List of all items
Structs
- assigner::AdjacencyUmiAssigner
- assigner::BkTree
- assigner::IdentityUmiAssigner
- assigner::NgramIndex
- assigner::PairedUmiAssigner
- assigner::SimpleErrorUmiAssigner
- bam_io::ChainedReader
- bam_io::IndexingBamWriter
- bam_io::RawBamWriter
- batched_sam_reader::BatchedSamReader
- bgzf_reader::RawBgzfBlock
- bgzf_writer::CompressedBlock
- bgzf_writer::InlineBgzfCompressor
- bitenc::BitEnc
- clipper::SamRecordClipper
- consensus::CodecConsensusCaller
- consensus::CodecConsensusOptions
- consensus::CodecConsensusStats
- consensus::ConsensusBaseBuilder
- consensus::ConsensusSequence
- consensus::CorrectionStats
- consensus::DuplexConsensusCaller
- consensus::DuplexConsensusRead
- consensus::FilterConfig
- consensus::FilterThresholds
- consensus::OverlappingBasesConsensusCaller
- consensus::VanillaConsensusRead
- consensus::VanillaUmiConsensusCaller
- consensus::VanillaUmiConsensusOptions
- consensus::base_builder::ConsensusBaseBuilder
- consensus::caller::ConsensusCallingStats
- consensus::caller::ConsensusOutput
- consensus::codec_caller::CodecConsensusCaller
- consensus::codec_caller::CodecConsensusOptions
- consensus::codec_caller::CodecConsensusStats
- consensus::duplex_caller::DuplexConsensusCaller
- consensus::duplex_caller::DuplexConsensusRead
- consensus::filter::FilterConfig
- consensus::filter::FilterThresholds
- consensus::overlapping::CorrectionStats
- consensus::overlapping::OverlappingBasesConsensusCaller
- consensus::sequence::ConsensusSequence
- consensus::simple_umi::SimpleConsensusCaller
- consensus::simple_umi::SimpleUmiConsensusCaller
- consensus::vanilla_caller::VanillaConsensusRead
- consensus::vanilla_caller::VanillaUmiConsensusCaller
- consensus::vanilla_caller::VanillaUmiConsensusOptions
- consensus_caller::ConsensusCallingStats
- consensus_caller::ConsensusOutput
- consensus_filter::FilterConfig
- consensus_filter::FilterThresholds
- duplex_consensus_caller::DuplexConsensusCaller
- duplex_consensus_caller::DuplexConsensusRead
- fastq::FastqSegment
- fastq::FastqSet
- fastq::ReadSetIterator
- grouper::FastqGrouper
- grouper::FastqRecord
- grouper::FastqTemplate
- grouper::FilterMetrics
- grouper::ProcessedPositionGroup
- grouper::RawPositionGroup
- grouper::RecordPositionGrouper
- grouper::SingleRawRecordGrouper
- grouper::SingleRecordGrouper
- grouper::TemplateGrouper
- logging::OperationTimer
- metrics::ClippingMetrics
- metrics::ClippingMetricsCollection
- metrics::ConsensusKvMetric
- metrics::ConsensusMetrics
- metrics::DuplexFamilySizeMetric
- metrics::DuplexMetricsCollector
- metrics::DuplexUmiMetric
- metrics::DuplexYieldMetric
- metrics::FamilySizeMetric
- metrics::FamilySizeMetrics
- metrics::UmiCorrectionMetrics
- metrics::UmiGroupingMetrics
- metrics::UmiMetric
- metrics::clip::ClipCounts
- metrics::clip::ClippingMetrics
- metrics::clip::ClippingMetricsCollection
- metrics::consensus::ConsensusKvMetric
- metrics::consensus::ConsensusMetrics
- metrics::correct::UmiCorrectionMetrics
- metrics::duplex::DuplexFamilySizeMetric
- metrics::duplex::DuplexMetricsCollector
- metrics::duplex::DuplexUmiMetric
- metrics::duplex::DuplexYieldMetric
- metrics::duplex::FamilySizeMetric
- metrics::duplex::UmiMetric
- metrics::group::FamilySizeMetrics
- metrics::group::UmiGroupingMetrics
- mi_group::MiGroup
- mi_group::MiGroupBatch
- mi_group::MiGroupIterator
- mi_group::MiGroupIteratorWithTransform
- mi_group::MiGrouper
- mi_group::RawMiGroup
- mi_group::RawMiGroupBatch
