIAN, typename std::iterator_traits< offsets_iterator >::value_type >, offsets_iterator > string_set, PagedText< SYMBOL_SIZE, BIG_ENDIAN > &BWT_ext, SparseSymbolSet &BWT_ext_dollars, BWTParams *params=NULL)
DCSView	plain_view (DCS &dcs)
DCSView	plain_view (const DCS &dcs)
void	calculateColbournAndLingDC (const uint32 r, uint32 &maxv, std::vector< uint32 > &samples)
SetBWTHandler *	open_bwt_file (const char *output_name, const char *params)
template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type , typename output_handler >
void	large_bwt (const ConcatenatedStringSet< PackedStream< storage_type, uint8, SYMBOL_SIZE, BIG_ENDIAN, uint64 >, uint64 * > string_set, output_handler &output, BWTParams *params=NULL)
template<typename TrieType , typename NodeVector >
void	build_suffix_trie (const TrieType &in_trie, NodeVector &out_nodes)
int	alloc_test ()
int	syncblocks_test ()
int	condition_test ()
int	rank_test (int argc, char *argv[])
int	work_queue_test (int argc, char *argv[])
int	string_set_test (int argc, char *argv[])
int	sum_tree_test ()
int	qgram_test (int argc, char *argv[])
int	sequence_test (int argc, char *argv[])
int	wavelet_test (int argc, char *argv[])
int	bloom_filter_test (int argc, char *argv[])
template<typename StreamType , typename SymbolType , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename W >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE vector_view < typename PackedStream < const_cached_iterator< const W * >, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T > ::iterator >	make_local_string (vector_view< PackedStream< StreamType, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T > > string, W *lmem)
bowtie2::cuda::ScoringQueuesDeviceView	device_view (bowtie2::cuda::ScoringQueues &queues)
bowtie2::cuda::HitQueuesDeviceView	device_view (bowtie2::cuda::HitQueues &queues)
bowtie2::cuda::ReadHitsIndexDeviceView	device_view (bowtie2::cuda::ReadHitsIndex &index)

Detailed Description

Define a vector_view POD type and plain_view() for std::vector.

.h

Typedef Documentation

typedef long nvbio::CounterT_default

Definition at line 46 of file shared_pointer.h.

Function Documentation

template<typename PredicateIterator >

bool nvbio::all	(	const host_tag	tag,
		const uint32	n,
		const PredicateIterator	pred
	)

Definition at line 50 of file primitives_inl.h.

template<typename T , uint32 DIM>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::all

(

const StaticVector< T, DIM > &

op)

Definition at line 171 of file static_vector_inl.h.

int nvbio::alloc_test

(

)

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8 nvbio::and_op	(	const simd4u8	op1,
		const simd4u8	op2
	)

Definition at line 237 of file simd_inl.h.

template<typename PredicateIterator >

bool nvbio::any	(	const host_tag	tag,
		const uint32	n,
		const PredicateIterator	pred
	)

Definition at line 35 of file primitives_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::any

(

const simd4u8

op)

Definition at line 71 of file simd.h.

template<typename T , uint32 DIM>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::any

(

const StaticVector< T, DIM > &

op)

Definition at line 161 of file static_vector_inl.h.

template<typename InputIterator , typename InputStream , typename Symbol , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >

NVBIO_HOST_DEVICE void nvbio::assign	(	const host_tag	tag,
		const IndexType	input_len,
		const InputIterator	input_string,
		PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType >	packed_string
	)

Definition at line 1395 of file packedstream_inl.h.

template<typename InputIterator , typename InputStream , typename Symbol , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >

NVBIO_HOST_DEVICE void nvbio::assign ( const IndexType  input_len, const InputIterator  input_string, PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType >  packed_string  )

related

Definition at line 1408 of file packedstream_inl.h.

template<typename TRankDictionary , typename TSuffixArray , typename TL2 >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index<TRankDictionary,TSuffixArray,TL2>::index_type nvbio::basic_inv_psi	(	const fm_index< TRankDictionary, TSuffixArray, TL2 > &	fmi,
		const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type	i
	)

Definition at line 395 of file fmindex_inl.h.

template<typename T >

thrust::device_vector<T>::iterator nvbio::begin

(

thrust::device_vector< T > &

vec)

return the begin iterator of a device vector

Definition at line 100 of file thrust_view.h.

template<typename T >

thrust::device_vector<T>::const_iterator nvbio::begin

(

const thrust::device_vector< T > &

vec)

return the begin iterator of a device vector

Definition at line 105 of file thrust_view.h.

template<typename T >

thrust::host_vector<T>::iterator nvbio::begin

(

thrust::host_vector< T > &

vec)

return the begin iterator of a host vector

Definition at line 110 of file thrust_view.h.

template<typename T >

thrust::host_vector<T>::const_iterator nvbio::begin

(

const thrust::host_vector< T > &

vec)

return the begin iterator of a host vector

Definition at line 115 of file thrust_view.h.

int nvbio::bloom_filter_test	(	int	argc,
		char *	argv[]
	)

template<typename options_type >

bool nvbio::bool_option	(	const options_type &	options,
		const char *	name,
		const bool	val
	)

Definition at line 38 of file options.h.

template<typename options_type >

bool nvbio::bool_option	(	const options_type &	options,
		const char *	name1,
		const char *	name2,
		const bool	val
	)

Definition at line 46 of file options.h.

void nvbio::build_buckets	(	const uint64	key_range,
		const uint32	n_keys,
		const uint64 *	keys,
		const uint32	bucket_size,
		nvbio::vector< host_tag, uint32 > &	buckets,
		const bool	upper = true
	)

build a set of buckets pointing to the lower/upper bounds of a sequence of keys

Definition at line 52 of file paged_text.cpp.

template<uint32 SYMBOL_SIZE, uint32 K, typename SymbolIterator , typename IndexType >

void nvbio::build_occurrence_table ( SymbolIterator  begin, SymbolIterator  end, IndexType *  occ, IndexType *  cnt  )

related

Definition at line 43 of file rank_dictionary_inl.h.

void nvbio::calculateColbournAndLingDC ( const uint32  r, uint32 &  maxv, std::vector< uint32 > &  samples  )

inline

Routune for calculating the elements of a difference cover using the technique of Colbourn and Ling.

