List of all items

Structs

• abundance::abundance_calculator_engine::AbundanceCalculatorEngine
• abundance::strain_abundances_calculator::StrainAbundanceCalculator
• activity_profile::activity_profile::ActivityProfile
• activity_profile::activity_profile_state::ActivityProfileState
• activity_profile::band_pass_activity_profile::BandPassActivityProfile
• ani_calculator::ani_calculator::ANICalculator
• annotator::tandem_repeat::TandemRepeat
• annotator::variant_annotation::Annotation
• annotator::variant_annotator_engine::VariantAnnotationEngine
• assembly::assembly_based_caller_utils::AssemblyBasedCallerUtils
• assembly::assembly_region::AssemblyRegion
• assembly::assembly_region_iterator::AssemblyRegionIterator
• assembly::assembly_region_trimmer::AssemblyRegionTrimmer
• assembly::assembly_region_trimmer::AssemblyRegionTrimmerResult
• assembly::assembly_region_walker::AssemblyRegionWalker
• assembly::assembly_result::AssemblyResult
• assembly::assembly_result_set::AssemblyResultSet
• assembly::kmer::Kmer
• assembly::kmer_counter::CountedKmer
• assembly::kmer_counter::KmerCounter
• bam_parsing::FlagFilter
• bam_parsing::OutputWriter
• bam_parsing::ReadsMapped
• bam_parsing::bam_generator::BamFileNamedReader
• bam_parsing::bam_generator::BamGeneratorSet
• bam_parsing::bam_generator::FilteredBamReader
• bam_parsing::bam_generator::IndexedBamFileNamedReader
• bam_parsing::bam_generator::NamedBamMaker
• bam_parsing::bam_generator::NamedBamMakerGenerator
• bam_parsing::bam_generator::PlaceholderBamFileReader
• bam_parsing::bam_generator::StreamingFilteredNamedBamReader
• bam_parsing::bam_generator::StreamingFilteredNamedBamReaderGenerator
• bam_parsing::bam_generator::StreamingNamedBamReader
• bam_parsing::bam_generator::StreamingNamedBamReaderGenerator
• bam_parsing::filter::ReferenceSortedBamFilter
• bam_parsing::mapping_index_maintenance::TemporaryIndexStruct
• bam_parsing::mapping_index_maintenance::VanillaBwaIndexStuct
• bam_parsing::mapping_parameters::MappingParameters
• bam_parsing::mapping_parameters::OneSampleMappingParameters
• bam_parsing::mapping_parameters::SingleReferenceMappingParameters
• evolve::codon_structs::CodonTable
• evolve::codon_structs::GeneInfo
• evolve::codon_structs::NCBITable
• genotype::genotype_allele_counts::GenotypeAlleleCounts
• genotype::genotype_builder::Genotype
• genotype::genotype_builder::GenotypesContext
• genotype::genotype_likelihood_calculator::GenotypeLikelihoodCalculator
• genotype::genotype_likelihood_calculators::GenotypeLikelihoodCalculators
• genotype::genotype_likelihoods::GenotypeLikelihoods
• genotype::genotype_likelihoods::GenotypeNumLikelihoodsCache
• genotype::genotype_prior_calculator::GenotypePriorCalculator
• genotype::genotyping_engine::GenotypingEngine
• genotype::genotyping_likelihoods::GenotypingLikelihoods
• graphs::adaptive_chain_pruner::AdaptiveChainPruner
• graphs::base_edge::BaseEdgeStruct
• graphs::base_graph::BaseGraph
• graphs::base_graph::TestGraph
• graphs::common_suffix_splitter::CommonSuffixSplitter
• graphs::graph_based_k_best_haplotype_finder::GraphBasedKBestHaplotypeFinder
• graphs::graph_utils::GraphUtils
