|
| CudaMemSupport (mgpu) | is_repeat_kmer | rank_word_traits< 8, uint32 > (nvbio) | supports_scheduler< GotohAligner< TYPE, ScoringScheme, AlgorithmTag >, DeviceStagedThreadScheduler > (nvbio::aln) |
| CudaTimer (mgpu) | is_segment_sorted_iterator (nvbio::cuda) | rank_word_traits< 8, uint64 > (nvbio) | supports_scheduler< GotohAligner< TYPE, ScoringScheme, AlgorithmTag >, DeviceThreadScheduler > (nvbio::aln) |
| above_threshold |
| is_segment_sorted_iterator (nvbio) | read_infixes | supports_scheduler< GotohAligner< TYPE, ScoringScheme, AlgorithmTag >, DeviceWarpScheduler > (nvbio::aln) |
| active_region | is_sorted_iterator (nvbio::cuda) | read_string (nvbio::io) | supports_scheduler< GotohAligner< TYPE, ScoringScheme, AlgorithmTag >, HostThreadScheduler > (nvbio::aln) |
| add_divide_functor (nvbio::priv) | D_KmerSet | is_sorted_iterator (nvbio) | ReadData (nvbio::io) | supports_scheduler< HammingDistanceAligner< TYPE, ScoringScheme, AlgorithmTag >, DeviceStagedThreadScheduler > (nvbio::aln) |
| add_functor (nvbio) | DataBuffer (nvbio::io) | is_true_functor (nvbio) | ReadDataDevice (nvbio::io) | supports_scheduler< HammingDistanceAligner< TYPE, ScoringScheme, AlgorithmTag >, DeviceThreadScheduler > (nvbio::aln) |
| Affine (nvbio) | DebugOutput::DbgAlignment (nvbio::io) | is_unique_kmer | ReadDataFile (nvbio::io) | supports_scheduler< HammingDistanceAligner< TYPE, ScoringScheme, AlgorithmTag >, HostThreadScheduler > (nvbio::aln) |
| Aligner (nvbio::bowtie2::cuda) | DebugOutput::DbgInfo (nvbio::io) | is_unique_suffix_id | ReadDataFile_BAM (nvbio::io) | supports_scheduler< SmithWatermanAligner< TYPE, ScoringScheme, AlgorithmTag >, DeviceStagedThreadScheduler > (nvbio::aln) |
| aligner_tag (nvbio::aln) | DCS (nvbio) | is_unique_uid | ReadDataFile_FASTQ_gz (nvbio::io) | supports_scheduler< SmithWatermanAligner< TYPE, ScoringScheme, AlgorithmTag >, DeviceThreadScheduler > (nvbio::aln) |
| Alignment (nvbio::aln) | DCS_predicate (nvbio::priv) | is_unpaired (nvbio::io) | ReadDataFile_FASTQ_parser (nvbio::io) | supports_scheduler< SmithWatermanAligner< TYPE, ScoringScheme, AlgorithmTag >, DeviceWarpScheduler > (nvbio::aln) |
| Alignment (nvbio::io) | DCS_string_suffix_index (nvbio::priv) | iterator_category_system (nvbio) | ReadDataFile_SAM (nvbio::io) | supports_scheduler< SmithWatermanAligner< TYPE, ScoringScheme, AlgorithmTag >, HostThreadScheduler > (nvbio::aln) |
| Alignment (nvbio::alndiff) | DCS_string_suffix_less (nvbio::priv) | iterator_category_system< bidirectional_device_iterator_tag > (nvbio) | ReadDataFile_TXT (nvbio::io) | sw_alignment_score_dispatch (nvbio::aln::priv::banded) |
| alignment_checkpointed_dispatch (nvbio::aln::priv) | DCSSuffixRanker (nvbio) | iterator_category_system< bidirectional_host_iterator_tag > (nvbio) | ReadDataFile_TXT_gz (nvbio::io) | sw_alignment_score_dispatch (nvbio::aln::priv) |
| alignment_checkpointed_dispatch< CHECKPOINTS, EditDistanceAligner< TYPE >, pattern_string, qual_string, text_string, column_type > (nvbio::aln::priv) | DCSView (nvbio) | iterator_category_system< bidirectional_universal_iterator_tag > (nvbio) | ReadDataRAM (nvbio::io) | sw_alignment_score_dispatch< BAND_LEN, TYPE, PatternBlockingTag, symbol_type > (nvbio::aln::priv) |
| alignment_checkpointed_dispatch< CHECKPOINTS, GotohAligner< TYPE, scoring_type >, pattern_string, qual_string, text_string, column_type > (nvbio::aln::priv) | DCTable (nvbio) | iterator_category_system< forward_device_iterator_tag > (nvbio) | ReadDataStream (nvbio::io) | sw_alignment_score_dispatch< BAND_LEN, TYPE, TextBlockingTag, symbol_type > (nvbio::aln::priv) |
| alignment_checkpointed_dispatch< CHECKPOINTS, HammingDistanceAligner< TYPE, scoring_type >, pattern_string, qual_string, text_string, column_type > (nvbio::aln::priv) | DCTable< 1024 > (nvbio) | iterator_category_system< forward_host_iterator_tag > (nvbio) | ReadDataView (nvbio::io) | sw_bandlen_selector (nvbio::aln::priv) |
| alignment_checkpointed_dispatch< CHECKPOINTS, SmithWatermanAligner< TYPE, scoring_type >, pattern_string, qual_string, text_string, column_type > (nvbio::aln::priv) | DCTable< 128 > (nvbio) | iterator_category_system< forward_universal_iterator_tag > (nvbio) | ReadHitBinder (nvbio::bowtie2::cuda) | sw_bandlen_selector< TYPE, DIM, simd4u8 > (nvbio::aln::priv) |
| alignment_end | DCTable< 2048 > (nvbio) | iterator_category_system< input_device_iterator_tag > (nvbio) | ReadHitReference (nvbio::bowtie2::cuda) | SWCheckpointContext (nvbio::aln::priv) |
| alignment_result (nvbio::aln::priv) | DCTable< 256 > (nvbio) | iterator_category_system< input_host_iterator_tag > (nvbio) | ReadHitsBinder (nvbio::bowtie2::cuda) | SWCheckpointedScoringContext (nvbio::aln::priv) |
| alignment_score_dispatch (nvbio::aln::priv) | DCTable< 512 > (nvbio) | iterator_category_system< input_universal_iterator_tag > (nvbio) | ReadHitsIndex (cufmi::bowtie2::cuda) | SWScoringContext (nvbio::aln::priv) |
| alignment_score_dispatch< EditDistanceAligner< TYPE, algorithm_tag >, pattern_string, qual_string, text_string, column_type > (nvbio::aln::priv) | DCTable< 64 > (nvbio) | iterator_category_system< output_device_iterator_tag > (nvbio) | ReadHitsIndex (nvbio::bowtie2::cuda) | SWSubmatrixContext (nvbio::aln::priv) |
| alignment_score_dispatch< GotohAligner< TYPE, scoring_type, algorithm_tag >, pattern_string, qual_string, text_string, column_type > (nvbio::aln::priv) | debruijn_graph | iterator_category_system< output_host_iterator_tag > (nvbio) | ReadHitsIndexDeviceView (nvbio::bowtie2::cuda) | syncblocks (nvbio::cuda) |
| alignment_score_dispatch< HammingDistanceAligner< TYPE, scoring_type, algorithm_tag >, pattern_string, qual_string, text_string, column_type > (nvbio::aln::priv) | DebugAlignmentStream (nvbio::alndiff) | iterator_category_system< output_universal_iterator_tag > (nvbio) | ReadHitsIndexDeviceView (cufmi::bowtie2::cuda) | syncblocks_storage (nvbio::cuda) |
| alignment_score_dispatch< SmithWatermanAligner< TYPE, scoring_type, algorithm_tag >, pattern_string, qual_string, text_string, column_type > (nvbio::aln::priv) | DebugOutput (nvbio::io) | iterator_category_system< random_access_device_iterator_tag > (nvbio) | ReadHitsReference (nvbio::bowtie2::cuda) |
|
| AlignmentCompare (nvbio::io) | DebugState (nvbio::bowtie2::cuda) | iterator_category_system< random_access_host_iterator_tag > (nvbio) | ReadHitsReference (cufmi::bowtie2::cuda) |
