[−] List of all items
Structs
- ComplementEvent
- SimpleEvent
- calling::cnvs::CNV
- calling::cnvs::CNVCall
- calling::cnvs::Call
- calling::cnvs::Caller
- calling::cnvs::CallerBuilder
- calling::cnvs::HMM
- calling::cnvs::Region
- calling::variants::BCFGrouper
- calling::variants::Call
- calling::variants::CallBuilder
- calling::variants::SampleInfo
- calling::variants::SampleInfoBuilder
- calling::variants::Variant
- calling::variants::VariantBuilder
- calling::variants::calling::Caller
- calling::variants::calling::CallerBuilder
- calling::variants::preprocessing::ObservationProcessor
- calling::variants::preprocessing::ObservationProcessorBuilder
- cli::PreprocessInput
- errors::InconsistentObservations
- errors::InvalidBAMSampleName
- errors::InvalidBCFRecord
- errors::InvalidContaminationSampleName
- errors::InvalidIndex
- errors::InvalidLocus
- errors::InvalidMinBayesFactor
- errors::InvalidObservationFormat
- errors::InvalidObservationSampleName
- errors::InvalidObservations
- errors::InvalidObservationsSpec
- errors::InvalidSampleName
- errors::MissingBCFTag
- errors::MissingCandidates
- errors::MissingPrefix
- errors::MissingSampleEvent
- errors::NoCandidateFound
- errors::NoRecordsFound
- errors::RecordMissingChrom
- errors::ReferenceContigNotFound
- errors::UniverseContigNotFound
- estimation::alignment_properties::AlignmentProperties
- estimation::alignment_properties::InsertSize
- estimation::effective_mutation_rate::Estimate
- grammar::Contamination
- grammar::Sample
- grammar::SampleInfo
- grammar::SampleInfoBuilder
- grammar::Scenario
- grammar::formula::FormulaParser
- grammar::formula::IUPAC
- grammar::formula::VAFRange
- grammar::formula::VAFUniverse
- grammar::vaftree::Node
- grammar::vaftree::VAFTree
- model::Contamination
- model::ContinuousAlleleFreqs
- model::DiscreteAlleleFreqs
- model::Event
- model::VariantTypeIter
- model::evidence::Clips
- model::evidence::fragments::IndelEvidence
- model::evidence::observation::Observation
- model::evidence::observation::ObservationBuilder
- model::evidence::reads::DeletionEmissionParams
- model::evidence::reads::EditDistanceCalculation
- model::evidence::reads::EditDistanceHit
- model::evidence::reads::IndelEvidence
- model::evidence::reads::IndelGapParams
- model::evidence::reads::InsertionEmissionParams
- model::evidence::reads::MNVEvidence
- model::evidence::reads::NoneEvidence
- model::evidence::reads::ReadEmission
- model::evidence::reads::ReferenceEmissionParams
- model::evidence::reads::SNVEvidence
- model::likelihood::ContaminatedSampleEvent
- model::likelihood::ContaminatedSampleLikelihoodModel
- model::likelihood::Event
- model::likelihood::SampleLikelihoodModel
- model::modes::generic::Data
- model::modes::generic::FlatPrior
- model::modes::generic::GenericLikelihood
- model::modes::generic::GenericModelBuilder
- model::modes::generic::GenericModelBuilderBuilder
- model::modes::generic::GenericPosterior
- model::modes::generic::SNV
- model::modes::tumor::TumorNormalPair
- model::sample::ProtocolStrandednessIter
- model::sample::Sample
- model::sample::SampleBuilder
- testcase::Testcase
- testcase::TestcaseBuilder
- utils::ReferenceBuffer
Enums
- cli::CallKind
- cli::EstimateKind
- cli::FilterMethod
- cli::PreprocessKind
- cli::VariantCallMode
- cli::Varlociraptor
- errors::Error
- grammar::UniverseDefinition
- grammar::formula::Formula
- grammar::formula::NormalizedFormula
- grammar::formula::Rule
- grammar::formula::VAFRangeOverlap
- grammar::formula::VAFSpectrum
- grammar::vaftree::NodeKind
- model::StrandBias
- model::Variant
- model::VariantType
- model::modes::generic::CacheEntry
- model::sample::ProtocolStrandedness
- model::sample::SubsampleCandidates
- testcase::Mode
- utils::MiniLogProb
- utils::Overlap
Traits
- Event
- model::AlleleFreqs
- model::evidence::reads::AbstractReadEvidence
- model::evidence::reads::RefBaseEmission
- model::likelihood::ContaminatedSamplePairView
- model::modes::UniverseDrivenPrior
- model::modes::tumor::TumorNormalPairView
Functions
- calling::cnvs::allele_freq_pdf
- calling::cnvs::depth_pmf
- calling::cnvs::likelihood
- calling::cnvs::marginal
- calling::variants::event_tag_name
- calling::variants::preprocessing::read_observations
- calling::variants::preprocessing::read_preprocess_options
- calling::variants::preprocessing::remove_observation_header_entries
- calling::variants::preprocessing::write_observations
- cli::est_or_load_alignment_properites
- cli::run
- conversion::decode_phred::decode_phred
- estimation::effective_mutation_rate::estimate
- estimation::tumor_mutational_burden::estimate
- filtration::fdr::control_fdr
- filtration::posterior_odds::filter_by_odds
- model::AlleleFreq
- model::evidence::fragments::estimate_insert_size
- model::evidence::fragments::isize_pmf
- model::evidence::fragments::n_fragment_positions
- model::evidence::max_indel
- model::evidence::observation::expected_depth
- model::evidence::observation::poisson_pmf
- model::evidence::read_len
- model::evidence::reads::prob_read_base
- model::evidence::reads::prob_read_base_miscall
- model::sample::estimate_alignment_properties
- utils::collect_prob_dist
- utils::collect_variants
- utils::events_to_tags
- utils::evidence_kass_raftery_to_letter
- utils::filter_by_threshold
- utils::filter_calls
- utils::generalized_cigar
- utils::get_event_tags
- utils::is_phred_scaled
- utils::is_repeat_variant
- utils::max_prob
- utils::select
- utils::tags_prob_sum
Typedefs
- calling::variants::calling::AlleleFreqCombination
- cli::PathMap
- errors::Result
- model::AlleleFreq
- model::likelihood::ContaminatedSampleCache
- model::likelihood::SingleSampleCache
- model::modes::generic::Cache
- model::sample::Pileup
Statics
- calling::variants::preprocessing::OBSERVATION_FORMAT_VERSION
- constants::PROB_ILLUMINA_DEL
- constants::PROB_ILLUMINA_INS
- constants::PROB_ILLUMINA_SUBST