• graphs::k_best_haplotype::KBestHaplotype
• graphs::k_best_haplotype_finder::KBestHaplotypeFinder
• graphs::low_weight_chain_pruner::LowWeightChainPruner
• graphs::multi_sample_edge::MultiSampleEdge
• graphs::path::Chain
• graphs::path::Path
• graphs::seq_graph::SeqGraph
• graphs::seq_vertex::SeqVertex
• graphs::shared_sequence_merger::SharedSequenceMerger
• graphs::shared_vertex_sequence_splitter::SharedVertexSequenceSplitter
• haplotype::called_haplotypes::CalledHaplotypes
• haplotype::event_map::EventMap
• haplotype::haplotype::Haplotype
• haplotype::haplotype_caller_engine::HaplotypeCallerEngine
• haplotype::haplotype_caller_genotyping_engine::HaplotypeCallerGenotypingEngine
• haplotype::haplotype_clustering_engine::HaplotypeClusteringEngine
• haplotype::homogenous_ploidy_model::HeterogeneousPloidyModel
• haplotype::homogenous_ploidy_model::HomogeneousPloidyModel
• haplotype::independent_samples_genotype_model::IndependentSamplesGenotypesModel
• haplotype::location_and_alleles::LocationsAndAlleles
• haplotype::ref_vs_any_result::RefVsAnyResult
• haplotype::reference_confidence_model::ReferenceConfidenceModel
• linkage::linkage_engine::LinkageEngine
• model::allele_frequency_calculator::AlleleFrequencyCalculator
• model::allele_frequency_calculator_result::AFCalculationResult
• model::allele_likelihood_matrix_mapper::AlleleLikelihoodMatrixMapper
• model::allele_likelihoods::AlleleLikelihoods
• model::allele_likelihoods::BestAllele
• model::allele_likelihoods::LOG_10_INFORMATIVE_THRESHOLD
• model::allele_likelihoods::NATURAL_LOG_INFORMATIVE_THRESHOLD
• model::allele_likelihoods::ReadIndexer
• model::allele_list::AlleleList
• model::allele_subsetting_utils::AlleleSubsettingUtils
• model::byte_array_allele::ByteArrayAllele
• model::location_and_alleles::LocationAndAlleles
• model::variant_context::VariantContext
• model::variant_context_utils::AlleleMapper
• model::variant_context_utils::VariantContextUtils
• model::variants::AbstractAllele
• model::variants::Base
• model::variants::EMPTY_ALLELE_BASES
• model::variants::NON_REF_ALLELE
• model::variants::SPAN_DEL_ALLELE
• model::variants::SV
• model::variants::VariantTypeIter
• pair_hmm::pair_hmm::PairHMM
• pair_hmm::pair_hmm_likelihood_calculation_engine::PairHMMInputScoreImputator
• pair_hmm::pair_hmm_likelihood_calculation_engine::PairHMMLikelihoodCalculationEngine
• pair_hmm::pair_hmm_model::PairHMMModel
• processing::lorikeet_engine::Elem
• processing::lorikeet_engine::LorikeetEngine
• read_orientation::beta_distribution_shape::BetaDistributionShape
• read_orientation::beta_distribution_shape::FLAT_BETA
• read_threading::abstract_read_threading_graph::DanglingChainMergeHelper
• read_threading::abstract_read_threading_graph::SequenceForKmers
• read_threading::multi_debruijn_vertex::MultiDeBruijnVertex
• read_threading::read_threading_assembler::ReadThreadingAssembler
• read_threading::read_threading_graph::ReadThreadingGraph
• reads::alignment_utils::AlignmentUtils
• reads::alignment_utils::HAPLOTYPE_TAG
• reads::alignment_utils::MismatchCount
• reads::bird_tool_reads::BirdToolRead
• reads::cigar_builder::CigarBuilder