| AlignmentData (nvbio::io) | DefaultMover (nvbio::cuda) | iterator_category_system< random_access_universal_iterator_tag > (nvbio) | ReadLoader (nvbio) | t_pool |
| AlignmentPair (nvbio::alndiff) | deinterleaved_iterator (nvbio) | iterator_reference (nvbio) | ReadReference (cufmi::bowtie2::cuda) | t_pool_job |
| AlignmentStats (nvbio::bowtie2::cuda) | DelayList (nvbio::cuda) | iterator_system (nvbio) | ReadsDef (nvbio::bowtie2::cuda) | t_res |
| AlignmentStats (nvbio::alndiff) | Deleter (nvbio::internals) | iterator_traits (nvbio) | ReadStream (nvbio) | t_results_queue |
| AlignmentStream (nvbio::alndiff) | device_copy_dispatch (nvbio::priv) | iterator_traits< PackedStream< InputStream, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > > (nvbio) | ReadStreamQualities (nvbio) | table_object (nvbio::html) |
| AlignmentStream (nvbio::aln::priv) | device_copy_dispatch< input_iterator, PackedStream< storage_type, uint8, SYMBOL_SIZE, BIG_ENDIAN, index_type >, index_type > (nvbio::priv) |
| ReduceBestApproxContext (nvbio::bowtie2::cuda) | tbx_conf_t |
| AlignmentStreamBase (nvbio::bowtie2::cuda::detail) | device_iterator_type (nvbio) | ReduceBestExactContext (nvbio::bowtie2::cuda) | tbx_intv_t |
| AlignmentStreamContext (nvbio::bowtie2::cuda::detail) | device_iterator_type< const T * > (nvbio) | kmer_count_tuple_sum | ref_entry | tbx_t |
| AlignmentStreamContext< OPPOSITE_SCORE_STREAM > (nvbio::bowtie2::cuda::detail) | device_iterator_type< T * > (nvbio) | kmer_key_rid_eq | RefData (BamTools) | td_object (nvbio::html) |
| AlignmentStreamContext< SCORE_STREAM > (nvbio::bowtie2::cuda::detail) | device_scatter_dispatch (nvbio::priv) | kmer_key_sid_eq | RefEdit (BamTools) | test_funct |
| AlignmentStreamContext< TRACEBACK_STREAM > (nvbio::bowtie2::cuda::detail) | device_scatter_dispatch< input_iterator, slot_iterator, PackedStream< storage_type, uint8, SYMBOL_SIZE, BIG_ENDIAN, index_type > > (nvbio::priv) | kmer_pos_sid_eq | Reference_cache (nvbio::aln::priv) | TestBacktracker (nvbio::aln) |
| AlignmentStrings (nvbio::bowtie2::cuda::detail) | device_tag (nvbio) | kmer_uid_eq | Reference_cache< 15u > (nvbio::aln::priv) | TextBlockingTag (nvbio::aln) |
| all_dispatch (nvbio::cuda) | device_view_subtype (nvbio) | kmer_word_extractor_functor | Reference_cache< 3u > (nvbio::aln::priv) | th_object (nvbio::html) |
| all_dispatch< 128 > (nvbio::cuda) | device_view_subtype< const T * > (nvbio) | KmerCode | Reference_cache< 5u > (nvbio::aln::priv) | Thread (nvbio) |
| all_dispatch< 16 > (nvbio::cuda) | device_view_subtype< null_type > (nvbio) | kmers_to_64b_functor | Reference_cache< 7u > (nvbio::aln::priv) | ThreadBase (nvbio) |
| all_dispatch< 2 > (nvbio::cuda) | device_view_subtype< T * > (nvbio) | knetFile_s | reference_subtype (nvbio) | Timer (nvbio::cuda) |
| all_dispatch< 256 > (nvbio::cuda) | device_view_subtype< thrust::device_vector< T > > (nvbio) | ks_isort_stack_t | reference_subtype< const T * > (nvbio) | Timer (nvbio) |
| all_dispatch< 32 > (nvbio::cuda) | DeviceBWTConfig (nvbio::cuda) | ks_tokaux_t | reference_subtype< null_type > (nvbio) | TimeSeries (nvbio) |
| all_dispatch< 4 > (nvbio::cuda) | DeviceBWTHandler (nvbio) | kswq_t | reference_subtype< T * > (nvbio) | to_char_functor (nvbio) |
| all_dispatch< 64 > (nvbio::cuda) | DeviceCigarArray (nvbio::io) | kswr_t | ReferenceIndex (BamTools) | to_const (nvbio) |
| all_dispatch< 8 > (nvbio::cuda) | DeviceCoreSetSuffixBucketer (nvbio::priv) |
| refs_t | to_const< const T & > (nvbio) |
| AllMappingPipelineState (nvbio::bowtie2::cuda) | DeviceOutputBatchSE (nvbio::io) | region1_t | to_const< const T * > (nvbio) |
| AllScoreStream (nvbio::bowtie2::cuda::detail) | DeviceSetSuffixBucketer (nvbio::priv) | LargeBWTSkeleton (nvbio::cuda) | remove_singletons (nvbio::priv) | to_const< iterator_reference< Iterator > > (nvbio) |
| AllTracebackStream (nvbio::bowtie2::cuda::detail) | DeviceStagedThreadScheduler (nvbio::aln) | LargeBWTStatus (nvbio::cuda) | reverse_functor (nvbio) | to_const< PackedStreamRef< Stream > > (nvbio) |
| AlphabetTraits (nvbio) | DeviceStringSetRadices (nvbio::priv) | LCG_random (nvbio) | ReverseXform (nvbio) | to_const< T & > (nvbio) |
| AlphabetTraits< ASCII > (nvbio) | DeviceThreadBlockScheduler (nvbio::aln) | ldg_pointer (nvbio::cuda) | right_mem_functor (nvbio::mem) | to_const< T * > (nvbio) |
| AlphabetTraits< DNA > (nvbio) | DeviceVectorArray (nvbio) | leading_bits (nvbio) | RoundedQualCost (nvbio::bowtie2::cuda) | topological_sort_functor |
| AlphabetTraits< DNA_IUPAC > (nvbio) | DeviceWarpScheduler (nvbio::aln) | left_mem_functor (nvbio::mem) | runtime_error (nvbio) | tr_object (nvbio::html) |
| AlphabetTraits< DNA_N > (nvbio) | difference_transform (nvbio::bowtie2::cuda) | length_functor (nvbio::priv) |
| TracebackPipelineState (nvbio::bowtie2::cuda) |
| AlphabetTraits< PROTEIN > (nvbio) | direction_vector_traits (nvbio::aln) | Linear (nvbio) | transform_iterator (nvbio) |
| AlphabetTraits< RNA > (nvbio) | direction_vector_traits< GotohAligner< TYPE, scoring_type, algorithm_tag > > (nvbio::aln) | lmem_cache_tag (nvbio) | s_align | TransformStringSet (nvbio) |
| AlphabetTraits< RNA_N > (nvbio) | DiscardBWTHandler (nvbio) | lmem_selector (nvbio) | sAbs (mgpu) | transpose_aligner (nvbio::aln) |
| any_dispatch (nvbio::cuda) | DiscardDelayList (nvbio::cuda) | lmem_selector< vector_view< PackedStream< StreamType, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T > > > (nvbio) | SAM_hdr | transpose_aligner< EditDistanceAligner< T_TYPE, AlgorithmTag > > (nvbio::aln) |
| any_dispatch< 128 > (nvbio::cuda) | dispatch_rank (nvbio) | load_pointer (nvbio::cuda) | SAM_hdr_item_s | transpose_aligner< GotohAligner< T_TYPE, scoring_scheme_type, AlgorithmTag > > (nvbio::aln) |
| any_dispatch< 16 > (nvbio::cuda) | dispatch_rank< 2, 64, PackedStream< TextStorage, uint8, 2u, true >, OccIterator, CountTable, uint4, uint4 > (nvbio) | local_set_suffix_word_functor (nvbio::priv) | SAM_hdr_tag_s | transpose_aligner< HammingDistanceAligner< T_TYPE, scoring_scheme_type, AlgorithmTag > > (nvbio::aln) |
| any_dispatch< 2 > (nvbio::cuda) | dispatch_rank< SYMBOL_SIZE, K, PackedStream< TextStorage, uint8, SYMBOL_SIZE, true, index_type >, OccIterator, CountTable, word_type, index_type > (nvbio) | local_set_suffix_word_functor< SYMBOL_SIZE, WORD_BITS, DOLLAR_BITS, ConcatenatedStringSet< PackedStream< storage_type, uint8, SYMBOL_SIZE, true, typename std::iterator_traits< offsets_iterator >::value_type >, offsets_iterator >, word_type > (nvbio::priv) | SAM_PG | transpose_aligner< SmithWatermanAligner< T_TYPE, scoring_scheme_type, AlgorithmTag > > (nvbio::aln) |