- mi_group::RawMiGroupIterator
- mi_group::RawMiGrouper
- overlapping_consensus::CorrectionStats
- overlapping_consensus::OverlappingBasesConsensusCaller
- progress::ProgressTracker
- read_info::LibraryIndex
- read_info::ReadInfo
- reference::ReferenceReader
- reorder_buffer::DrainReady
- reorder_buffer::ReorderBuffer
- sam::ConsensusTagsBuilder
- sam::FragBuilder
- sam::PairBuilder
- sam::RecordBuilder
- sam::SamBuilder
- sam::builder::ConsensusTagsBuilder
- sam::builder::FragBuilder
- sam::builder::PairBuilder
- sam::builder::RecordBuilder
- sam::builder::RecordPairBuilder
- sam::builder::SamBuilder
- simple_umi_consensus::SimpleConsensusCaller
- simple_umi_consensus::SimpleUmiConsensusCaller
- sort::SortStats
- sort::external::ExternalSorter
- sort::inline_buffer::PackedCoordKey
- sort::inline_buffer::RecordBuffer
- sort::inline_buffer::RecordRef
- sort::inline_buffer::TemplateInlineHeader
- sort::inline_buffer::TemplateKey
- sort::inline_buffer::TemplateRecordBuffer
- sort::inline_buffer::TemplateRecordRef
- sort::keys::CoordinateKey
- sort::keys::PrimaryAlignmentInfo
- sort::keys::QuerynameKey
- sort::keys::RawCoordinateKey
- sort::keys::RawQuerynameKey
- sort::keys::SortContext
- sort::pipeline::MergeEntry
- sort::pipeline::ParallelMergeConfig
- sort::radix::PackedCoordinateKey
- sort::raw::GenericKeyedChunkReader
- sort::raw::GenericKeyedChunkWriter
- sort::raw::LibraryLookup
- sort::raw::RawExternalSorter
- sort::raw_bam_reader::BatchedRawBamReader
- sort::raw_bam_reader::RawBamRecordReader
- sort::read_ahead::RawReadAheadReader
- sort::read_ahead::ReadAheadReader
- template::Builder
- template::Template
- template::TemplateIterator
- umi::AdjacencyUmiAssigner
- umi::IdentityUmiAssigner
- umi::PairedUmiAssigner
- umi::SimpleErrorUmiAssigner
- umi::TagInfo
- umi::TagSets
- umi::assigner::AdjacencyUmiAssigner
- umi::assigner::BkTree
- umi::assigner::IdentityUmiAssigner
- umi::assigner::NgramIndex
- umi::assigner::PairedUmiAssigner
- umi::assigner::SimpleErrorUmiAssigner
- umi::parallel_assigner::ParallelAdjacencyAssigner
- umi::parallel_assigner::ParallelEditAssigner
- umi::parallel_assigner::ParallelIdentityAssigner
- umi::parallel_assigner::ParallelPairedAssigner
- umi::parallel_assigner::UnionFind
- unified_pipeline::ActiveSteps
- unified_pipeline::BamPipelineConfig
- unified_pipeline::BamPipelineState
- unified_pipeline::BamStepContext
- unified_pipeline::BgzfBatchConfig
- unified_pipeline::BgzfWorkerState
- unified_pipeline::BoundaryBatch
- unified_pipeline::BoundaryState
- unified_pipeline::ChaseBottleneckScheduler
- unified_pipeline::CompressedBlockBatch
- unified_pipeline::DecodedRecord
- unified_pipeline::DecompressedBatch
- unified_pipeline::FastqBoundaryBatch
- unified_pipeline::FastqBoundaryState
- unified_pipeline::FastqDecompressedBatch
- unified_pipeline::FastqDecompressedChunk
- unified_pipeline::FastqFormat
- unified_pipeline::FastqParsedBatch
- unified_pipeline::FastqParsedStream
- unified_pipeline::FastqPipelineConfig
- unified_pipeline::FastqPipelineState
- unified_pipeline::FastqStepContext
- unified_pipeline::FastqStreamBoundaries
- unified_pipeline::FastqWorkerState
- unified_pipeline::FixedPriorityScheduler
- unified_pipeline::GroupKey
- unified_pipeline::GroupKeyConfig
- unified_pipeline::GroupState
- unified_pipeline::MemoryTracker
- unified_pipeline::OutputPipelineQueues
- unified_pipeline::OutputQueueDepths
- unified_pipeline::PerStreamChunk
- unified_pipeline::PipelineConfig