• reads::cigar_builder::CigarBuilderResult
• reads::cigar_utils::ALIGNMENT_TO_BEST_HAPLOTYPE_SW_PARAMETERS
• reads::cigar_utils::CigarUtils
• reads::cigar_utils::NEW_SW_PARAMETERS
• reads::clipping_op::ClippingOp
• reads::read_clipper::ReadClipper
• reads::read_utils::ReadUtils
• reference::reference_reader::ReferenceReader
• reference::reference_reader_utils::GenomesAndContigs
• reference::reference_reader_utils::ReferenceReaderUtils
• reference::reference_writer::ReferenceWriter
• smith_waterman::bindings::SWParameters
• smith_waterman::smith_waterman_aligner::ALIGNMENT_TO_BEST_HAPLOTYPE_SW_PARAMETERS
• smith_waterman::smith_waterman_aligner::NEW_SW_PARAMETERS
• smith_waterman::smith_waterman_aligner::ORIGINAL_DEFAULT
• smith_waterman::smith_waterman_aligner::STANDARD_NGS
• smith_waterman::smith_waterman_aligner::SmithWatermanAligner
• smith_waterman::smith_waterman_aligner::SmithWatermanAlignmentResult
• test_utils::allele_list_unit_tester::AlleleListUnitTester
• test_utils::random_dna::RandomDNA
• test_utils::read_clipper_test_utils::BASES
• test_utils::read_clipper_test_utils::CORE_CIGAR_ELEMENTS
• test_utils::read_clipper_test_utils::CORE_CIGAR_ELEMENTS_INCLUDING_SKIPS
• test_utils::read_clipper_test_utils::LEADING_CLIPS
• test_utils::read_clipper_test_utils::QUALS
• test_utils::read_clipper_test_utils::ReadClipperTestUtils
• test_utils::read_clipper_test_utils::TRAILING_CLIPS
• test_utils::read_likelihoods_unit_tester::ReadLikelihoodsUnitTester
• test_utils::variant_context_test_utils::VariantContextTestUtils
• utils::artificial_read_utils::ArtificialReadUtils
• utils::base_utils::BASES
• utils::base_utils::BASES_EXTENDED
• utils::base_utils::BASE_CHARS
• utils::base_utils::BASE_CHARS_EXTENDED
• utils::base_utils::BaseUtils
• utils::dirichlet::Dirichlet
• utils::fragment_collection::FragmentCollection
• utils::interval_utils::IntervalUtils
• utils::math_utils::INV_LOG_2
• utils::math_utils::LOG10_E
• utils::math_utils::LOG10_ONE_HALF
• utils::math_utils::LOG10_ONE_THIRD
• utils::math_utils::LOG_ONE_THIRD
• utils::math_utils::MathUtils
• utils::math_utils::RunningAverage
• utils::natural_log_utils::LOG_ONE_HALF
• utils::natural_log_utils::LOG_ONE_THIRD
• utils::natural_log_utils::NaturalLogUtils
• utils::quality_utils::QualityUtils
• utils::simple_interval::CoordMath
• utils::simple_interval::SimpleInterval
• utils::utils::FilterParameters
• utils::vcf_constants::AS_QUAL_KEY
• utils::vcf_constants::DEPTH_KEY
• utils::vcf_constants::GENOTYPE_KEY
• utils::vcf_constants::GENOTYPE_POSTERIORS_KEY
• utils::vcf_constants::GENOTYPE_PRIOR_KEY
• utils::vcf_constants::HAPLOTYPE_CALLER_PHASING_GT_KEY
• utils::vcf_constants::HAPLOTYPE_CALLER_PHASING_ID_KEY
• utils::vcf_constants::LOW_QUAL_FILTER_NAME
• utils::vcf_constants::MLE_ALLELE_COUNT_KEY
• utils::vcf_constants::MLE_ALLELE_FREQUENCY_KEY
• utils::vcf_constants::NUMBER_OF_DISCOVERED_ALLELES_KEY
• utils::vcf_constants::PHASE_QUALITY_KEY
• utils::vcf_constants::PHASE_SET_KEY
• utils::vcf_constants::PHRED_SCALED_POSTERIORS_KEY
• utils::vcf_constants::STRAND_COUNT_BY_SAMPLE_KEY
• utils::vcf_constants::VCFConstants