| any_dispatch< 256 > (nvbio::cuda) | divide_by_two | localize_functor (nvbio) | SAM_RG | transpose_tag (nvbio::aln) |
| any_dispatch< 32 > (nvbio::cuda) | divide_ri_functor (nvbio) | localize_suffix_functor (nvbio::priv) | SAM_SQ | transpose_tag< PatternBlockingTag > (nvbio::aln) |
| any_dispatch< 4 > (nvbio::cuda) | DollarExtractor (nvbio::priv) | localized_seed_functor (nvbio) | same_type (nvbio) | transpose_tag< TextBlockingTag > (nvbio::aln) |
| any_dispatch< 64 > (nvbio::cuda) | dynamic_cast_marker (nvbio::internals) | locate_results (nvbio::fmindex) | same_type< T, T > (nvbio) | tree_desc_s |
| any_dispatch< 8 > (nvbio::cuda) |
| locate_ssa_results (nvbio::mem) | SamOutput (nvbio::io) | trie_copy (nvbio) |
| Arch (nvbio::cuda) | locate_ssa_results (nvbio::fmindex) | SampleKmersStage | trie_copy< ALPHABET_SIZE_T, CompressedTrie > (nvbio) |
| args_t | edge_weights_functor | logic_error (nvbio) | sBankConflictDivisor (mgpu) | TrieNode (nvbio) |
| assembly_pipeline | edit_distance_scoring_tag (nvbio::bowtie2::cuda) | lookup_ssa_results (nvbio::mem) | scan_dispatch (nvbio::cuda) | TrieNode5 (nvbio) |
| AtomicInt32 (nvbio) | EditDistanceAligner (nvbio::aln) | lookup_ssa_results (nvbio::fmindex) | scan_dispatch< T, Op, 16 > (nvbio::cuda) | TrieNode< 2, TYPE_T > (nvbio) |
| AtomicInt64 (nvbio) | EditDistanceScoringScheme (nvbio::bowtie2::cuda) | LRU (nvbio) | scan_dispatch< T, Op, 2 > (nvbio::cuda) | TrieNode< 3, TYPE_T > (nvbio) |
|
| EditDistanceSWScheme (nvbio::aln::priv) | LZ4_stream_t | scan_dispatch< T, Op, 32 > (nvbio::cuda) | TrieNode< 4, TYPE_T > (nvbio) |
| EditDistanceTag (nvbio::aln) | LZ4_stream_t_internal | scan_dispatch< T, Op, 4 > (nvbio::cuda) | TrieNode< 5, TYPE_T > (nvbio) |
| Backtracker (nvbio::bowtie2::cuda::detail) | equal_functor (nvbio) | LZ4_streamDecode_t | scan_dispatch< T, Op, 8 > (nvbio::cuda) | trivial_quality_string (nvbio::aln) |
| bad_alloc (nvbio) | equal_to_functor (nvbio) | LZ4_streamDecode_t_internal | sConflictFreeStorage (mgpu) | trivial_quality_string_set (nvbio::aln) |
| bam1_core_t | ErrorCorrectStage | LZ4_streamHC_t | ScopedLock (nvbio) | TrustedKmersStage |
| bam1_t | extract_active_region_source_sink | LZ4F_cctx_internal_t | ScopedTimer (nvbio::cuda) | TypeIdMap (mgpu) |
| BAM_alignment (nvbio::io) | extract_non_overlapped_repeats | LZ4F_compressOptions_t | ScopedTimer (nvbio) |
|
| BAM_alignment_batch_raw | extract_repeat_adjacencies | LZ4F_dctx_internal_t | ScoreMatrices (nvbio::aln) |
| BAM_alignment_batch_SoA | extract_super_kmers_functor | LZ4F_decompressOptions_t | ScoreMatrices< N, M, aln::EditDistanceTag > (nvbio::aln) | UberScoringScheme (nvbio::bowtie2::cuda) |
| BAM_alignment_data_block (nvbio::io) | extract_unique_adjacencies | LZ4F_frameInfo_t | ScoreMatrices< N, M, aln::GotohTag > (nvbio::aln) | uint4_as_uint32_iterator (nvbio) |
| BAM_alignment_header |
| LZ4F_preferences_t | ScoreMatrices< N, M, aln::SmithWatermanTag > (nvbio::aln) | uncached_tag (nvbio) |
| BAM_alignment_record | LZ4FileWriter (nvbio) | ScoreStream (nvbio::aln) | uniform_seeds_functor (nvbio) |
| BAM_CRQ_index | faidx1_t | LZ4HC_Data_Structure | ScoringQueues (cufmi::bowtie2::cuda) | unsigned_type (nvbio) |
| bam_hdr_t | FakeTimer (nvbio) | LZ4OutputFile (nvbio) | ScoringQueues (nvbio::bowtie2::cuda) | unsigned_type< int32 > (nvbio) |
| BAM_header (nvbio::io) | FASTA_inc_reader (nvbio) |
| ScoringQueuesDeviceView (cufmi::bowtie2::cuda) | unsigned_type< int64 > (nvbio) |
| BAM_header | FASTA_reader (nvbio) | ScoringQueuesDeviceView (nvbio::bowtie2::cuda) | unsigned_type< uint32 > (nvbio) |
| BAM_NAUX_index | FASTQ_buffer (nvbio) | make_aligner_dispatch (nvbio::bowtie2::cuda) | ScoringSchemeSelector (nvbio::bowtie2::cuda) | unsigned_type< uint64 > (nvbio) |
| bam_pileup1_t | FASTQ_file (nvbio) | make_aligner_dispatch< EndToEndAlignment, scheme_type > (nvbio::bowtie2::cuda) | ScoringSchemeSelector< edit_distance_scoring_tag > (nvbio::bowtie2::cuda) |
|
| BAM_reference (nvbio::io) | FASTQ_gzfile (nvbio) | make_aligner_dispatch< LocalAlignment, scheme_type > (nvbio::bowtie2::cuda) | ScoringSchemeSelector< smith_waterman_scoring_tag > (nvbio::bowtie2::cuda) |
| BamAlignment (BamTools) | FASTQ_reader (nvbio) | MappedFile (nvbio) | ScoringSchemeTag (nvbio::bowtie2::cuda) | variant_t |
| BAMAlignmentStream (nvbio::alndiff) | Field_traits (nvbio) | ServerMappedFile::mapping_error (nvbio) | ScoringSchemeTag< EditDistanceScoringScheme > (nvbio::bowtie2::cuda) | vector (nvbio) |
| BamOutput (nvbio::io) | Field_traits< int16 > (nvbio) | MappedFile::mapping_error (nvbio) | ScoringSchemeTag< SmithWatermanScoringScheme< MMCost, NCost > > (nvbio::bowtie2::cuda) | vector< device_tag, T > (nvbio) |
| BamReader (BamTools) | Field_traits< int32 > (nvbio) | MapqFunctorPE (nvbio::bowtie2::cuda) | sDiv2RoundUp (mgpu) | vector< host_tag, T > (nvbio) |
| BamReader::BamReaderPrivate | Field_traits< int64 > (nvbio) | MapqFunctorSE (nvbio::bowtie2::cuda) | sDiv2RoundUp< count, 0 > (mgpu) | vector_loader (nvbio) |
| BamWriter (BamTools) | Field_traits< int8 > (nvbio) | mark_kmer_uniqueness | sDivSafe (mgpu) | vector_loader< 1, char > (nvbio) |
| BamWriter::BamWriterPrivate | Filter (nvbio::alndiff) | mark_unique_prefix_kmer | sDivSafe< X, 0 > (mgpu) | vector_loader< 1, int16 > (nvbio) |
| banded_alignment_checkpointed_dispatch (nvbio::aln::priv) | filter_results (nvbio::qgram) | MatrixElement (mgpu) | sDivUp (mgpu) | vector_loader< 1, int32 > (nvbio) |
| banded_alignment_score_dispatch (nvbio::aln::priv) | filter_results (nvbio::mem) | MatrixStats (mgpu) | SEAnalyzer (nvbio::alndiff) | vector_loader< 1, int64 > (nvbio) |
| BandedScoreUnit (nvbio::aln) | filter_results (nvbio::fmindex) | max_functor (nvbio) | seed_mapper (nvbio::bowtie2::cuda::detail) | vector_loader< 1, int8 > (nvbio) |
| simd4u8::base_rep_tag (nvbio) | filter_results< qgram_index_type, index_iterator, uint2 > (nvbio::qgram) | alignment_result::max_operator (nvbio::aln::priv) | seed_mapper< APPROX_MAPPING > (nvbio::bowtie2::cuda::detail) | vector_loader< 1, T > (nvbio) |