See http://citeseer.ist.psu.edu/211575.html

Parameters

r	the r parameter, determining the DC size as in Corollary 2.3
samples	output vector of DC samples

Definition at line 42 of file dcs_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8 nvbio::char_to_dna

(

const char

c)

convert an ASCII DNA representation to its 2-bit symbol

Definition at line 78 of file dna.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8 nvbio::char_to_iupac16

(

const char

c)

convert an ASCII DNA representation to its 4-bit symbol

Definition at line 89 of file dna.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8 nvbio::char_to_protein

(

const char

c)

convert an ASCII character to a Protein symbol

Definition at line 90 of file alphabet_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8 nvbio::char_to_rna

(

const char

c)

convert an ASCII RNA representation to its 2-bit symbol

Definition at line 48 of file alphabet_inl.h.

int nvbio::condition_test

(

)

template<typename T , typename U , typename CounterT >

SharedPointer<T, CounterT> nvbio::const_pointer_cast

(

const SharedPointer< U, CounterT > &

r)

Definition at line 526 of file shared_pointer.h.

template<typename input_storage , typename output_storage , uint32 SYMBOL_SIZE, typename index_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::copy	(	const uint32	len,
		const PackedStream< input_storage, uint8, SYMBOL_SIZE, true, index_type >	in,
		PackedStream< output_storage, uint8, SYMBOL_SIZE, true, index_type >	out
	)

Definition at line 61 of file paged_text_inl.h.

template<typename input_storage , typename output_storage , uint32 SYMBOL_SIZE, typename index_type >

NVBIO_FORCEINLINE NVBIO_HOST void nvbio::copy	(	const uint32	len,
		const PackedStream< input_storage, uint8, SYMBOL_SIZE, true, index_type >	in,
		PackedStream< output_storage, uint8, SYMBOL_SIZE, true, index_type >	out,
		const uint32	occ_intv_log,
		const uint32	occ_intv,
		uint32 *	partials,
		uint32 *	occ,
		const uint32 *	count_table
	)

Definition at line 143 of file paged_text_inl.h.

template<typename InputIterator , typename FlagsIterator , typename OutputIterator >

uint32 nvbio::copy_flagged	(	const host_tag	tag,
		const uint32	n,
		InputIterator	in,
		FlagsIterator	flags,
		OutputIterator	out,
		nvbio::vector< host_tag, uint8 > &	temp_storage
	)

Definition at line 598 of file primitives_inl.h.

template<typename InputIterator , typename OutputIterator , typename Predicate >

uint32 nvbio::copy_if	(	const host_tag	tag,
		const uint32	n,
		InputIterator	in,
		OutputIterator	out,
		const Predicate	pred,
		nvbio::vector< host_tag, uint8 > &	temp_storage
	)

Definition at line 625 of file primitives_inl.h.

template<typename key_iterator1 , typename key_iterator2 >

uint2 nvbio::corank	(	const int32	i,
		const key_iterator1	A,
		const int32	m,
		const key_iterator2	B,
		const int32	n
	)

Definition at line 1190 of file primitives_inl.h.

template<typename T >

device_iterator_type<T>::type nvbio::device_iterator

(

const T

it)

a convenience function to wrap naked device pointers as thrust::device_ptr

Definition at line 152 of file vector.h.

template<typename T >

vector_view<T*,uint64> nvbio::device_view

(

thrust::device_vector< T > &

vec)

return the plain view of a device vector

Definition at line 50 of file thrust_view.h.

template<typename T >

vector_view<const T*,uint64> nvbio::device_view

(

const thrust::device_vector< T > &

vec)

return the plain view of a device vector

Definition at line 55 of file thrust_view.h.

bowtie2::cuda::ScoringQueuesDeviceView nvbio::device_view ( bowtie2::cuda::ScoringQueues &  queues)

inline

Definition at line 567 of file scoring_queues.h.

bowtie2::cuda::HitQueuesDeviceView nvbio::device_view ( bowtie2::cuda::HitQueues &  queues)

inline

Definition at line 572 of file scoring_queues.h.

bowtie2::cuda::ReadHitsIndexDeviceView nvbio::device_view ( bowtie2::cuda::ReadHitsIndex &  index)

inline

Definition at line 577 of file scoring_queues.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE char nvbio::dna_to_char

(

const uint8

c)

convert a 2-bit DNA symbol to its ASCII character

Definition at line 36 of file dna.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8 nvbio::dna_to_iupac16

(

const uint8

c)

convert a 2-bit DNA symbol to a IUPAC16 symbol

Definition at line 47 of file dna.h.

template<typename SymbolIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::dna_to_string	(	const SymbolIterator	begin,
		const uint32	n,
		char *	string
	)

convert a 2-bit DNA string to an ASCII string

Definition at line 112 of file dna.h.

template<typename SymbolIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::dna_to_string	(	const SymbolIterator	begin,
		const SymbolIterator	end,
		char *	string
	)

convert a 2-bit DNA string to an ASCII string

Definition at line 126 of file dna.h.

template<typename T , typename U , typename CounterT >

SharedPointer<T, CounterT> nvbio::dynamic_pointer_cast

(

const SharedPointer< U, CounterT > &

r)

Definition at line 532 of file shared_pointer.h.

template<typename InputIterator , typename OutputIterator , typename BinaryOp , typename Identity >

void nvbio::exclusive_scan	(	host_tag	tag,
		const uint32	n,
		InputIterator	in,
		OutputIterator	out,
		BinaryOp	op,
		Identity	identity,
		nvbio::vector< host_tag, uint8 > &	temp_storage
	)

Definition at line 431 of file primitives_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::find_nthbit	(	const uint32	mask,
		const uint32	n
	)

Definition at line 163 of file popcount_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::find_nthbit	(	const uint8	mask,
		const uint32	n
	)

Definition at line 188 of file popcount_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::find_nthbit	(	const uint16	mask,
		const uint32	n
	)

Definition at line 195 of file popcount_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::find_nthbit16	(	const uint32	mask,
		const uint32	n
	)

Definition at line 138 of file popcount_inl.h.

template<typename Iterator , typename Predicate >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Iterator nvbio::find_pivot	(	Iterator	begin,
		const uint32	n,
		const Predicate	predicate
	)

find the first element in a sequence for which a given predicate evaluates to true

Parameters

begin	sequence start iterator
n	sequence size
predicate	unary predicate

Definition at line 55 of file algorithms.h.

template<typename options_type >

float nvbio::float_option	(	const options_type &	options,
		const char *	name,
		const float	val
	)

Definition at line 114 of file options.h.

template<typename options_type >

float nvbio::float_option	(	const options_type &	options,
		const char *	name1,
		const char *	name2,
		const uint32	val
	)

Definition at line 122 of file options.h.

template<typename Iterator , typename Functor >

void nvbio::for_each	(	const host_tag	tag,
		const uint64	n,
		const Iterator	in,
		Functor	functor
	)

Definition at line 256 of file primitives_inl.h.

template<typename Iterator , typename Functor >

void nvbio::for_each	(	const device_tag	tag,
		const uint64	n,
		const Iterator	in,
		Functor	functor
	)

Definition at line 272 of file primitives_inl.h.

template<typename StreamIterator >

int32 nvbio::gen_bwt	(	const uint32	n,
		const StreamIterator	T,
		int32 *	buffer,
		StreamIterator	bwt
	)

helper function to generate the BWT of a string given a temporary buffer.

Definition at line 68 of file bwt.h.

template<typename StreamIterator >

int64 nvbio::gen_bwt	(	const uint32	n,
		const StreamIterator	T,
		int64 *	buffer,
		StreamIterator	bwt
	)

helper function to generate the BWT of a string given a temporary buffer.

Definition at line 76 of file bwt.h.

void nvbio::gen_bwt_count_table ( uint32 *  count_table)

inline

Definition at line 87 of file bwt.h.

template<typename StreamIterator >

uint32 nvbio::gen_bwt_from_sa	(	const uint32	n,
		const StreamIterator	T,
		const int32 *	SA,
		StreamIterator	bwt
	)

helper function to generate the BWT of a string given its suffix array.

Definition at line 52 of file bwt.h.

template<typename StreamIterator >

uint32 nvbio::gen_sa	(	const uint32	n,
		const StreamIterator	T,
		int32 *	SA
	)

helper function to generate a suffix array padded by 1, where the 0-th entry is the SA size.