- unified_pipeline::PipelineFunctions
- unified_pipeline::PipelineStats
- unified_pipeline::PipelineValidationError
- unified_pipeline::QueueDepths
- unified_pipeline::QueueSample
- unified_pipeline::RawBlockBatch
- unified_pipeline::ReorderBufferState
- unified_pipeline::SerializedBatch
- unified_pipeline::StreamBoundaryState
- unified_pipeline::WorkerCoreState
- unified_pipeline::WorkerState
- unified_pipeline::deadlock::DeadlockConfig
- unified_pipeline::deadlock::DeadlockState
- unified_pipeline::deadlock::QueueSnapshot
- unified_pipeline::queue::OrderedQueue
- unified_pipeline::queue::QueueStats
- unified_pipeline::rebalancer::DynamicRebalancer
- unified_pipeline::rebalancer::InitialAllocation
- unified_pipeline::rebalancer::RebalancerConfig
- unified_pipeline::scheduler::BackpressureState
- vanilla_consensus_caller::VanillaConsensusRead
- vanilla_consensus_caller::VanillaUmiConsensusCaller
- vanilla_consensus_caller::VanillaUmiConsensusOptions
- variant_review::BaseCounts
- variant_review::ConsensusVariantReviewInfo
- variant_review::Variant
Enums
- RejectionReason
- assigner::Strategy
- bam_io::BgzfReaderEnum
- bam_io::BgzfWriterEnum
- clipper::ClippingMode
- consensus::AgreementStrategy
- consensus::ConsensusType
- consensus::DisagreementStrategy
- consensus::FilterResult
- consensus::caller::RejectionReason
- consensus::filter::ConsensusType
- consensus::filter::FilterResult
- consensus::overlapping::AgreementStrategy
- consensus::overlapping::DisagreementStrategy
- consensus_caller::RejectionReason
- consensus_filter::ConsensusType
- consensus_filter::FilterResult
- errors::FgumiError
- fastq::SkipReason
- metrics::ReadType
- metrics::clip::ReadType
- overlapping_consensus::AgreementStrategy
- overlapping_consensus::DisagreementStrategy
- rejection::RejectionReason
- sam::PairOrientation
- sam::Strand
- sam::builder::Strand
- sam::record_utils::PairOrientation
- sort::keys::SortOrder
- template::MoleculeId
- template::PairOrientation
- umi::MoleculeId
- umi::Strategy
- umi::UmiValidation
- umi::assigner::Strategy
- unified_pipeline::DecodedRecordData
- unified_pipeline::PipelineStep
- unified_pipeline::StepResult
- unified_pipeline::StreamReader
- unified_pipeline::deadlock::DeadlockAction
- unified_pipeline::scheduler::Direction
- unified_pipeline::scheduler::SchedulerStrategy
Traits
- assigner::UmiAssigner
- consensus::ConsensusCaller
- consensus::caller::ConsensusCaller
- consensus_caller::ConsensusCaller
- metrics::Metric
- metrics::ProcessingMetrics
- sort::keys::RawSortKey
- sort::keys::SortKey
- umi::UmiAssigner
- umi::assigner::UmiAssigner
- unified_pipeline::BatchWeight
- unified_pipeline::Grouper
- unified_pipeline::HasCompressor
- unified_pipeline::HasHeldBoundaries
- unified_pipeline::HasHeldCompressed
- unified_pipeline::HasHeldProcessed
- unified_pipeline::HasHeldSerialized
- unified_pipeline::HasRecycledBuffers
- unified_pipeline::HasWorkerCore
- unified_pipeline::MemoryEstimate
- unified_pipeline::MonitorableState
- unified_pipeline::OutputPipelineState
- unified_pipeline::PipelineLifecycle
- unified_pipeline::ProcessPipelineState
- unified_pipeline::SerializePipelineState
- unified_pipeline::StepContext
- unified_pipeline::WorkerStateCommon
- unified_pipeline::WritePipelineState
- unified_pipeline::scheduler::Scheduler
Functions
- alignment_tags::md_tag
- alignment_tags::nm_tag
- alignment_tags::regenerate_alignment_tags
- alignment_tags::regenerate_alignment_tags_raw
- alignment_tags::uq_tag
