[−] List of all items
Structs
- ComplementEvent
- SimpleEvent
- call::Call
- call::CallBuilder
- call::Caller
- call::CallerBuilder
- call::SampleInfo
- call::SampleInfoBuilder
- call::Variant
- call::VariantBuilder
- call_cnvs::CNV
- call_cnvs::CNVCall
- call_cnvs::Call
- call_cnvs::Caller
- call_cnvs::CallerBuilder
- call_cnvs::HMM
- call_cnvs::Region
- estimation::alignment_properties::AlignmentProperties
- estimation::alignment_properties::InsertSize
- estimation::effective_mutation_rate::Estimate
- grammar::Contamination
- grammar::Event
- grammar::Sample
- grammar::Scenario
- grammar::vafrange::VAFRangeParser
- 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::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::FlatPrior
- model::modes::generic::GenericLikelihood
- model::modes::generic::GenericModelBuilder
- model::modes::generic::GenericPosterior
- model::modes::tumor::TumorNormalPair
- model::sample::RecordBuffer
- model::sample::Sample
- model::sample::SampleBuilder
- testcase::Testcase
- testcase::TestcaseBuilder
- utils::ReferenceBuffer
Enums
- BCFError
- cli::CallKind
- cli::FilterMethod
- cli::VariantCallMode
- cli::Varlociraptor
- errors::CLIError
- errors::CallCNVError
- errors::TestcaseError
- grammar::vafrange::Rule
- grammar::vafrange::VAFRange
- model::StrandBias
- model::Variant
- model::VariantType
- model::evidence::observation::Evidence
- model::modes::generic::CacheEntry
- model::sample::RecordBufferError
- model::sample::SubsampleCandidates
- utils::Overlap
Traits
- Event
- model::AlleleFreqs
- model::evidence::reads::AbstractReadEvidence
- model::evidence::reads::RefBaseEmission
- model::likelihood::ContaminatedSamplePairView
- model::modes::tumor::TumorNormalPairView
Functions
- call::event_tag_name
- call_cnvs::allele_freq_pdf
- call_cnvs::depth_pmf
- call_cnvs::likelihood
- call_cnvs::marginal
- cli::est_or_load_alignment_properites
- cli::run
- conversion::decode_phred::decode_phred
- estimation::effective_mutation_rate::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::is_repeat_variant
- utils::max_prob
- utils::select
- utils::tags_prob_sum
Typedefs
- call::AlleleFreqCombination
- model::AlleleFreq
- model::likelihood::ContaminatedSampleCache
- model::likelihood::SingleSampleCache
- model::modes::generic::Cache
- model::sample::Pileup