Definition at line 39 of file bwt.h.

template<uint32 I>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8 nvbio::get

(

const simd4u8

op)

Definition at line 249 of file simd_inl.h.

template<typename DeleterT , typename T , typename CounterT >

DeleterT* nvbio::get_deleter ( const SharedPointer< T, CounterT > &  p)

inline

Definition at line 545 of file shared_pointer.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64 nvbio::hibits_2bit	(	const uint64	mask,
		const uint32	i
	)

Definition at line 335 of file popcount_inl.h.

template<uint32 N>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint64 nvbio::hibits_nbit	(	const uint64	mask,
		const uint32	i
	)

Definition at line 436 of file popcount_inl.h.

template<typename InputIterator , typename OutputIterator , typename BinaryOp >

void nvbio::inclusive_scan	(	host_tag	tag,
		const uint32	n,
		InputIterator	in,
		OutputIterator	out,
		BinaryOp	op,
		nvbio::vector< host_tag, uint8 > &	temp_storage
	)

Definition at line 406 of file primitives_inl.h.

template<typename options_type >

int2 nvbio::int2_option	(	const options_type &	options,
		const char *	name,
		const int2	val
	)

Definition at line 152 of file options.h.

template<typename options_type >

int64 nvbio::int64_option	(	const options_type &	options,
		const char *	name,
		const int64	val
	)

Definition at line 95 of file options.h.

template<typename options_type >

int64 nvbio::int64_option	(	const options_type &	options,
		const char *	name1,
		const char *	name2,
		const uint32	val
	)

Definition at line 103 of file options.h.

template<typename options_type >

int32 nvbio::int_option	(	const options_type &	options,
		const char *	name,
		const int32	val
	)

Definition at line 76 of file options.h.

template<typename options_type >

int32 nvbio::int_option	(	const options_type &	options,
		const char *	name1,
		const char *	name2,
		const uint32	val
	)

Definition at line 84 of file options.h.

template<typename TRankDictionary , typename TSuffixArray , typename TL2 >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index<TRankDictionary,TSuffixArray,TL2>::range_type nvbio::inv_psi	(	const fm_index< TRankDictionary, TSuffixArray, TL2 > &	fmi,
		const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type	i
	)

Definition at line 427 of file fmindex_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE char nvbio::iupac16_to_char

(

const uint8

c)

convert a 4-bit DNA symbol to its ASCII character

Definition at line 56 of file dna.h.

template<typename SymbolIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::iupac16_to_string	(	const SymbolIterator	begin,
		const uint32	n,
		char *	string
	)

convert a 2-bit DNA string to an ASCII string

Definition at line 140 of file dna.h.

template<typename SymbolIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::iupac16_to_string	(	const SymbolIterator	begin,
		const SymbolIterator	end,
		char *	string
	)

convert a 2-bit DNA string to an ASCII string

Definition at line 154 of file dna.h.

void nvbio::load_bns	(	BNTSeq &	bns,
		const char *	prefix
	)

Definition at line 83 of file bnt.cpp.

void nvbio::load_bns	(	BNTSeqLoader *	bns,
		const char *	prefix
	)

Definition at line 197 of file bnt.cpp.

void nvbio::load_bns_info	(	BNTInfo &	bns,
		const char *	prefix
	)

Definition at line 165 of file bnt.cpp.

template<typename TRankDictionary , typename TSuffixArray , typename TL2 >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index<TRankDictionary,TSuffixArray,TL2>::index_type nvbio::locate	(	const fm_index< TRankDictionary, TSuffixArray, TL2 > &	fmi,
		const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type	i
	)

Definition at line 471 of file fmindex_inl.h.

template<typename TRankDictionary , typename TSuffixArray , typename TL2 >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index<TRankDictionary,TSuffixArray,TL2>::range_type nvbio::locate_ssa_iterator	(	const fm_index< TRankDictionary, TSuffixArray, TL2 > &	fmi,
		const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type	i
	)

Definition at line 516 of file fmindex_inl.h.

template<typename TRankDictionary , typename TSuffixArray , typename TL2 >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index<TRankDictionary,TSuffixArray,TL2>::index_type nvbio::lookup_ssa_iterator	(	const fm_index< TRankDictionary, TSuffixArray, TL2 > &	fmi,
		const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::range_type	it
	)

Definition at line 558 of file fmindex_inl.h.

template<typename Iterator , typename Value , typename index_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Iterator nvbio::lower_bound	(	const Value	x,
		Iterator	begin,
		const index_type	n
	)

find the lower bound in a sequence

Parameters

x	element to find
begin	sequence start iterator
n	sequence size

Definition at line 91 of file algorithms.h.

template<typename KeyIterator , typename ValueIterator , typename OutputIterator >

void nvbio::lower_bound	(	const device_tag	tag,
		const uint32	n,
		ValueIterator	values,
		const uint32	n_keys,
		KeyIterator	keys,
		OutputIterator	indices
	)

Definition at line 910 of file primitives_inl.h.

template<typename KeyIterator , typename ValueIterator , typename OutputIterator >

void nvbio::lower_bound	(	const host_tag	tag,
		const uint32	n,
		ValueIterator	values,
		const uint32	n_keys,
		KeyIterator	keys,
		OutputIterator	indices
	)

Definition at line 932 of file primitives_inl.h.

template<typename Iterator , typename Value , typename index_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE index_type nvbio::lower_bound_index	(	const Value	x,
		Iterator	begin,
		const index_type	n
	)

find the lower bound in a sequence

Parameters

x	element to find
begin	sequence start iterator
n	sequence size

Definition at line 171 of file algorithms.h.

template<typename StreamIterator , typename SymbolType , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator >

CachedPackedSparseStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator, typename std::iterator_traits<StreamIterator>::value_type>::cached_string_set nvbio::make_cached_string_set

(

const SparseStringSet< PackedStream< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T >, LengthIterator >

string_set)

A utility function to convert a plain packed-sparse string set into a cached one

Definition at line 1245 of file string_set.h.

template<typename StreamIterator , typename SymbolType , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator >

CachedPackedConcatStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator, typename std::iterator_traits<StreamIterator>::value_type>::cached_string_set nvbio::make_cached_string_set

(

const ConcatenatedStringSet< PackedStream< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T >, LengthIterator >

string_set)

A utility function to convert a plain packed-concatenated string set into a cached one

Definition at line 1277 of file string_set.h.

template<typename StreamType , typename SymbolType , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename W >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE vector_view< typename PackedStream<const_cached_iterator<const W*>,SymbolType,SYMBOL_SIZE_T,BIG_ENDIAN_T>::iterator > nvbio::make_local_string	(	vector_view< PackedStream< StreamType, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T > >	string,
		W *	lmem
	)

Definition at line 58 of file utils.h.

template<typename TRankDictionary , typename TSuffixArray , typename TL2 , typename Iterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index<TRankDictionary,TSuffixArray,TL2>::range_type nvbio::match ( const fm_index< TRankDictionary, TSuffixArray, TL2 > &  fmi, const Iterator  pattern, const uint32  pattern_len  )

related

Definition at line 286 of file fmindex_inl.h.