- assigner::count_mismatches
- assigner::matches_within_threshold
- bam_io::create_bam_reader
- bam_io::create_bam_reader_for_pipeline
- bam_io::create_bam_writer
- bam_io::create_indexing_bam_writer
- bam_io::create_optional_bam_writer
- bam_io::create_raw_bam_reader
- bam_io::create_raw_bam_writer
- bam_io::is_stdin_path
- bam_io::is_stdout_path
- bam_io::write_bai_index
- bgzf_reader::decompress_block
- bgzf_reader::decompress_block_into
- bgzf_reader::decompress_block_slice_into
- bgzf_reader::read_raw_blocks
- clipper::cigar_utils::aligned_bases
- clipper::cigar_utils::clipped_bases
- clipper::cigar_utils::is_cigar_prefix
- clipper::cigar_utils::reference_length
- clipper::cigar_utils::simplify_cigar
- consensus::apply_overlapping_consensus
- consensus::calculate_error_rate
- consensus::caller::calculate_error_rate
- consensus::caller::log_consensus_statistics
- consensus::caller::make_prefix_from_header
- consensus::compute_read_stats
- consensus::count_no_calls
- consensus::filter::compute_read_stats
- consensus::filter::compute_read_stats_raw
- consensus::filter::count_no_calls
- consensus::filter::filter_duplex_read
- consensus::filter::filter_duplex_read_raw
- consensus::filter::filter_read
- consensus::filter::filter_read_raw
- consensus::filter::is_duplex_consensus
- consensus::filter::is_duplex_consensus_raw
- consensus::filter::mask_bases
- consensus::filter::mask_bases_raw
- consensus::filter::mask_duplex_bases
- consensus::filter::mask_duplex_bases_raw
- consensus::filter::mean_base_quality
- consensus::filter::template_passes
- consensus::filter::template_passes_raw
- consensus::filter_duplex_read
- consensus::filter_read
- consensus::is_duplex_consensus
- consensus::log_consensus_statistics
- consensus::mask_bases
- consensus::mask_duplex_bases
- consensus::mean_base_quality
- consensus::overlapping::apply_overlapping_consensus
- consensus::overlapping::apply_overlapping_consensus_raw
- consensus::simple_umi::consensus_umis
- consensus::tags::is_consensus
- consensus::tags::is_duplex_consensus
- consensus::tags::is_simplex_consensus
- consensus::tags::per_base::all_tags
- consensus::tags::per_base::tag
- consensus::tags::per_base::tags_to_reverse
- consensus::tags::per_base::tags_to_reverse_complement
- consensus::tags::per_read::all_tags
- consensus::tags::per_read::tag
- consensus::tags::qualities_to_tag_value
- consensus::tags::sequence_to_tag_value
- consensus::tags::tag
- consensus::template_passes
- consensus_caller::calculate_error_rate
- consensus_caller::log_consensus_statistics
- consensus_caller::make_prefix_from_header
- consensus_filter::compute_read_stats
- consensus_filter::compute_read_stats_raw
- consensus_filter::count_no_calls
- consensus_filter::filter_duplex_read
- consensus_filter::filter_duplex_read_raw
- consensus_filter::filter_read
- consensus_filter::filter_read_raw
- consensus_filter::is_duplex_consensus
- consensus_filter::is_duplex_consensus_raw
- consensus_filter::mask_bases
- consensus_filter::mask_bases_raw
- consensus_filter::mask_duplex_bases
- consensus_filter::mask_duplex_bases_raw
- consensus_filter::mean_base_quality
- consensus_filter::template_passes
- consensus_filter::template_passes_raw
- consensus_tags::is_consensus
- consensus_tags::is_duplex_consensus
- consensus_tags::is_simplex_consensus
- consensus_tags::per_base::all_tags
- consensus_tags::per_base::tag
- consensus_tags::per_base::tags_to_reverse
- consensus_tags::per_base::tags_to_reverse_complement