| BaseScoringPipelineState (nvbio::bowtie2::cuda) | filter_results< qgram_index_type, index_iterator, uint32 > (nvbio::qgram) | maximum_vector_width (nvbio) | seed_mapper< CASE_PRUNING_MAPPING > (nvbio::bowtie2::cuda::detail) | vector_loader< 1, uint16 > (nvbio) |
| BatchedAlignmentScore (nvbio::aln) | find_k_best_paths_functor | maximum_vector_width< char > (nvbio) | seed_mapper< EXACT_MAPPING > (nvbio::bowtie2::cuda::detail) | vector_loader< 1, uint32 > (nvbio) |
| BatchedAlignmentScore< stream_type, DeviceStagedThreadScheduler > (nvbio::aln) | find_max_kmer_overlaps | maximum_vector_width< int16 > (nvbio) | SeedHit (nvbio::bowtie2::cuda) | vector_loader< 1, uint64 > (nvbio) |
| BatchedAlignmentScore< stream_type, DeviceThreadBlockScheduler< BLOCKDIM, MINBLOCKS > > (nvbio::aln) | SeedHit::Flags (nvbio::bowtie2::cuda) | maximum_vector_width< int32 > (nvbio) | SeedHitDequeArray (nvbio::bowtie2::cuda) | vector_loader< 1, uint8 > (nvbio) |
| BatchedAlignmentScore< stream_type, DeviceWarpScheduler > (nvbio::aln) | flip_edges | maximum_vector_width< int64 > (nvbio) | SeedHitDequeArrayDeviceStorage (nvbio::bowtie2::cuda) | vector_loader< 16, char > (nvbio) |
| BatchedAlignmentScore< stream_type, HostThreadScheduler > (nvbio::aln) | fm_index (nvbio) | maximum_vector_width< int8 > (nvbio) | SeedHitDequeArrayDeviceView (nvbio::bowtie2::cuda) | vector_loader< 16, int8 > (nvbio) |
| BatchedAlignmentTraceback (nvbio::aln) | fm_index_device_data (nvbio) | maximum_vector_width< uint16 > (nvbio) | SeedHitDequeArrayHostStorage (nvbio::bowtie2::cuda) | vector_loader< 16, uint8 > (nvbio) |
| BatchedAlignmentTraceback< CHECKPOINTS, stream_type, DeviceThreadBlockScheduler< BLOCKDIM, MINBLOCKS > > (nvbio::aln) | FMIndexData (nvbio::io) | maximum_vector_width< uint32 > (nvbio) | SeedHitDequeReference (nvbio::bowtie2::cuda) | vector_loader< 2, char > (nvbio) |
| BatchedBandedAlignmentScore (nvbio::aln) | FMIndexDataCore (nvbio::io) | maximum_vector_width< uint64 > (nvbio) | select_bit_functor (nvbio) | vector_loader< 2, int16 > (nvbio) |
| BatchedBandedAlignmentScore< BAND_LEN, stream_type, DeviceStagedThreadScheduler > (nvbio::aln) | FMIndexDataDevice (nvbio::io) | maximum_vector_width< uint8 > (nvbio) | select_dispatch (nvbio::aln) | vector_loader< 2, int32 > (nvbio) |
| BatchedBandedAlignmentScore< BAND_LEN, stream_type, DeviceThreadBlockScheduler< BLOCKDIM, MINBLOCKS > > (nvbio::aln) | FMIndexDataHost (nvbio::io) | MD5_CTX | select_dispatch< BAND_LEN, simd4u8 > (nvbio::aln) | vector_loader< 2, int64 > (nvbio) |
| BatchedBandedAlignmentScore< BAND_LEN, stream_type, HostThreadScheduler > (nvbio::aln) | FMIndexDataMMAP (nvbio::io) | mem_functor (nvbio::mem) | SelectBestApproxContext (nvbio::bowtie2::cuda) | vector_loader< 2, int8 > (nvbio) |
| BatchedBandedAlignmentTraceback (nvbio::aln) | FMIndexDataMMAPInfo (nvbio::io) | mem_handler (nvbio::mem) | sequence_string (nvbio::io) | vector_loader< 2, uint16 > (nvbio) |
| BatchedBandedAlignmentTraceback< BAND_LEN, CHECKPOINTS, stream_type, DeviceThreadScheduler > (nvbio::aln) | FMIndexDataMMAPServer (nvbio::io) | MEMFilter (nvbio) | SequenceData (nvbio::io) | vector_loader< 2, uint32 > (nvbio) |
| bcf1_t | FMIndexDef (nvbio::bowtie2::cuda) | MEMFilter< device_tag, fm_index_type > (nvbio) | SequenceDataAccess (nvbio::io) | vector_loader< 2, uint64 > (nvbio) |
| bcf_dec_t | FMIndexFilter (nvbio) | MEMFilter< host_tag, fm_index_type > (nvbio) | SequenceDataEdit (nvbio::io) | vector_loader< 2, uint8 > (nvbio) |
| bcf_fmt_t | FMIndexFilter< device_tag, fm_index_type > (nvbio) | MEMFilterDevice (nvbio) | SequenceDataEncoder (nvbio::io) | vector_loader< 3, char > (nvbio) |
| bcf_hdr_t | FMIndexFilter< host_tag, fm_index_type > (nvbio) | MEMFilterHost (nvbio) | SequenceDataEncoderImpl (nvbio::io) | vector_loader< 3, int16 > (nvbio) |
| bcf_hrec_t | FMIndexFilterDevice (nvbio) | MEMHit (nvbio) | SequenceDataFile (nvbio::io) | vector_loader< 3, int32 > (nvbio) |
| bcf_idinfo_t | FMIndexFilterHost (nvbio) | mempool_t | SequenceDataFile_BAM (nvbio::io) | vector_loader< 3, int8 > (nvbio) |
| bcf_idpair_t | fmt_aux_t | MEMRange (nvbio) | SequenceDataFile_FASTA_gz (nvbio::io) | vector_loader< 3, uint16 > (nvbio) |
| bcf_info_t | for_each_enactor (nvbio) | merge_keys (nvbio::priv) | SequenceDataFile_FASTQ_gz (nvbio::io) | vector_loader< 3, uint32 > (nvbio) |
| bcf_sr_t | for_each_enactor< device_tag > (nvbio) | mFILE | SequenceDataFile_FASTQ_parser (nvbio::io) | vector_loader< 3, uint8 > (nvbio) |
| bcf_srs_t | FormatOpMarkArray (mgpu) | min_functor (nvbio) | SequenceDataFile_SAM (nvbio::io) | vector_loader< 4, char > (nvbio) |
| Best2Sink (nvbio::aln) | FormatOpMaskBit (mgpu) | minus_one (nvbio::priv) | SequenceDataFile_TXT (nvbio::io) | vector_loader< 4, int16 > (nvbio) |
| BestAlignments (nvbio::io) | FormatOpPrintf (mgpu) | MultiPassQueueTag (nvbio::cuda) | SequenceDataFile_TXT_gz (nvbio::io) | vector_loader< 4, int32 > (nvbio) |
| BestAnchorScoreStream (nvbio::bowtie2::cuda::detail) | forward_packer (nvbio) | Mutex (nvbio) | SequenceDataInfo (nvbio::io) | vector_loader< 4, int8 > (nvbio) |
| BestApproxScoringPipelineState (nvbio::bowtie2::cuda) | forward_packer< BIG_ENDIAN, SYMBOL_SIZE, Symbol, InputStream, IndexType, uint4 > (nvbio) | MyersBitVectors (nvbio::aln::priv) | SequenceDataInputStream (nvbio::io) | vector_loader< 4, uint16 > (nvbio) |
| BestColumnSink (nvbio::aln) | ForwardPackedStream (nvbio) | MyersBitVectors< 2 > (nvbio::aln::priv) | SequenceDataMMAP (nvbio::io) | vector_loader< 4, uint32 > (nvbio) |
| BestOppositeScoreStream (nvbio::bowtie2::cuda::detail) | from_char_functor (nvbio) | MyersBitVectors< 4 > (nvbio::aln::priv) | SequenceDataMMAPServer (nvbio::io) | vector_loader< 4, uint8 > (nvbio) |
| BestPairedAlignments (nvbio::io) |
| MyersBitVectors< 5 > (nvbio::aln::priv) | SequenceDataOutputFile_FASTA (nvbio::io) | vector_loader< 8, char > (nvbio) |
| BestScoreStream (nvbio::bowtie2::cuda::detail) | MyersTag (nvbio::aln) | SequenceDataOutputFile_FASTQ (nvbio::io) | vector_loader< 8, int8 > (nvbio) |
| BestSink (nvbio::aln) | gather_functor (nvbio) |
| SequenceDataOutputFile_TXT (nvbio::io) | vector_loader< 8, uint8 > (nvbio) |
| BestSink< simd4u8 > (nvbio::aln) | genome_infixes | SequenceDataOutputStream (nvbio::io) | vector_traits (nvbio) |
| BestTracebackStream (nvbio::bowtie2::cuda::detail) | genome_loc | negate_functor (nvbio) | SequenceDataStorage (nvbio::io) | vector_traits< char > (nvbio) |