template<typename TRankDictionary , typename TSuffixArray , typename TL2 , typename Iterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index<TRankDictionary,TSuffixArray,TL2>::range_type nvbio::match	(	const fm_index< TRankDictionary, TSuffixArray, TL2 > &	fmi,
		const Iterator	pattern,
		const uint32	pattern_len,
		const typename fm_index< TRankDictionary, TSuffixArray, TL2 >::range_type	in_range
	)

Definition at line 313 of file fmindex_inl.h.

template<typename TRankDictionary , typename TSuffixArray , typename TL2 , typename Iterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index<TRankDictionary,TSuffixArray,TL2>::range_type nvbio::match_reverse ( const fm_index< TRankDictionary, TSuffixArray, TL2 > &  fmi, const Iterator  pattern, const uint32  pattern_len  )

related

Definition at line 355 of file fmindex_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8 nvbio::max	(	const simd4u8	op1,
		const simd4u8	op2
	)

Definition at line 210 of file simd_inl.h.

template<typename T , uint32 DIM>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StaticVector< T, DIM > nvbio::max	(	const StaticVector< T, DIM > &	op1,
		const StaticVector< T, DIM > &	op2
	)

Definition at line 151 of file static_vector_inl.h.

template<typename input_iterator1 , typename input_iterator2 , typename output_iterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::merge	(	input_iterator1	first1,
		input_iterator1	end1,
		input_iterator2	first2,
		input_iterator2	end2,
		output_iterator	output
	)

merge two ranges

Parameters

first1	beginning of the first range
end1	end of the first range
first2	beginning of the second range
end2	end of the second range
output	beginning of the output range

Definition at line 206 of file algorithms.h.

template<typename key_iterator1 , typename key_iterator2 , typename value_iterator1 , typename value_iterator2 , typename key_iterator , typename value_iterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::merge_by_key	(	key_iterator1	first1,
		key_iterator1	end1,
		key_iterator2	first2,
		key_iterator2	end2,
		value_iterator1	values1,
		value_iterator2	values2,
		key_iterator	output_keys,
		value_iterator	output_values
	)

merge two ranges

Parameters

first1	beginning of the first range
end1	end of the first range
first2	beginning of the second range
end2	end of the second range
output	beginning of the output range

Definition at line 265 of file algorithms.h.

template<typename key_iterator1 , typename key_iterator2 , typename value_iterator1 , typename value_iterator2 , typename key_output , typename value_output >

void nvbio::merge_by_key	(	const host_tag	tag,
		const uint32	A_len,
		const uint32	B_len,
		const key_iterator1	A_keys,
		const key_iterator2	B_keys,
		const value_iterator1	A_values,
		const value_iterator2	B_values,
		key_output	C_keys,
		value_output	C_values
	)

Definition at line 1236 of file primitives_inl.h.

template<typename key_iterator1 , typename key_iterator2 , typename value_iterator1 , typename value_iterator2 , typename key_output , typename value_output >

void nvbio::merge_by_key	(	const device_tag	tag,
		const uint32	A_len,
		const uint32	B_len,
		const key_iterator1	A_keys,
		const key_iterator2	B_keys,
		const value_iterator1	A_values,
		const value_iterator2	B_values,
		key_output	C_keys,
		value_output	C_values
	)

Definition at line 1321 of file primitives_inl.h.

template<typename Iterator , typename Compare >

NVBIO_HOST_DEVICE bool nvbio::merge_sort	(	uint32	n,
		Iterator	A,
		Iterator	B,
		const Compare	cmp
	)

Merge sort

Parameters

n	number of entries
A	array to sort
B	temporary buffer

Returns

true if the results are in B, false otherwise

Definition at line 83 of file merge_sort.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8 nvbio::min	(	const simd4u8	op1,
		const simd4u8	op2
	)

Definition at line 223 of file simd_inl.h.

template<typename T , uint32 DIM>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StaticVector< T, DIM > nvbio::min	(	const StaticVector< T, DIM > &	op1,
		const StaticVector< T, DIM > &	op2
	)

Definition at line 141 of file static_vector_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8 nvbio::operator!=	(	const simd4u8	op1,
		const simd4u8	op2
	)

Definition at line 90 of file simd_inl.h.

template<typename StringType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator!= ( const string_iterator< StringType > &  it1, const string_iterator< StringType > &  it2  )

related

Definition at line 90 of file string_iterator_inl.h.

template<typename T1 , typename T2 >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator!=	(	const is_sorted_iterator< T1, T2 >	it1,
		const is_sorted_iterator< T1, T2 >	it2
	)

Definition at line 157 of file primitives_inl.h.

template<typename T , uint32 DIM>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator!=	(	const StaticVector< T, DIM > &	op1,
		const StaticVector< T, DIM > &	op2
	)

Definition at line 193 of file static_vector_inl.h.

template<typename T1 , typename T2 , typename H >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator!=	(	const is_segment_sorted_iterator< T1, T2, H >	it1,
		const is_segment_sorted_iterator< T1, T2, H >	it2
	)

Definition at line 219 of file primitives_inl.h.

template<typename InputStream , typename Symbol , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator!= ( const PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &  it1, const PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &  it2  )

related

inequality test

Definition at line 775 of file packedstream_inl.h.

template<typename InputStream , typename Symbol , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator!= ( const ForwardPackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &  it1, const ForwardPackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &  it2  )

related

inequality test

Definition at line 1092 of file packedstream_inl.h.

template<typename T , uint32 DIM>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StaticVector< T, DIM > nvbio::operator*	(	const StaticVector< T, DIM > &	op1,
		const StaticVector< T, DIM > &	op2
	)

Definition at line 103 of file static_vector_inl.h.

template<typename T , uint32 DIM>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StaticVector< T, DIM > & nvbio::operator*=	(	StaticVector< T, DIM > &	op1,
		const StaticVector< T, DIM > &	op2
	)

Definition at line 113 of file static_vector_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8 nvbio::operator+	(	const simd4u8	op1,
		const simd4u8	op2
	)

Definition at line 155 of file simd_inl.h.

template<typename T1 , typename T2 >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE is_sorted_iterator<T1,T2> nvbio::operator+	(	const is_sorted_iterator< T1, T2 >	it,
		const int64	i
	)

Definition at line 143 of file primitives_inl.h.

template<typename T , uint32 DIM>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StaticVector< T, DIM > nvbio::operator+	(	const StaticVector< T, DIM > &	op1,
		const StaticVector< T, DIM > &	op2
	)

Definition at line 65 of file static_vector_inl.h.

template<typename StringType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_iterator<StringType> nvbio::operator+	(	const string_iterator< StringType >	it,
		const typename string_iterator< StringType >::difference_type	distance
	)

Definition at line 163 of file string_iterator_inl.h.

template<typename T1 , typename T2 , typename H >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE is_segment_sorted_iterator<T1,T2,H> nvbio::operator+	(	const is_segment_sorted_iterator< T1, T2, H >	it,
		const int64	i
	)

Definition at line 205 of file primitives_inl.h.

template<typename StringType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_iterator<StringType>& nvbio::operator++ ( string_iterator< StringType > &  it)

related

Definition at line 101 of file string_iterator_inl.h.

template<typename StringType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_iterator<StringType> nvbio::operator++ ( string_iterator< StringType > &  it, int  dummy  )

related

Definition at line 111 of file string_iterator_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8 & nvbio::operator+=	(	simd4u8 &	op1,
		const simd4u8	op2
	)

