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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_DEVICEsgn (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_DEVICEread (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 *, uint64device_view (thrust::device_vector< T > &vec)
 
template<typename T >
vector_view< const T *, uint64device_view (const thrust::device_vector< T > &vec)
 
template<typename T >
vector_view< T *, uint64plain_view (thrust::device_vector< T > &vec)
 
template<typename T >
vector_view< const T *, uint64plain_view (const thrust::device_vector< T > &vec)
 
template<typename T >
vector_view< T *, uint64plain_view (thrust::host_vector< T > &vec)
 
template<typename T >
vector_view< const T *, uint64plain_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
raw_pointer (const vector_view< T > &vec)
 
template<typename T , typename I >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE
begin (vector_view< T, I > &vec)
 
template<typename T , typename I >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE
begin (const vector_view< T, I > &vec)
 
template<typename T >
vector_view< T *, uint64plain_view (std::vector< T > &vec)
 
template<typename T >
vector_view< const T *, uint64plain_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)
 
OutputStreamopen_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)
 
SetBWTHandleropen_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

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
rthe r parameter, determining the DC size as in Corollary 2.3
samplesoutput 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 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
beginsequence start iterator
nsequence size
predicateunary 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
xelement to find
beginsequence start iterator
nsequence 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
xelement to find
beginsequence start iterator
nsequence 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
first1beginning of the first range
end1end of the first range
first2beginning of the second range
end2end of the second range
outputbeginning 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
first1beginning of the first range
end1end of the first range
first2beginning of the second range
end2end of the second range
outputbeginning 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
nnumber of entries
Aarray to sort
Btemporary 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