| BGZF | get_char_functor (nvbio) | node_type (nvbio::priv::wtree) | SequenceDataTraits (nvbio::io) | vector_traits< char2 > (nvbio) |
| BGZFCompressor::bgzf_extra_data (nvbio::io) | get_global_id | noncopyable (mgpu) | SequenceDataViewCore (nvbio::io) | vector_traits< char3 > (nvbio) |
| bgzf_mtaux_t | get_kmer_reg_id | not_equal_functor (nvbio) | SequenceStats | vector_traits< char4 > (nvbio) |
| BGZFCompressor (nvbio::io) | get_kmer_seq_id | not_equal_to_functor (nvbio) | SequenceStreamLoader (nvbio) | vector_traits< double > (nvbio) |
| BgzfData (BamTools) | get_kmer_size | null_type (nvbio) | ServerMappedFile (nvbio) | vector_traits< float > (nvbio) |
| BGZFileWriter (nvbio) | get_prefix_global_id | NullSink (nvbio::aln) | set_global_id | vector_traits< float2 > (nvbio) |
| BgzfThread (BamTools) | get_prefix_global_id_by_idx | num_adj_repeats | set_global_id_region_id | vector_traits< float3 > (nvbio) |
| bgzidx1_t | get_suffix_global_id_by_idx | num_non_overlapped_repeats | SetBWTHandler (nvbio) | vector_traits< float4 > (nvbio) |
| binary_switch (nvbio) | global_set_suffix_word_functor (nvbio::priv) |
| SetSuffixFlattener (nvbio::priv) | vector_traits< int > (nvbio) |
| binary_switch< A, B, 0 > (nvbio) | global_to_sorted_id | SharedCount (nvbio::internals) | vector_traits< int2 > (nvbio) |
| binary_transform_iterator (nvbio) | global_to_uid | offset_functor (nvbio::priv) | SharedPointer (nvbio) | vector_traits< int3 > (nvbio) |
| BinaryCast (nvbio) | gotoh_alignment_score_dispatch (nvbio::aln::priv) | OffsetXform (nvbio) | SharedPointerTraits (nvbio::internals) | vector_traits< int4 > (nvbio) |
| bind_first_functor (nvbio) | gotoh_alignment_score_dispatch (nvbio::aln::priv::banded) | SequenceDataFile::Options (nvbio::io) | SharedPointerTraits< void > (nvbio::internals) | vector_traits< int64 > (nvbio) |
| bind_second_functor (nvbio) | gotoh_alignment_score_dispatch< BAND_LEN, TYPE, PatternBlockingTag, symbol_type > (nvbio::aln::priv) | Options | SharedPointerTraits< void const > (nvbio::internals) | vector_traits< int64_2 > (nvbio) |
| bins_t | gotoh_alignment_score_dispatch< BAND_LEN, TYPE, TextBlockingTag, symbol_type > (nvbio::aln::priv) | OrderedQueueTag (nvbio::cuda) | SharedPointerTraits< void const volatile > (nvbio::internals) | vector_traits< int64_3 > (nvbio) |
| Bits (nvbio::priv) | gotoh_bandlen_selector (nvbio::aln::priv) | OutputFile (nvbio::io) | SharedPointerTraits< void volatile > (nvbio::internals) | vector_traits< int64_4 > (nvbio) |
| block_occupancy_functor | gotoh_bandlen_selector< TYPE, DIM, simd4u8 > (nvbio::aln::priv) | OutputStage | shift_left (nvbio) | vector_traits< short > (nvbio) |
| block_strided_iterator (nvbio) | gotoh_use_vectorization (nvbio::aln::priv) | OutputStageData | shift_right (nvbio) | vector_traits< short2 > (nvbio) |
| blocked_bloom_filter (nvbio) | gotoh_use_vectorization< vector_view< const T * > > (nvbio::aln::priv) | OutputStream (nvbio) | signed_type (nvbio) | vector_traits< short3 > (nvbio) |
| bloom_filter (nvbio) | gotoh_use_vectorization< vector_view< T * > > (nvbio::aln::priv) |
| signed_type< int32 > (nvbio) | vector_traits< short4 > (nvbio) |
| BloomFilters | GotohAligner (nvbio::aln) | signed_type< int64 > (nvbio) | vector_traits< StaticVectorBase< T, DIM_T > > (nvbio) |
| bns_files_mismatch (nvbio) | GotohCheckpointContext (nvbio::aln::priv) | pack_read (nvbio::bowtie2::cuda) | signed_type< uint32 > (nvbio) | vector_traits< uchar2 > (nvbio) |
| bns_fopen_failure (nvbio) | GotohCheckpointContext (nvbio::aln::priv::banded) | packed_read (nvbio::bowtie2::cuda) | signed_type< uint64 > (nvbio) | vector_traits< uchar3 > (nvbio) |
| BNT (nvbio::io) | GotohCheckpointedScoringContext (nvbio::aln::priv) | packed_seed (nvbio::bowtie2::cuda) | simd4u8 (nvbio) | vector_traits< uchar4 > (nvbio) |
| BNTAmb (nvbio) | GotohCheckpointedScoringContext (nvbio::aln::priv::banded) | PackedStream (nvbio) | SimpleFunc (nvbio::bowtie2::cuda) | vector_traits< uint2 > (nvbio) |
| BNTAnnData (nvbio) | GotohScoringContext (nvbio::aln::priv) | PackedStreamRef (nvbio) | SimpleGotohScheme (nvbio::aln) | vector_traits< uint3 > (nvbio) |
| BNTAnnInfo (nvbio) | GotohScoringContext (nvbio::aln::priv::banded) | PackedStringLoader (nvbio) | SimpleSmithWatermanScheme (nvbio::aln) | vector_traits< uint4 > (nvbio) |
| BNTInfo (nvbio) | GotohSubmatrixContext (nvbio::aln::priv) | PackedStringLoader< StorageIterator, SYMBOL_SIZE_T, BIG_ENDIAN_T, lmem_cache_tag< CACHE_SIZE > > (nvbio) | sink_score | vector_traits< uint64 > (nvbio) |
| BNTSeq (nvbio) | GotohSubmatrixContext (nvbio::aln::priv::banded) | PackedStringLoader< StorageIterator, SYMBOL_SIZE_T, BIG_ENDIAN_T, uncached_tag > (nvbio) | sIntegerDiv (mgpu) | vector_traits< uint64_2 > (nvbio) |
| BNTSeqLoader (nvbio) | GotohTag (nvbio::aln) | PackedVector (nvbio) | sIsPow2 (mgpu) | vector_traits< uint64_3 > (nvbio) |
| body_object (nvbio::html) | graph_functor | packer (nvbio) | sLogPow2 (mgpu) | vector_traits< uint64_4 > (nvbio) |
| BooleanStats (nvbio::alndiff) | gz_header_s | packer< BIG_ENDIAN_T, 2u, Symbol, InputStream, IndexType, uint32 > (nvbio) | sLogPow2< 0, roundUp > (mgpu) | vector_traits< unsigned char > (nvbio) |
| BowtieMapq2 (nvbio::bowtie2::cuda) | gz_state | packer< BIG_ENDIAN_T, 2u, Symbol, InputStream, IndexType, uint4 > (nvbio) | sLogPow2< 1, roundUp > (mgpu) | vector_traits< unsigned int > (nvbio) |
| BowtieMapq3 (nvbio::bowtie2::cuda) | gzFile_s | packer< BIG_ENDIAN_T, 2u, Symbol, InputStream, IndexType, uint64 > (nvbio) | sMax (mgpu) | vector_traits< unsigned short > (nvbio) |
| BufferedTextFile (nvbio::io) | GzipCompressor (nvbio::io) | packer< BIG_ENDIAN_T, 4u, Symbol, InputStream, IndexType, uint32 > (nvbio) | sMin (mgpu) | vector_traits< ushort2 > (nvbio) |
| BWTBGZWriter (nvbio) | GZOutputFile (nvbio) | packer< BIG_ENDIAN_T, 4u, Symbol, InputStream, IndexType, uint4 > (nvbio) | smith_waterman_scoring_tag (nvbio::bowtie2::cuda) | vector_traits< ushort3 > (nvbio) |
| BWTEBlock (nvbio) |
| packer< BIG_ENDIAN_T, 4u, Symbol, InputStream, IndexType, uint64 > (nvbio) | SmithWatermanAligner (nvbio::aln) | vector_traits< ushort4 > (nvbio) |
| BWTEContext (nvbio) | packer< BIG_ENDIAN_T, 8u, Symbol, InputStream, IndexType, uint4 > (nvbio) | SmithWatermanCheckpointContext (nvbio::aln::priv::banded) | vector_type (nvbio) |