- consensus_tags::per_read::all_tags
- consensus_tags::per_read::tag
- consensus_tags::qualities_to_tag_value
- consensus_tags::sequence_to_tag_value
- consensus_tags::tag
- dna::complement_base
- dna::complement_base_preserve_case
- dna::reverse_complement
- dna::reverse_complement_str
- grouper::build_templates_from_records
- grouper::parse_fastq_records
- grouper::strip_read_suffix
- header::add_pg_record
- header::add_pg_to_builder
- header::build_program_record
- header::get_last_program_id
- header::make_unique_program_id
- logging::format_duration
- logging::format_percent
- logging::format_rate
- logging::log_consensus_summary
- logging::log_umi_grouping_summary
- metrics::format_float
- metrics::read_metrics
- metrics::write_metrics
- metrics::writer::read_metrics
- metrics::writer::read_metrics_auto
- metrics::writer::write_metrics
- metrics::writer::write_metrics_auto
- overlapping_consensus::apply_overlapping_consensus
- overlapping_consensus::apply_overlapping_consensus_raw
- phred::ln_error_prob_two_trials
- phred::ln_normalize
- phred::ln_not
- phred::ln_prob_to_phred
- phred::ln_sum_exp
- phred::ln_sum_exp_array
- phred::phred_to_ln_correct_prob
- phred::phred_to_ln_error_prob
- read_info::build_library_lookup
- read_info::compute_group_key
- reference::find_dict_path
- rejection::format_count
- sam::alignment_end
- sam::alignment_tags::md_tag
- sam::alignment_tags::nm_tag
- sam::alignment_tags::regenerate_alignment_tags
- sam::alignment_tags::regenerate_alignment_tags_raw
- sam::alignment_tags::uq_tag
- sam::buf_value_to_smallest_signed_int
- sam::builder::cigar_ref_len
- sam::builder::cigar_seq_len
- sam::builder::create_default_test_fasta
- sam::builder::create_ref_dict
- sam::builder::create_test_fasta
- sam::builder::degrading_qualities
- sam::builder::parse_cigar
- sam::builder::repeat_n
- sam::builder::uniform_qualities
- sam::check_sort
- sam::cigar_reference_length
- sam::create_default_test_fasta
- sam::create_ref_dict
- sam::create_test_fasta
- sam::degrading_qualities
- sam::get_pair_orientation
- sam::is_fr_pair
- sam::is_fr_pair_from_tags
- sam::is_sorted
- sam::is_template_coordinate_sorted
- sam::leading_clipping
- sam::leading_soft_clipping
- sam::mate_unclipped_end
- sam::mate_unclipped_start
- sam::num_bases_extending_past_mate
- sam::parse_cigar
- sam::parse_cigar_string
- sam::read_pos_at_ref_pos
- sam::record_utils::alignment_end
- sam::record_utils::cigar_reference_length
- sam::record_utils::get_pair_orientation
- sam::record_utils::is_fr_pair
- sam::record_utils::is_fr_pair_from_tags
- sam::record_utils::leading_clipping
- sam::record_utils::leading_soft_clipping
- sam::record_utils::mate_unclipped_end
- sam::record_utils::mate_unclipped_start
- sam::record_utils::num_bases_extending_past_mate
- sam::record_utils::parse_cigar_string
- sam::record_utils::read_pos_at_ref_pos
- sam::record_utils::reference_length
- sam::record_utils::trailing_clipping
- sam::record_utils::trailing_soft_clipping
- sam::record_utils::unclipped_end
- sam::record_utils::unclipped_five_prime_position
- sam::record_utils::unclipped_start
- sam::reference_length
- sam::regenerate_alignment_tags
- sam::repeat_n
- sam::revcomp_buf_value
- sam::reverse_buf_value
- sam::to_smallest_signed_int
- sam::trailing_clipping
- sam::trailing_soft_clipping
- sam::unclipped_end
- sam::unclipped_five_prime_position
- sam::unclipped_start
- sam::uniform_qualities
- simple_umi_consensus::consensus_umis