Definition at line 168 of file simd_inl.h.

template<typename StringType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_iterator<StringType>& nvbio::operator+=	(	string_iterator< StringType > &	it,
		const typename string_iterator< StringType >::difference_type	distance
	)

Definition at line 143 of file string_iterator_inl.h.

template<typename T , uint32 DIM>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StaticVector< T, DIM > & nvbio::operator+=	(	StaticVector< T, DIM > &	op1,
		const StaticVector< T, DIM > &	op2
	)

Definition at line 75 of file static_vector_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8 nvbio::operator-	(	const simd4u8	op1,
		const simd4u8	op2
	)

Definition at line 182 of file simd_inl.h.

template<typename T1 , typename T2 >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int64 nvbio::operator-	(	const is_sorted_iterator< T1, T2 >	it1,
		const is_sorted_iterator< T1, T2 >	it2
	)

Definition at line 150 of file primitives_inl.h.

template<typename T , uint32 DIM>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StaticVector< T, DIM > nvbio::operator-	(	const StaticVector< T, DIM > &	op1,
		const StaticVector< T, DIM > &	op2
	)

Definition at line 84 of file static_vector_inl.h.

template<typename StringType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_iterator<StringType> nvbio::operator-	(	const string_iterator< StringType >	it,
		const typename string_iterator< StringType >::difference_type	distance
	)

Definition at line 172 of file string_iterator_inl.h.

template<typename StringType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_iterator<StringType>::difference_type nvbio::operator- ( const string_iterator< StringType >  it1, const string_iterator< StringType >  it2  )

related

Definition at line 181 of file string_iterator_inl.h.

template<typename T1 , typename T2 , typename H >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int64 nvbio::operator-	(	const is_segment_sorted_iterator< T1, T2, H >	it1,
		const is_segment_sorted_iterator< T1, T2, H >	it2
	)

Definition at line 212 of file primitives_inl.h.

template<typename StringType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_iterator<StringType>& nvbio::operator-- ( string_iterator< StringType > &  it)

related

Definition at line 122 of file string_iterator_inl.h.

template<typename StringType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_iterator<StringType> nvbio::operator-- ( string_iterator< StringType > &  it, int  dummy  )

related

Definition at line 132 of file string_iterator_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8 & nvbio::operator-=	(	simd4u8 &	op1,
		const simd4u8	op2
	)

Definition at line 195 of file simd_inl.h.

template<typename StringType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_iterator<StringType>& nvbio::operator-=	(	string_iterator< StringType > &	it,
		const typename string_iterator< StringType >::difference_type	distance
	)

Definition at line 153 of file string_iterator_inl.h.

template<typename T , uint32 DIM>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StaticVector< T, DIM > & nvbio::operator-=	(	StaticVector< T, DIM > &	op1,
		const StaticVector< T, DIM > &	op2
	)

Definition at line 94 of file static_vector_inl.h.

template<typename T , uint32 DIM>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StaticVector< T, DIM > nvbio::operator/	(	const StaticVector< T, DIM > &	op1,
		const StaticVector< T, DIM > &	op2
	)

Definition at line 122 of file static_vector_inl.h.

template<typename T , uint32 DIM>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE StaticVector< T, DIM > & nvbio::operator/=	(	StaticVector< T, DIM > &	op1,
		const StaticVector< T, DIM > &	op2
	)

Definition at line 132 of file static_vector_inl.h.

template<typename StringType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator< ( const string_iterator< StringType > &  it1, const string_iterator< StringType > &  it2  )

related

Definition at line 40 of file string_iterator_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8 nvbio::operator<	(	const simd4u8	op1,
		const simd4u8	op2
	)

Definition at line 142 of file simd_inl.h.

template<typename InputStream , typename Symbol , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator< ( const PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &  it1, const PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &  it2  )

related

less than

Definition at line 745 of file packedstream_inl.h.

template<typename InputStream , typename Symbol , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator< ( const ForwardPackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &  it1, const ForwardPackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &  it2  )

related

less than

Definition at line 1062 of file packedstream_inl.h.

template<typename CharT , typename TraitsT , typename T , typename CounterT >

std::basic_ostream<CharT, TraitsT>& nvbio::operator<<	(	std::basic_ostream< CharT, TraitsT > &	os,
		const SharedPointer< T, CounterT > &	p
	)

Definition at line 539 of file shared_pointer.h.

template<typename StringType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator<= ( const string_iterator< StringType > &  it1, const string_iterator< StringType > &  it2  )

related

Definition at line 50 of file string_iterator_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8 nvbio::operator<=	(	const simd4u8	op1,
		const simd4u8	op2
	)

Definition at line 129 of file simd_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8 nvbio::operator==	(	const simd4u8	op1,
		const simd4u8	op2
	)

Definition at line 77 of file simd_inl.h.

template<typename StringType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator== ( const string_iterator< StringType > &  it1, const string_iterator< StringType > &  it2  )

related

Definition at line 80 of file string_iterator_inl.h.

template<typename T1 , typename T2 >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator==	(	const is_sorted_iterator< T1, T2 >	it1,
		const is_sorted_iterator< T1, T2 >	it2
	)

Definition at line 164 of file primitives_inl.h.

template<typename T , uint32 DIM>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator==	(	const StaticVector< T, DIM > &	op1,
		const StaticVector< T, DIM > &	op2
	)

Definition at line 182 of file static_vector_inl.h.

template<typename T1 , typename T2 , typename H >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator==	(	const is_segment_sorted_iterator< T1, T2, H >	it1,
		const is_segment_sorted_iterator< T1, T2, H >	it2
	)

Definition at line 226 of file primitives_inl.h.

template<typename InputStream , typename Symbol , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator== ( const PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &  it1, const PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &  it2  )

related

equality test

Definition at line 765 of file packedstream_inl.h.

template<typename InputStream , typename Symbol , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator== ( const ForwardPackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &  it1, const ForwardPackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &  it2  )

related

equality test

Definition at line 1082 of file packedstream_inl.h.

template<typename StringType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator> ( const string_iterator< StringType > &  it1, const string_iterator< StringType > &  it2  )

related

Definition at line 60 of file string_iterator_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8 nvbio::operator>	(	const simd4u8	op1,
		const simd4u8	op2
	)

Definition at line 116 of file simd_inl.h.

template<typename InputStream , typename Symbol , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator> ( const PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &  it1, const PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &  it2  )

related

greater than

Definition at line 755 of file packedstream_inl.h.

template<typename InputStream , typename Symbol , uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename IndexType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator> ( const ForwardPackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &  it1, const ForwardPackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > &  it2  )

related

greater than

Definition at line 1072 of file packedstream_inl.h.

template<typename StringType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::operator>= ( const string_iterator< StringType > &  it1, const string_iterator< StringType > &  it2  )

related

Definition at line 70 of file string_iterator_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8 nvbio::operator>=	(	const simd4u8	op1,
		const simd4u8	op2
	)

Definition at line 103 of file simd_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8 nvbio::operator~

(

const simd4u8

op)

Definition at line 74 of file simd.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8 nvbio::or_op	(	const simd4u8	op1,
		const simd4u8	op2
	)

Definition at line 242 of file simd_inl.h.

uint64 nvbio::peak_resident_memory

(

)

Definition at line 43 of file system.cpp.

template<typename T >

vector_view<T*,uint64> nvbio::plain_view

(

thrust::device_vector< T > &

vec)

return the plain view of a device vector

Definition at line 60 of file thrust_view.h.

template<typename T >

vector_view<const T*,uint64> nvbio::plain_view

(

const thrust::device_vector< T > &

vec)

return the plain view of a device vector

Definition at line 65 of file thrust_view.h.

template<typename T >

vector_view<T*,uint64> nvbio::plain_view

(

thrust::host_vector< T > &

vec)

return the plain view of a device vector

Definition at line 70 of file thrust_view.h.

template<typename T >

vector_view<const T*,uint64> nvbio::plain_view

(

const thrust::host_vector< T > &

vec)

return the plain view of a device vector

Definition at line 75 of file thrust_view.h.