| BWTLZ4Writer (nvbio) | hamming_alignment_score_dispatch (nvbio::aln::priv) | packer< BIG_ENDIAN_T, SYMBOL_SIZE, Symbol, InputStream, IndexType, uint32 > (nvbio) | SmithWatermanCheckpointedScoringContext (nvbio::aln::priv::banded) | vector_type< char, 1 > (nvbio) |
| BWTParams (nvbio) | hamming_alignment_score_dispatch< BAND_LEN, TYPE, PatternBlockingTag, symbol_type > (nvbio::aln::priv) | packer< BIG_ENDIAN_T, SYMBOL_SIZE, Symbol, InputStream, IndexType, uint64 > (nvbio) | SmithWatermanScoringContext (nvbio::aln::priv::banded) | vector_type< char, 2 > (nvbio) |
|
| hamming_alignment_score_dispatch< BAND_LEN, TYPE, TextBlockingTag, symbol_type > (nvbio::aln::priv) | packer< BIG_ENDIAN_T, SYMBOL_SIZE, Symbol, InputStream, IndexType, uint8 > (nvbio) | SmithWatermanScoringScheme (nvbio::bowtie2::cuda) | vector_type< char, 3 > (nvbio) |
| hamming_bandlen_selector (nvbio::aln::priv) | PagedText (nvbio) | SmithWatermanSubmatrixContext (nvbio::aln::priv::banded) | vector_type< char, 4 > (nvbio) |
| cache_overflow (nvbio) | hamming_bandlen_selector< TYPE, DIM, simd4u8 > (nvbio::aln::priv) | PairedAlignments (nvbio::io) | SmithWatermanTag (nvbio::aln) | vector_type< float, 1 > (nvbio) |
| cache_t | HammingCheckpointContext (nvbio::aln::priv) | Params (nvbio::bowtie2::cuda) | SNP_sequence_index (nvbio::io) | vector_type< float, 2 > (nvbio) |
| cached_iterator (nvbio) | HammingCheckpointedScoringContext (nvbio::aln::priv) | ParamsPOD (nvbio::bowtie2::cuda) | SNPDatabase (nvbio::io) | vector_type< float, 3 > (nvbio) |
| CachedPackedConcatStringSet (nvbio) | HammingDistanceAligner (nvbio::aln) | PatternBlockingTag (nvbio::aln) | sNumFactorsOf2 (mgpu) | vector_type< float, 4 > (nvbio) |
| CachedPackedConcatStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator, uint32 > (nvbio) | HammingDistanceTag (nvbio::aln) | PEAnalyzer (nvbio::alndiff) | sNumFactorsOf2< X, 1 > (mgpu) | vector_type< int, 1 > (nvbio) |
| CachedPackedConcatStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator, uint4 > (nvbio) | HammingScoringContext (nvbio::aln::priv) | PersistentThreadsQueueTag (nvbio::cuda) | SortBuffers (nvbio::cuda) | vector_type< int, 2 > (nvbio) |
| CachedPackedSparseStringSet (nvbio) | HammingSubmatrixContext (nvbio::aln::priv) | PersistentWarpsQueueTag (nvbio::cuda) | SortedDictionaryNode (nvbio) | vector_type< int, 3 > (nvbio) |
| CachedPackedSparseStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator, uint32 > (nvbio) | has_second (nvbio::io) | PingPongQueues (nvbio::cuda) | SortedDictionarySuffixTrie (nvbio) | vector_type< int, 4 > (nvbio) |
| CachedPackedSparseStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator, uint4 > (nvbio) | has_second_paired (nvbio::io) | PingPongQueuesView (nvbio::cuda) | SortEnactor (nvbio::cuda) | vector_type< int64, 1 > (nvbio) |
| CacheManager | has_second_unpaired (nvbio::io) | Pipeline (nvbio) | SortingKeys (nvbio::bowtie2::cuda) | vector_type< int64, 2 > (nvbio) |
| cast_functor (nvbio) | hash_functor1 | PipelineContext (nvbio) | copy_dispatch::source_dispatch (nvbio) | vector_type< int64, 3 > (nvbio) |
| checkpoint_storage_type (nvbio::aln) | hash_functor2 | PipelineSinkThread (nvbio::priv) | spare_bams | vector_type< int64, 4 > (nvbio) |
| checkpoint_storage_type< EditDistanceAligner< TYPE, algorithm_tag > > (nvbio::aln) | header_object (nvbio::html) | PipelineStageThread (nvbio::priv) | sparse_string_set_tag (nvbio) | vector_type< short, 1 > (nvbio) |
| checkpoint_storage_type< GotohAligner< TYPE, scoring_type, algorithm_tag > > (nvbio::aln) | hFILE | PipelineThreadBase (nvbio::priv) | SparseMatrix (mgpu) | vector_type< short, 2 > (nvbio) |
| checkpoint_storage_type< HammingDistanceAligner< TYPE, scoring_type, algorithm_tag > > (nvbio::aln) | hFILE_backend | plain_view_subtype (nvbio) | SparseStringSet (nvbio) | vector_type< short, 3 > (nvbio) |
| checkpoint_storage_type< SmithWatermanAligner< TYPE, scoring_type, algorithm_tag > > (nvbio::aln) | hFILE_fd | plain_view_subtype< const QGramIndexDevice > (nvbio) | SparseSymbolSet (nvbio) | vector_type< short, 4 > (nvbio) |
| Chunk (BamTools) | hFILE_mem | plain_view_subtype< const QGramIndexHost > (nvbio) | split_mem_functor (nvbio::mem) | vector_type< uint64, 1 > (nvbio) |
| ChunkLoader (nvbio::priv) | hFILE_net | plain_view_subtype< const QGramSetIndexDevice > (nvbio) | sRoundDown (mgpu) | vector_type< uint64, 2 > (nvbio) |
| ChunkLoader< SYMBOL_SIZE, BIG_ENDIAN, storage_type, offsets_iterator, host_tag, device_tag > (nvbio::priv) | hgacc_t | plain_view_subtype< const QGramSetIndexHost > (nvbio) | sRoundUp (mgpu) | vector_type< uint64, 3 > (nvbio) |
| ChunkLoader< SYMBOL_SIZE, BIG_ENDIAN, storage_type, offsets_iterator, system_tag, system_tag > (nvbio::priv) | hi_bits_functor (nvbio) | plain_view_subtype< const QGroupIndexDevice > (nvbio) | SSA_index_multiple (nvbio) | vector_type< uint64, 4 > (nvbio) |
| Cigar (nvbio::io) | hi_bits_functor< uint16, uint32 > (nvbio) | plain_view_subtype< const QGroupIndexHost > (nvbio) | SSA_index_multiple_context (nvbio) | vector_type< unsigned char, 1 > (nvbio) |
| cigar | hi_bits_functor< uint32, uint32 > (nvbio) | plain_view_subtype< const std::vector< T > > (nvbio) | SSA_index_multiple_device (nvbio) | vector_type< unsigned char, 2 > (nvbio) |
| cigar_op | hi_bits_functor< uint32, uint64 > (nvbio) | plain_view_subtype< const T * > (nvbio) | SSA_value_multiple (nvbio) | vector_type< unsigned char, 3 > (nvbio) |
| CigarOp (BamTools) | hi_bits_functor< uint8, uint32 > (nvbio) | plain_view_subtype< const T > (nvbio) | SSA_value_multiple_context (nvbio) | vector_type< unsigned char, 4 > (nvbio) |
| closest_diagonal (nvbio::qgram) | Histogram (nvbio::alndiff) | plain_view_subtype< const thrust::device_vector< T > > (nvbio) | SSA_value_multiple_device (nvbio) | vector_type< unsigned int, 1 > (nvbio) |
| closest_diagonal< uint2 > (nvbio::qgram) | Histogram2d (nvbio::alndiff) | plain_view_subtype< const thrust::host_vector< T > > (nvbio) | stackinfo3 (divsufsortxx::helper) | vector_type< unsigned int, 2 > (nvbio) |
| closest_diagonal< uint4 > (nvbio::qgram) | hit_compare (nvbio::bowtie2::cuda) | plain_view_subtype< null_type > (nvbio) | stackinfo4 (divsufsortxx::helper) | vector_type< unsigned int, 3 > (nvbio) |
| code | ReadHitsIndexDeviceView::HitArray (cufmi::bowtie2::cuda) | plain_view_subtype< QGramIndexDevice > (nvbio) | StagedAlignmentUnitBase (nvbio::aln) | vector_type< unsigned int, 4 > (nvbio) |