- sort::inline_buffer::extract_coordinate_key_inline
- sort::inline_buffer::parallel_radix_sort_record_refs
- sort::inline_buffer::parallel_radix_sort_template_refs
- sort::inline_buffer::radix_sort_record_refs
- sort::inline_buffer::radix_sort_template_refs
- sort::keys::queryname_flag_order
- sort::pipeline::parallel_merge
- sort::pipeline::parallel_merge_buffered
- sort::radix::binary_insertion_sort
- sort::radix::heap_make
- sort::radix::heap_pop
- sort::radix::heap_replace_top
- sort::radix::heap_sift_down
- sort::radix::hybrid_sort
- sort::radix::insertion_sort_by_key
- sort::radix::pack_coordinate_for_radix
- sort::radix::radix_sort_coordinate
- sort::radix::radix_sort_coordinate_adaptive
- sort::radix::radix_sort_u64
- sort::raw::extract_template_key_inline
- tag_reversal::reverse_per_base_tags
- tag_reversal::reverse_per_base_tags_raw
- template::estimate_record_buf_heap_size
- umi::assigner::count_mismatches
- umi::assigner::matches_within_threshold
- umi::extract_mi_base
- umi::parallel_assigner::discover_edges_parallel_k
- umi::parallel_assigner::discover_edges_parallel_k1
- umi::validate_umi
- unified_pipeline::deadlock::check_deadlock_and_restore
- unified_pipeline::deadlock::now_secs
- unified_pipeline::decode_records
- unified_pipeline::extract_panic_message
- unified_pipeline::finalize_pipeline
- unified_pipeline::generic_worker_loop
- unified_pipeline::handle_worker_backoff
- unified_pipeline::handle_worker_panic
- unified_pipeline::join_monitor_thread
- unified_pipeline::join_worker_threads
- unified_pipeline::read_raw_block_batch
- unified_pipeline::rebalancer::initial_allocation_for_command
- unified_pipeline::rebalancer::parse_memory_limit
- unified_pipeline::run_bam_pipeline
- unified_pipeline::run_bam_pipeline_from_reader
- unified_pipeline::run_bam_pipeline_from_reader_with_secondary
- unified_pipeline::run_bam_pipeline_with_grouper
- unified_pipeline::run_bam_pipeline_with_header
- unified_pipeline::run_fastq_pipeline
- unified_pipeline::run_monitor_loop
- unified_pipeline::scheduler::create_scheduler
- unified_pipeline::serialize_bam_record
- unified_pipeline::serialize_bam_record_into
- unified_pipeline::serialize_bam_records
- unified_pipeline::serialize_bam_records_into
- unified_pipeline::serialize_bam_records_to_compressor
- unified_pipeline::shared_try_step_compress
- unified_pipeline::shared_try_step_process
- unified_pipeline::shared_try_step_serialize
- unified_pipeline::shared_try_step_write_new
- unified_pipeline::should_monitor_exit
- unified_pipeline::try_advance_held
- unified_pipeline::try_push_or_hold
- unified_pipeline::write_compressed_batch
- validation::optional_string_to_tag
- validation::string_to_tag
- validation::validate_error_rate
- validation::validate_file_exists
- validation::validate_files_exist
- validation::validate_min_max
- validation::validate_positive
- validation::validate_quality_score
- validation::validate_tag
- variant_review::format_insert_string
- variant_review::read_number_suffix
Type Aliases
- assigner::Umi
- bam_io::BamReaderAuto
- bam_io::BamWriter
- bam_io::RawBamReaderAuto
- clipper::cigar_utils::SimplifiedCigar
- errors::Result
- phred::LogProbability
- phred::PhredScore
- read_info::LibraryLookup
- template::TemplateBatch
- umi::Umi
- umi::assigner::Umi
Constants
- assigner::BOTTOM_STRAND_DUPLEX
- assigner::DEFAULT_INDEX_THRESHOLD
- assigner::TOP_STRAND_DUPLEX
- bgzf_reader::BGZF_EOF
- bgzf_reader::BGZF_FOOTER_SIZE
- bgzf_reader::BGZF_HEADER_SIZE