DCSView nvbio::plain_view ( DCS &  dcs)

inline

return the plain view of a DCS

Definition at line 181 of file dcs.h.

DCSView nvbio::plain_view ( const DCS &  dcs)

inline

return the plain view of a DCS

Definition at line 196 of file dcs.h.

io::ReadData::plain_view_type nvbio::plain_view ( io::ReadData &  read_data)

inline

return a plain view of a ReadData object

Definition at line 543 of file reads.h.

io::ReadData::const_plain_view_type nvbio::plain_view ( const io::ReadData &  read_data)

inline

return a plain view of a const ReadData object

Definition at line 551 of file reads.h.

io::SequenceData::plain_view_type nvbio::plain_view ( io::SequenceData &  sequence_data)

inline

Definition at line 724 of file sequence.h.

io::SequenceData::const_plain_view_type nvbio::plain_view ( const io::SequenceData &  sequence_data)

inline

Definition at line 732 of file sequence.h.

template<typename system_tag >

io::SequenceDataStorage<system_tag>::plain_view_type nvbio::plain_view

(

io::SequenceDataStorage< system_tag > &

sequence_data)

return a plain view of a SequenceData object

Definition at line 741 of file sequence.h.

template<typename system_tag >

io::SequenceDataStorage<system_tag>::const_plain_view_type nvbio::plain_view

(

const io::SequenceDataStorage< system_tag > &

sequence_data)

return a plain view of a const SequenceData object

Definition at line 750 of file sequence.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::popc

(

const uint64

i)

Definition at line 65 of file popcount_inl.h.

template<uint8 c>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::popc_2bit

(

const uint64

x)

Definition at line 70 of file paged_text.cpp.

template<uint8 c>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::popc_2bit	(	const uint64	mask,
		const uint32	i
	)

Definition at line 83 of file paged_text.cpp.

uint32 nvbio::popc_2bit	(	const uint64 *	page,
		const uint32	n,
		const uint32	mod,
		const uint32	c
	)

Definition at line 150 of file paged_text.cpp.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::popc_2bit	(	const uint64	x,
		int	c
	)

Definition at line 249 of file popcount_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::popc_2bit	(	const uint64	mask,
		int	c,
		const uint32	i
	)

Definition at line 355 of file popcount_inl.h.

template<typename CountTable >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::popc_2bit_all	(	const uint64	b,
		const CountTable	count_table
	)

Definition at line 313 of file popcount_inl.h.

template<typename CountTable >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::popc_2bit_all	(	const uint64	mask,
		const CountTable	count_table,
		const uint32	i
	)

Definition at line 498 of file popcount_inl.h.

template<uint32 N>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::popc_nbit	(	const uint64	x,
		int	c
	)

Definition at line 402 of file popcount_inl.h.

template<uint32 N>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::popc_nbit	(	const uint64	mask,
		int	c,
		const uint32	i
	)

Definition at line 463 of file popcount_inl.h.

template<typename out_coord_type , typename in_coord_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE out_coord_type nvbio::project_coords

(

const in_coord_type

i)

project a given set of coordinates to a lower-dimensional object

Definition at line 94 of file seeds_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE char nvbio::protein_to_char

(

const uint8

c)

convert a Protein symbol to its ASCII character

Definition at line 59 of file alphabet_inl.h.

int nvbio::qgram_test	(	int	argc,
		char *	argv[]
	)

template<typename KeyIterator >

void nvbio::radix_sort	(	const host_tag	tag,
		const uint32	n,
		KeyIterator	keys,
		nvbio::vector< host_tag, uint8 > &	temp_storage
	)

Definition at line 1131 of file primitives_inl.h.

template<typename KeyIterator , typename ValueIterator >

void nvbio::radix_sort	(	const host_tag	tag,
		const uint32	n,
		KeyIterator	keys,
		ValueIterator	values,
		nvbio::vector< host_tag, uint8 > &	temp_storage
	)

Definition at line 1161 of file primitives_inl.h.

template<typename TRankDictionary , typename TSuffixArray , typename TL2 >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index<TRankDictionary,TSuffixArray,TL2>::index_type nvbio::rank	(	const fm_index< TRankDictionary, TSuffixArray, TL2 > &	fmi,
		typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type	k,
		uint8	c
	)

Definition at line 41 of file fmindex_inl.h.

template<typename TRankDictionary , typename TSuffixArray , typename TL2 >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE fm_index<TRankDictionary,TSuffixArray,TL2>::range_type nvbio::rank	(	const fm_index< TRankDictionary, TSuffixArray, TL2 > &	fmi,
		typename fm_index< TRankDictionary, TSuffixArray, TL2 >::range_type	range,
		uint8	c
	)

Definition at line 71 of file fmindex_inl.h.

template<typename BitStreamIterator , typename IndexIterator , typename SymbolType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE WaveletTree<BitStreamIterator,IndexIterator,SymbolType>::index_type nvbio::rank	(	const WaveletTree< BitStreamIterator, IndexIterator, SymbolType > &	tree,
		const typename WaveletTree< BitStreamIterator, IndexIterator, SymbolType >::index_type	i,
		const uint32	c
	)

Definition at line 383 of file wavelet_tree_inl.h.

template<typename BitStreamIterator , typename IndexIterator , typename SymbolType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE WaveletTree<BitStreamIterator,IndexIterator,SymbolType>::range_type nvbio::rank	(	const WaveletTree< BitStreamIterator, IndexIterator, SymbolType > &	tree,
		const typename WaveletTree< BitStreamIterator, IndexIterator, SymbolType >::range_type	range,
		const uint32	c
	)

Definition at line 442 of file wavelet_tree_inl.h.

template<uint32 SYMBOL_SIZE_T, uint32 K, typename TextString , typename OccIterator , typename CountTable , typename IndexType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE IndexType nvbio::rank ( const rank_dictionary< SYMBOL_SIZE_T, K, TextString, OccIterator, CountTable > &  dict, const IndexType  i, const uint32  c  )

related

Definition at line 589 of file rank_dictionary_inl.h.

template<uint32 SYMBOL_SIZE_T, uint32 K, typename TextString , typename OccIterator , typename CountTable , typename IndexType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE vector_type<IndexType,2>::type nvbio::rank	(	const rank_dictionary< SYMBOL_SIZE_T, K, TextString, OccIterator, CountTable > &	dict,
		const typename vector_type< IndexType, 2 >::type	range,
		const uint32	c
	)