| collapse_same_start_kmers | ReadHitsIndexDeviceView::HitArray (nvbio::bowtie2::cuda) | plain_view_subtype< QGramIndexHost > (nvbio) | StagedScoreUnit (nvbio::aln) | vector_type< unsigned short, 1 > (nvbio) |
| Collector (nvbio) | HitQueues (nvbio::bowtie2::cuda) | plain_view_subtype< QGramSetIndexDevice > (nvbio) | static_cast_marker (nvbio::internals) | vector_type< unsigned short, 2 > (nvbio) |
| column_storage_type (nvbio::aln) | HitQueues (cufmi::bowtie2::cuda) | plain_view_subtype< QGramSetIndexHost > (nvbio) | static_tree_desc_s | vector_type< unsigned short, 3 > (nvbio) |
| column_storage_type< EditDistanceAligner< TYPE, algorithm_tag > > (nvbio::aln) | HitQueuesDeviceView (cufmi::bowtie2::cuda) | plain_view_subtype< QGroupIndexDevice > (nvbio) | StaticVector (nvbio) | vector_type< unsigned short, 4 > (nvbio) |
| column_storage_type< GotohAligner< TYPE, scoring_type, algorithm_tag > > (nvbio::aln) | HitQueuesDeviceView (nvbio::bowtie2::cuda) | plain_view_subtype< QGroupIndexHost > (nvbio) | StaticVectorBase (nvbio) | vector_view (nvbio) |
| column_storage_type< HammingDistanceAligner< TYPE, scoring_type, algorithm_tag > > (nvbio::aln) | HitReference (cufmi::bowtie2::cuda) | plain_view_subtype< std::vector< T > > (nvbio) | StaticVectorBase< T, 2 > (nvbio) | VectorArrayView (nvbio) |
| column_storage_type< SmithWatermanAligner< TYPE, scoring_type, algorithm_tag > > (nvbio::aln) | HitReference (nvbio::bowtie2::cuda) | plain_view_subtype< T * > (nvbio) | StaticVectorBase< T, 3 > (nvbio) | vectorized_string (nvbio) |
| complement_functor (nvbio) | host_device_buffer (nvbio::cuda) | plain_view_subtype< thrust::device_vector< T > > (nvbio) | StaticVectorBase< T, 4 > (nvbio) | vectorized_string< const char * > (nvbio) |
| component_functor (nvbio) | host_device_buffer_sync (nvbio::cuda) | plain_view_subtype< thrust::host_vector< T > > (nvbio) | Stats (nvbio::bowtie2::cuda) | vectorized_string< vector_view< const T *, IndexType > > (nvbio) |
| composition_functor (nvbio) | host_device_buffer_zero_copy (nvbio::cuda) | pod_reader (nvbio) | Stats (nvbio::alndiff) | vectorized_string< vector_view< PackedStream< InputStream, Symbol, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > > > (nvbio) |
| CompressionSort (nvbio::cuda) | host_tag (nvbio) | pod_type (nvbio) | StatsPartition (nvbio::alndiff) | debruijn_graph::view |
| compute_prefix_global_id | HostBWTConfigCPUBucketer (nvbio::cuda) | pod_type< io::Alignment > (nvbio) | store_kmer_unique_ids | ServerMappedFile::view_error (nvbio) |
| compute_suffix_global_id | HostBWTConfigGPUBucketer (nvbio::cuda) | pod_type< io::BestAlignments > (nvbio) | stream_traits (nvbio) | MappedFile::view_error (nvbio) |
| ComputeThreadPE (nvbio::bowtie2::cuda) | HostBWTHandler (nvbio) | pod_writer (nvbio) | stream_traits< const T * > (nvbio) |
|
| ComputeThreadSE (nvbio::bowtie2::cuda) | HostBWTHandler< PackedStream< word_type *, uint8, SYMBOL_SIZE, BIG_ENDIAN, uint64 > > (nvbio) | polymorphic_cast_marker (nvbio::internals) | stream_traits< ForwardPackedStream< InputStream, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > > (nvbio) |
| concatenated_string_set_tag (nvbio) | HostCigarArray (nvbio::io) | pool_alloc_t | stream_traits< PackedStream< InputStream, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, IndexType > > (nvbio) | wavelet_ranker (nvbio) |
| ConcatenatedStringSet (nvbio) | HostCoreSetSuffixBucketer (nvbio::priv) | pool_t | stream_traits< T * > (nvbio) | WaveletTree (nvbio) |
| condition (nvbio::cuda) | HostOutputBatchPE (nvbio::io) | popc_functor (nvbio) | StreamAdapter (nvbio::bowtie2::cuda) | WaveletTreeStorage (nvbio) |
| condition_set_storage (nvbio::cuda) | HostOutputBatchSE (nvbio::io) | populate_unique_kmer_data | StreamAdapterBase (nvbio::bowtie2::cuda) | WeakCount (nvbio::internals) |
| condition_set_view (nvbio::cuda) | HostSetSuffixBucketer (nvbio::priv) | Prefix (nvbio) | StreamAdapterBase< Iterator, uint32 > (nvbio::bowtie2::cuda) | WeakPointer (nvbio) |
| config_s | HostStringSetRadices (nvbio::priv) | PrefixCore (nvbio) | StreamAdapterBase< Iterator, uint4 > (nvbio::bowtie2::cuda) | word_selector (nvbio::priv) |
| const_cached_iterator (nvbio) | HostThreadScheduler (nvbio::aln) | PrefixCore< StringType, CoordType, 1u > (nvbio) | strided_iterator (nvbio) | word_selector< 10 > (nvbio::priv) |
| const_cast_marker (nvbio::internals) | HostVectorArray (nvbio) | PrefixCore< StringType, CoordType, 2u > (nvbio) | strided_packed_string_set_tag (nvbio) | word_selector< 12 > (nvbio::priv) |
| Constant (nvbio) | html_object (nvbio::html) | PrefixDoublingSufSort (nvbio::cuda) | strided_string_set_tag (nvbio) | word_selector< 14 > (nvbio::priv) |
| ConstantCost (nvbio::bowtie2::cuda) | hts_cram_idx_t | PrefixSet (nvbio) | StridedPackedStringSet (nvbio) | word_selector< 16 > (nvbio::priv) |
| WorkQueue< OrderedQueueTag, WorkUnitT, BLOCKDIM >::Context (nvbio::cuda) | hts_itr_t | PrefixSetCore (nvbio) | StridedStringSet (nvbio) | word_selector< 18 > (nvbio::priv) |
| WorkQueue< MultiPassQueueTag, WorkUnitT, BLOCKDIM >::Context (nvbio::cuda) | hts_pair64_t | PrefixSetCore< SequenceType, PrefixIterator, 1u > (nvbio) | string_alloc_t | word_selector< 20 > (nvbio::priv) |
| AlignmentStreamBase::context_type (nvbio::bowtie2::cuda::detail) | HTSBAMReader | PrefixSetCore< SequenceType, PrefixIterator, 2u > (nvbio) | string_bwt_functor (nvbio::priv) | word_selector< 22 > (nvbio::priv) |
| AlignmentStream::context_type (nvbio::aln::priv) | HTSBAMWriter | print_super_kmer_functor | string_iterator (nvbio) | word_selector< 24 > (nvbio::priv) |
| coord_to_seq | htsFile | priority_deque (boost::container) | string_qgram_functor (nvbio) | word_selector< 26 > (nvbio::priv) |
| copy_dispatch (nvbio) |
| priority_deque (nvbio) | string_qgram_search_functor (nvbio) | word_selector< 28 > (nvbio::priv) |
| copy_insert_pages (nvbio) | priority_queue (nvbio) | string_seed_functor (nvbio) | word_selector< 30 > (nvbio::priv) |
| copy_merge_pages (nvbio) | if_equal (nvbio) | project_coords_functor (nvbio) | string_set_bwt_functor (nvbio::priv) | word_selector< 32 > (nvbio::priv) |
| count_overlapped_adjacencies | if_true (nvbio) | project_coords_functor< in_coord_type, uint2 > (nvbio) | string_set_length_functor (nvbio) | word_selector< 4 > (nvbio::priv) |
| CountedBase (nvbio::internals) | if_true< false, T, F > (nvbio) | project_coords_functor< in_coord_type, uint3 > (nvbio) | string_set_qgram_functor (nvbio) | word_selector< 48 > (nvbio::priv) |
