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