Definition at line 601 of file rank_dictionary_inl.h.

template<typename TRankDictionary , typename TSuffixArray , typename TL2 >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE TRankDictionary::vec4_type nvbio::rank4	(	const fm_index< TRankDictionary, TSuffixArray, TL2 > &	fmi,
		typename fm_index< TRankDictionary, TSuffixArray, TL2 >::index_type	k
	)

Definition at line 112 of file fmindex_inl.h.

template<typename TRankDictionary , typename TSuffixArray , typename TL2 >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::rank4	(	const fm_index< TRankDictionary, TSuffixArray, TL2 > &	fmi,
		typename fm_index< TRankDictionary, TSuffixArray, TL2 >::range_type	range,
		typename TRankDictionary::vec4_type *	outl,
		typename TRankDictionary::vec4_type *	outh
	)

Definition at line 149 of file fmindex_inl.h.

template<uint32 K, typename TextString , typename OccIterator , typename CountTable , typename IndexType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE vector_type<IndexType,4>::type nvbio::rank4 ( const rank_dictionary< 2, K, TextString, OccIterator, CountTable > &  dict, const IndexType  i  )

related

Definition at line 614 of file rank_dictionary_inl.h.

template<uint32 K, typename TextString , typename OccIterator , typename CountTable >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::rank4 ( const rank_dictionary< 2, K, TextString, OccIterator, CountTable > &  dict, const uint2  range, uint4 *  outl, uint4 *  outh  )

related

Definition at line 627 of file rank_dictionary_inl.h.

template<uint32 K, typename TextString , typename OccIterator , typename CountTable >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::rank4 ( const rank_dictionary< 2, K, TextString, OccIterator, CountTable > &  dict, const uint64_2  range, uint64_4 *  outl, uint64_4 *  outh  )

related

Definition at line 640 of file rank_dictionary_inl.h.

template<uint32 SYMBOL_SIZE, uint32 K, typename TextString , typename OccIterator , typename CountTable >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE rank_dictionary<SYMBOL_SIZE,K,TextString,OccIterator,CountTable>::vector_type nvbio::rank_all	(	const rank_dictionary< SYMBOL_SIZE, K, TextString, OccIterator, CountTable > &	dict,
		const typename rank_dictionary< SYMBOL_SIZE, K, TextString, OccIterator, CountTable >::index_type	i
	)

Definition at line 654 of file rank_dictionary_inl.h.

template<uint32 SYMBOL_SIZE, uint32 K, typename TextString , typename OccIterator , typename CountTable >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::rank_all	(	const rank_dictionary< SYMBOL_SIZE, K, TextString, OccIterator, CountTable > &	dict,
		const typename rank_dictionary< SYMBOL_SIZE, K, TextString, OccIterator, CountTable >::index_type	i,
		typename rank_dictionary< SYMBOL_SIZE, K, TextString, OccIterator, CountTable >::vector_type *	out
	)

Definition at line 672 of file rank_dictionary_inl.h.

template<uint32 SYMBOL_SIZE, uint32 K, typename TextString , typename OccIterator , typename CountTable >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::rank_all	(	const rank_dictionary< SYMBOL_SIZE, K, TextString, OccIterator, CountTable > &	dict,
		const typename rank_dictionary< SYMBOL_SIZE, K, TextString, OccIterator, CountTable >::range_type	range,
		typename rank_dictionary< SYMBOL_SIZE, K, TextString, OccIterator, CountTable >::vector_type *	outl,
		typename rank_dictionary< SYMBOL_SIZE, K, TextString, OccIterator, CountTable >::vector_type *	outh
	)

Definition at line 687 of file rank_dictionary_inl.h.

int nvbio::rank_test	(	int	argc,
		char *	argv[]
	)

template<typename T >

T* nvbio::raw_pointer

(

thrust::device_vector< T > &

vec)

return the raw pointer of a device vector

Definition at line 80 of file thrust_view.h.

template<typename T >

const T* nvbio::raw_pointer

(

const thrust::device_vector< T > &

vec)

return the raw pointer of a device vector

Definition at line 85 of file thrust_view.h.

template<typename T >

T* nvbio::raw_pointer

(

thrust::host_vector< T > &

vec)

return the raw pointer of a device vector

Definition at line 90 of file thrust_view.h.

template<typename T >

const T* nvbio::raw_pointer

(

const thrust::host_vector< T > &

vec)

return the plain view of a device vector

Definition at line 95 of file thrust_view.h.

template<typename T >

NVBIO_FORCEINLINE NVBIO_DEVICE T nvbio::read

(

const T *

ptr)

Definition at line 43 of file pod.h.

template<typename InputIterator , typename BinaryOp >

std::iterator_traits<InputIterator>::value_type nvbio::reduce	(	host_tag	tag,
		const uint32	n,
		InputIterator	in,
		BinaryOp	op,
		nvbio::vector< host_tag, uint8 > &	temp_storage
	)

Definition at line 387 of file primitives_inl.h.

template<typename KeyIterator , typename ValueIterator , typename OutputKeyIterator , typename OutputValueIterator , typename ReductionOp >

uint32 nvbio::reduce_by_key	(	const host_tag	tag,
		const uint32	n,
		KeyIterator	keys_in,
		ValueIterator	values_in,
		OutputKeyIterator	keys_out,
		OutputValueIterator	values_out,
		ReductionOp	reduction_op,
		nvbio::vector< host_tag, uint8 > &	temp_storage
	)

Definition at line 681 of file primitives_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE char nvbio::rna_to_char

(

const uint8

c)

convert a 2-bit RNA symbol to its ASCII character

Definition at line 37 of file alphabet_inl.h.

template<typename InputIterator , typename OutputIterator , typename CountIterator >

uint32 nvbio::runlength_encode	(	const host_tag	tag,
		const uint32	n,
		InputIterator	in,
		OutputIterator	out,
		CountIterator	counts,
		nvbio::vector< host_tag, uint8 > &	temp_storage
	)

Definition at line 651 of file primitives_inl.h.

void nvbio::save_bns	(	const BNTSeq &	bns,
		const char *	prefix
	)

Definition at line 37 of file bnt.cpp.

template<uint32 SYMBOL_COUNT>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::save_occurrences	(	const uint32	k,
		const uint32	occ_intv_log,
		const uint32	occ_intv,
		const uint32 *	partials,
		uint32 *	occ
	)

Definition at line 130 of file paged_text_inl.h.

int nvbio::sequence_test	(	int	argc,
		char *	argv[]
	)

template<uint32 I>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::set	(	simd4u8	op,
		const uint8	v
	)

Definition at line 255 of file simd_inl.h.

template<typename system_tag , typename string_iterator , typename index_type , typename symbol_type >

void nvbio::setup	(	const index_type	string_len,
		const string_iterator &	string,
		WaveletTreeStorage< system_tag, index_type, symbol_type > &	out_tree
	)

Definition at line 129 of file wavelet_tree_inl.h.

template<typename T , typename U , typename CounterT >

SharedPointer<T, CounterT> nvbio::static_pointer_cast

(

const SharedPointer< U, CounterT > &

r)

Definition at line 520 of file shared_pointer.h.