| CountedBase_impl (nvbio::internals) | if_true< true, T, F > (nvbio) | project_coords_functor< in_coord_type, uint32 > (nvbio) | string_suffix_difference (nvbio::priv) | word_selector< 6 > (nvbio::priv) |
| cram_beta_decoder | ServerMappedFile::Impl (nvbio) | project_coords_functor< in_coord_type, uint4 > (nvbio) | string_suffix_less (nvbio::priv) | word_selector< 64 > (nvbio::priv) |
| cram_block | MappedFile::Impl (nvbio) | project_coords_functor< uint32, uint32 > (nvbio) | string_suffix_word_functor (nvbio::priv) | word_selector< 8 > (nvbio::priv) |
| cram_block_compression_hdr | ThreadBase::Impl (nvbio) | project_coords_functor< uint64, uint64 > (nvbio) | string_suffix_word_functor< SYMBOL_SIZE, WORD_BITS, DOLLAR_BITS, PackedStream< storage_type, symbol_type, SYMBOL_SIZE, true, index_type >, word_type > (nvbio::priv) | worker_t |
| cram_block_slice_hdr | FASTQ_gzfile::Impl (nvbio) |
| string_t | WorkQueue (nvbio::cuda) |
| cram_byte_array_len_decoder | Mutex::Impl (nvbio) | string_traits (nvbio) | WorkQueue (nvbio) |
| cram_byte_array_len_encoder | in_range_functor (nvbio::priv) | qgram_locate_functor (nvbio) | string_traits< const T * > (nvbio) | WorkQueue< MultiPassQueueTag, WorkUnitT, BLOCKDIM > (nvbio::cuda) |
| cram_byte_array_stop_decoder | index_transform_iterator (nvbio) | QGramFilter (nvbio) | string_traits< T * > (nvbio) | WorkQueue< OrderedQueueTag, WorkUnitT, BLOCKDIM > (nvbio::cuda) |
| cram_codec | Infix (nvbio) | QGramFilter< device_tag, qgram_index_type, query_iterator, index_iterator > (nvbio) | string_traits< vector_view< Iterator, IndexType > > (nvbio) | WorkQueue< PersistentThreadsQueueTag, WorkUnitT, BLOCKDIM > (nvbio::cuda) |
| cram_container | InfixCore (nvbio) | QGramFilter< host_tag, qgram_index_type, query_iterator, index_iterator > (nvbio) | StringBWTHandler (nvbio) | WorkQueue< PersistentWarpsQueueTag, WorkUnitT, BLOCKDIM > (nvbio::cuda) |
| cram_decode_job | InfixCore< StringType, CoordType, 2u > (nvbio) | QGramFilterDevice (nvbio) | StringBWTSSAHandler (nvbio) | WorkQueueStats (nvbio::cuda) |
| cram_external_decoder | InfixCore< StringType, CoordType, 4u > (nvbio) | QGramFilterHost (nvbio) | StringPrefetcher (nvbio) | WorkQueueStatsView (nvbio::cuda) |
| cram_fd | InfixSet (nvbio) | QGramIndexCore (nvbio) | StringPrefetcher< Infix< PackedStream< StorageIterator, uint8, SYMBOL_SIZE_T, BIG_ENDIAN_T >, InfixCoordType >, lmem_cache_tag< CACHE_SIZE > > (nvbio) |
|
| cram_feature | InfixSetCore (nvbio) | QGramIndexDevice (nvbio) | StringPrefetcher< Infix< vector_view< PackedStream< StorageIterator, uint8, SYMBOL_SIZE_T, BIG_ENDIAN_T > >, InfixCoordType >, lmem_cache_tag< CACHE_SIZE > > (nvbio) |
| cram_file_def | InfixSetCore< SequenceType, InfixIterator, 2u > (nvbio) | QGramIndexHost (nvbio) | StringPrefetcher< vector_view< const T * >, lmem_cache_tag< CACHE_SIZE > > (nvbio) | XXH32_state_t |
| cram_gamma_decoder | InfixSetCore< SequenceType, InfixIterator, 4u > (nvbio) | QGramIndexViewCore (nvbio) | StringPrefetcher< vector_view< PackedStream< StorageIterator, uint8, SYMBOL_SIZE_T, BIG_ENDIAN_T > >, lmem_cache_tag< CACHE_SIZE > > (nvbio) | XXH64_state_t |
| cram_huffman_code | inflate_state | QGramSetIndexDevice (nvbio) | StringPrefetcher< vector_view< T * >, lmem_cache_tag< CACHE_SIZE > > (nvbio) | XXH_istate32_t |
| cram_huffman_decoder | DebugAlignmentStream::Info (nvbio::alndiff) | QGramSetIndexHost (nvbio) | AlignmentStream::strings_type (nvbio::aln::priv) | XXH_istate64_t |
| cram_huffman_encoder | inplace_or (nvbio) | qgroup_setup_I (nvbio::qgroup) | StringSetIterator (nvbio) |
|
| cram_index | inplace_or< uint2 > (nvbio) | qgroup_setup_P (nvbio::qgroup) | StringSSAHandler (nvbio) |
| cram_job | inplace_or< uint32 > (nvbio) | qgroup_setup_SS (nvbio::qgroup) | StringSuffixBucketer (nvbio::priv) | z_stream_s |
| cram_map | inplace_or< uint4 > (nvbio) | QGroupIndexDevice (nvbio) | substring_wrapper (divsufsortxx::substring) | zfp |
| cram_metrics | inplace_or< uint64 > (nvbio) | QGroupIndexHost (nvbio) | Suffix (nvbio) |
|
| cram_range | inplace_or< uint64_2 > (nvbio) | QGroupIndexViewCore (nvbio) | suffix_component_functor (nvbio::priv) |
| cram_record | inplace_or< uint64_4 > (nvbio) | QualCost (nvbio::bowtie2::cuda) | suffix_offset_functor (nvbio::priv) | __bam_mplp_t |
| cram_slice | InplaceQueueTag (nvbio::cuda) | quality_nop (nvbio) | SuffixCore (nvbio) | __bgzidx_t |
| cram_stats | InputStage |
| SuffixCore< StringType, CoordType, 1u > (nvbio) | __faidx_t |
| cram_subexp_decoder | InputStageData | SuffixCore< StringType, CoordType, 2u > (nvbio) | __hts_idx_t |
| cstate_t | InputThreadPE (nvbio::bowtie2::cuda) | range_size (nvbio::qgram) | SuffixSet (nvbio) | __kstring_t |
| ct_data_s | InputThreadSE (nvbio::bowtie2::cuda) | range_size (nvbio::mem) | SuffixSetCore (nvbio) | __linkbuf_t |
| cuda_error (nvbio) | internal_state | range_size (nvbio::fmindex) | SuffixSetCore< SequenceType, SuffixIterator, 1u > (nvbio) | _bcf_sr_regions_t |
| CudaAlloc (mgpu) | intrusive_ptr (mgpu) | rank_dictionary (nvbio) | SuffixSetCore< SequenceType, SuffixIterator, 2u > (nvbio) | _bcf_sweep_t |
| CudaAllocBuckets (mgpu) | IOStats (nvbio::io) | rank_functor (nvbio::fmindex) | SuffixTrie (nvbio) | _profile |
| CudaAllocSimple (mgpu) | is_aligned (nvbio::io) | rank_span_size (nvbio::mem) | SumTree (nvbio) | _region_t |
| CudaBase (mgpu) | is_concordant (nvbio::io) | rank_string_id (nvbio::mem) | super_coord_to_seq | _trbudget_t |
| CudaContext (mgpu) | is_discordant (nvbio::io) | rank_word_traits (nvbio) | supports_scheduler (nvbio::aln) | _U32_S |
| CudaDevice (mgpu) | is_false_functor (nvbio) | rank_word_traits< 2, uint32 > (nvbio) | supports_scheduler< EditDistanceAligner< TYPE, AlgorithmTag >, DeviceStagedThreadScheduler > (nvbio::aln) | _U64_S |
| CudaDeviceMem (mgpu) | is_invalid_super_kmer | rank_word_traits< 2, uint64 > (nvbio) | supports_scheduler< EditDistanceAligner< TYPE, AlgorithmTag >, DeviceThreadScheduler > (nvbio::aln) | |
| CudaEvent (mgpu) | is_not_concordant (nvbio::io) | rank_word_traits< 4, uint32 > (nvbio) | supports_scheduler< EditDistanceAligner< TYPE, AlgorithmTag >, DeviceWarpScheduler > (nvbio::aln) | |
| CudaException (mgpu) | is_paired (nvbio::io) | rank_word_traits< 4, uint64 > (nvbio) | supports_scheduler< EditDistanceAligner< TYPE, AlgorithmTag >, HostThreadScheduler > (nvbio::aln) | |
| | | | |
1.8.4