- consensus::tags::MOLECULAR_ID
- consensus::tags::ORIGINAL_UMI_BASES
- consensus::tags::ORIGINAL_UMI_QUALS
- consensus::tags::UMI_BASES
- consensus::tags::UMI_QUALS
- consensus::tags::per_base::AB_CONSENSUS_BASES
- consensus::tags::per_base::AB_CONSENSUS_QUALS
- consensus::tags::per_base::AB_RAW_READ_COUNT
- consensus::tags::per_base::AB_RAW_READ_ERRORS
- consensus::tags::per_base::ALL_TAGS
- consensus::tags::per_base::BA_CONSENSUS_BASES
- consensus::tags::per_base::BA_CONSENSUS_QUALS
- consensus::tags::per_base::BA_RAW_READ_COUNT
- consensus::tags::per_base::BA_RAW_READ_ERRORS
- consensus::tags::per_base::RAW_READ_COUNT
- consensus::tags::per_base::RAW_READ_ERRORS
- consensus::tags::per_base::TAGS_TO_REVERSE
- consensus::tags::per_base::TAGS_TO_REVERSE_COMPLEMENT
- consensus::tags::per_read::AB_MIN_RAW_READ_COUNT
- consensus::tags::per_read::AB_RAW_READ_COUNT
- consensus::tags::per_read::AB_RAW_READ_ERROR_RATE
- consensus::tags::per_read::ALL_TAGS
- consensus::tags::per_read::BA_MIN_RAW_READ_COUNT
- consensus::tags::per_read::BA_RAW_READ_COUNT
- consensus::tags::per_read::BA_RAW_READ_ERROR_RATE
- consensus::tags::per_read::MIN_RAW_READ_COUNT
- consensus::tags::per_read::RAW_READ_COUNT
- consensus::tags::per_read::RAW_READ_ERROR_RATE
- consensus_tags::MOLECULAR_ID
- consensus_tags::ORIGINAL_UMI_BASES
- consensus_tags::ORIGINAL_UMI_QUALS
- consensus_tags::UMI_BASES
- consensus_tags::UMI_QUALS
- consensus_tags::per_base::AB_CONSENSUS_BASES
- consensus_tags::per_base::AB_CONSENSUS_QUALS
- consensus_tags::per_base::AB_RAW_READ_COUNT
- consensus_tags::per_base::AB_RAW_READ_ERRORS
- consensus_tags::per_base::ALL_TAGS
- consensus_tags::per_base::BA_CONSENSUS_BASES
- consensus_tags::per_base::BA_CONSENSUS_QUALS
- consensus_tags::per_base::BA_RAW_READ_COUNT
- consensus_tags::per_base::BA_RAW_READ_ERRORS
- consensus_tags::per_base::RAW_READ_COUNT
- consensus_tags::per_base::RAW_READ_ERRORS
- consensus_tags::per_base::TAGS_TO_REVERSE
- consensus_tags::per_base::TAGS_TO_REVERSE_COMPLEMENT
- consensus_tags::per_read::AB_MIN_RAW_READ_COUNT
- consensus_tags::per_read::AB_RAW_READ_COUNT
- consensus_tags::per_read::AB_RAW_READ_ERROR_RATE
- consensus_tags::per_read::ALL_TAGS
- consensus_tags::per_read::BA_MIN_RAW_READ_COUNT
- consensus_tags::per_read::BA_RAW_READ_COUNT
- consensus_tags::per_read::BA_RAW_READ_ERROR_RATE
- consensus_tags::per_read::MIN_RAW_READ_COUNT
- consensus_tags::per_read::RAW_READ_COUNT
- consensus_tags::per_read::RAW_READ_ERROR_RATE
- metrics::FLOAT_PRECISION
- phred::LN_ONE
- phred::MAX_PHRED
- phred::MIN_PHRED
- phred::NO_CALL_BASE
- phred::NO_CALL_BASE_LOWER
- sam::MAPPED_PG_ID
- sam::REFERENCE_LENGTH
- sam::builder::DEFAULT_BASE_QUALITY
- sam::builder::DEFAULT_MAPQ
- sam::builder::DEFAULT_READ_GROUP_ID
- sam::builder::DEFAULT_READ_LENGTH
- sam::builder::DEFAULT_REFERENCE_LENGTH
- sam::builder::DEFAULT_SAMPLE_NAME
- sam::builder::MAPPED_PG_ID
- sam::builder::REFERENCE_LENGTH
- sort::inline_buffer::TEMPLATE_HEADER_SIZE
- sort::keys::PA_TAG
- umi::assigner::BOTTOM_STRAND_DUPLEX
- umi::assigner::DEFAULT_INDEX_THRESHOLD
- umi::assigner::TOP_STRAND_DUPLEX
- unified_pipeline::BACKPRESSURE_THRESHOLD_BYTES
- unified_pipeline::DEFAULT_TARGET_TEMPLATES_PER_BATCH
- unified_pipeline::MAX_BACKOFF_US
- unified_pipeline::MAX_THREADS
- unified_pipeline::MIN_BACKOFF_US
- unified_pipeline::PROGRESS_LOG_INTERVAL
- unified_pipeline::Q5_BACKPRESSURE_THRESHOLD_BYTES
- unified_pipeline::SERIALIZATION_BUFFER_CAPACITY