template<typename options_type >

std::string nvbio::string_option	(	const options_type &	options,
		const char *	name,
		const char *	val
	)

Definition at line 133 of file options.h.

template<typename options_type >

std::string nvbio::string_option	(	const options_type &	options,
		const char *	name1,
		const char *	name2,
		const char *	val
	)

Definition at line 141 of file options.h.

int nvbio::string_set_test	(	int	argc,
		char *	argv[]
	)

template<typename SymbolIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::string_to_dna	(	const char *	begin,
		const char *	end,
		SymbolIterator	symbols
	)

convert an ASCII DNA string to its 2-bit representation

Definition at line 168 of file dna.h.

template<typename SymbolIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::string_to_dna	(	const char *	begin,
		SymbolIterator	symbols
	)

convert a NULL-terminated ASCII DNA string to its 2-bit representation

Definition at line 180 of file dna.h.

template<typename SymbolIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::string_to_iupac16	(	const char *	begin,
		const char *	end,
		SymbolIterator	symbols
	)

convert an ASCII DNA string to its 4-bit representation

Definition at line 191 of file dna.h.

template<typename SymbolIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::string_to_iupac16	(	const char *	begin,
		SymbolIterator	symbols
	)

convert a NULL-terminated ASCII DNA string to its 4-bit representation

Definition at line 203 of file dna.h.

int nvbio::sum_tree_test

(

)

Definition at line 39 of file sum_tree_test.cpp.

template<typename T , typename CounterT >

void nvbio::swap ( SharedPointer< T, CounterT > &  a, SharedPointer< T, CounterT > &  b  )

inline

Definition at line 514 of file shared_pointer.h.

template<typename T , typename CounterT >

void nvbio::swap ( WeakPointer< T, CounterT > &  a, WeakPointer< T, CounterT > &  b  )

inline

Definition at line 637 of file shared_pointer.h.

int nvbio::syncblocks_test

(

)

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE simd4u8 nvbio::ternary_op	(	const simd4u8	mask,
		const simd4u8	op1,
		const simd4u8	op2
	)

Definition at line 262 of file simd_inl.h.

template<uint32 SYMBOL_SIZE_T, uint32 K, typename TextString , typename OccIterator , typename CountTable >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8 nvbio::text ( const rank_dictionary< SYMBOL_SIZE_T, K, TextString, OccIterator, CountTable > &  dict, const uint32  i  )

related

Definition at line 185 of file rank_dictionary_inl.h.

template<uint32 SYMBOL_SIZE_T, uint32 K, typename TextString , typename OccIterator , typename CountTable >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint8 nvbio::text ( const rank_dictionary< SYMBOL_SIZE_T, K, TextString, OccIterator, CountTable > &  dict, const uint64  i  )

related

Definition at line 193 of file rank_dictionary_inl.h.

template<typename BitStreamIterator , typename IndexIterator , typename IndexType , typename SymbolType >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE SymbolType nvbio::text ( const WaveletTree< BitStreamIterator, IndexIterator, SymbolType > &  tree, const IndexType  i  )

related

Definition at line 457 of file wavelet_tree_inl.h.

template<typename Iterator , typename Output , typename Functor >

void nvbio::transform	(	const device_tag	tag,
		const uint64	n,
		const Iterator	in,
		const Output	out,
		const Functor	functor
	)

Definition at line 295 of file primitives_inl.h.

template<typename Iterator , typename Output , typename Functor >

void nvbio::transform	(	const host_tag	tag,
		const uint32	n,
		const Iterator	in,
		const Output	out,
		const Functor	functor
	)

Definition at line 308 of file primitives_inl.h.

template<typename Iterator1 , typename Iterator2 , typename Output , typename Functor >

void nvbio::transform	(	const device_tag	tag,
		const uint32	n,
		const Iterator1	in1,
		const Iterator2	in2,
		const Output	out,
		const Functor	functor
	)

Definition at line 325 of file primitives_inl.h.

template<typename Iterator1 , typename Iterator2 , typename Output , typename Functor >

void nvbio::transform	(	const host_tag	tag,
		const uint32	n,
		const Iterator1	in1,
		const Iterator2	in2,
		const Output	out,
		const Functor	functor
	)

Definition at line 339 of file primitives_inl.h.

template<typename options_type >

uint32 nvbio::uint_option	(	const options_type &	options,
		const char *	name,
		const uint32	val
	)

Definition at line 57 of file options.h.

template<typename options_type >

uint32 nvbio::uint_option	(	const options_type &	options,
		const char *	name1,
		const char *	name2,
		const uint32	val
	)

Definition at line 65 of file options.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::unpack_add	(	uint4 *	op1,
		const uint32	op2
	)

Definition at line 96 of file rank_dictionary_inl.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::unpack_add	(	uint64_4 *	op1,
		const uint32	op2
	)

Definition at line 104 of file rank_dictionary_inl.h.

template<typename Iterator , typename Value , typename index_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE Iterator nvbio::upper_bound	(	const Value	x,
		Iterator	begin,
		const index_type	n
	)

find the upper bound in a sequence

Parameters

x	element to find
begin	sequence start iterator
n	sequence size

Definition at line 130 of file algorithms.h.

template<typename KeyIterator , typename ValueIterator , typename OutputIterator >

void nvbio::upper_bound	(	const device_tag	tag,
		const uint32	n,
		ValueIterator	values,
		const uint32	n_keys,
		KeyIterator	keys,
		OutputIterator	indices
	)

Definition at line 977 of file primitives_inl.h.

template<typename KeyIterator , typename ValueIterator , typename OutputIterator >

void nvbio::upper_bound	(	const host_tag	tag,
		const uint32	n,
		ValueIterator	values,
		const uint32	n_keys,
		KeyIterator	keys,
		OutputIterator	indices
	)

Definition at line 999 of file primitives_inl.h.

template<typename Iterator , typename Value , typename index_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE index_type nvbio::upper_bound_index	(	const Value	x,
		Iterator	begin,
		const index_type	n
	)

find the upper bound in a sequence

Parameters

x	element to find
begin	sequence start iterator
n	sequence size

Definition at line 185 of file algorithms.h.

template<uint32 VECTOR_WIDTH, typename T >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::vector_load	(	const T *	ptr,
		T *	vec
	)

load a vector using vectorized-loads

Definition at line 185 of file vector_loads.h.

NVBIO_FORCEINLINE NVBIO_DEVICE uint32 nvbio::warp_dec

(

uint32 *

count)

Definition at line 67 of file atomics.h.

NVBIO_FORCEINLINE NVBIO_DEVICE void nvbio::warp_decff

(

uint32 *

count)

Definition at line 59 of file atomics.h.

NVBIO_FORCEINLINE NVBIO_DEVICE uint32 nvbio::warp_inc

(

uint32 *

count)

Definition at line 45 of file atomics.h.

NVBIO_FORCEINLINE NVBIO_DEVICE void nvbio::warp_incff

(

uint32 *

count)

Definition at line 37 of file atomics.h.

int nvbio::wavelet_test	(	int	argc,
		char *	argv[]
	)

int nvbio::work_queue_test	(	int	argc,
		char *	argv[]
	)

template<typename T >

NVBIO_FORCEINLINE NVBIO_DEVICE void nvbio::write	(	T *	ptr,
		const T &	e
	)

Definition at line 38 of file pod.h.