Enums

• GenomeExclusionTypes
• activity_profile::activity_profile_state::ActivityProfileDataType
• annotator::variant_annotation::AnnotationType
• annotator::variant_annotation::VariantAnnotations
• assembly::assembly_result::Status
• bam_parsing::bam_generator::MappingProgram
• bam_parsing::mapping_parameters::ReadFormat
• genotype::genotype_builder::AttributeObject
• genotype::genotype_builder::GenotypeAssignmentMethod
• genotype::genotype_builder::GenotypeType
• graphs::chain_pruner::ChainPruner
• graphs::vertex_based_transformer::VertexBasedTransformer
• graphs::vertex_based_transformer::VertexBasedTransformerOptions
• model::allele_list::Permutation
• model::variant_context::VariantType
• model::variant_context_utils::FilteredRecordMergeType
• model::variant_context_utils::GenotypeMergeType
• model::variants::Filter
• model::variants::SVType
• model::variants::StrandBias
• model::variants::Variant
• model::variants::VariantType
• pair_hmm::pair_hmm_likelihood_calculation_engine::AVXMode
• pair_hmm::pair_hmm_likelihood_calculation_engine::PCRErrorModel
• processing::lorikeet_engine::ReadType
• read_threading::abstract_read_threading_graph::TraversalDirection
• reads::read_clipper::ClippingRepresentation
• smith_waterman::bindings::SWOverhangStrategy
• utils::base_utils::Base
• utils::errors::BirdToolError

Traits

• activity_profile::activity_profile::Profile
• bam_parsing::bam_generator::IndexedNamedBamReader
• bam_parsing::bam_generator::NamedBamReader
• bam_parsing::bam_generator::NamedBamReaderGenerator
• bam_parsing::mapping_index_maintenance::MappingIndex
• evolve::codon_structs::Translations
• graphs::base_edge::BaseEdge
• graphs::base_vertex::BaseVertex
• graphs::kmer_searchable_graph::KmerSearchableGraph
• haplotype::homogenous_ploidy_model::PloidyModel
• model::allele_list::AlleleListPermutation
• model::byte_array_allele::Allele
• read_error_corrector::read_error_corrector::ReadErrorCorrector
• read_threading::abstract_read_threading_graph::AbstractReadThreadingGraph
• utils::simple_interval::Locatable

Functions

• bam_parsing::bam_generator::build_mapping_command
• bam_parsing::bam_generator::complete_processes
• bam_parsing::bam_generator::generate_bam_maker_generator_from_reads
• bam_parsing::bam_generator::generate_filtered_bam_readers_from_bam_files
• bam_parsing::bam_generator::generate_filtered_named_bam_readers_from_reads
• bam_parsing::bam_generator::generate_indexed_named_bam_readers_from_bam_files
• bam_parsing::bam_generator::generate_named_bam_readers_from_bam_files
• bam_parsing::bam_generator::generate_named_bam_readers_from_reads
• bam_parsing::bam_generator::generate_placeholder
• bam_parsing::mapping_index_maintenance::check_reference_existence
• bam_parsing::mapping_index_maintenance::generate_bwa_index
• bam_parsing::mapping_index_maintenance::generate_concatenated_fasta_file
• bam_parsing::mapping_index_maintenance::generate_minimap2_index
• cli::build_cli
• cli::call_full_help
• cli::consensus_full_help
• cli::genotype_full_help
• cli::summarise_full_help
• evolve::codon_structs::get_codons
• external_command_checker::check_for_bcftools
• external_command_checker::check_for_bwa
• external_command_checker::check_for_bwa_mem2
• external_command_checker::check_for_dashing
• external_command_checker::check_for_fastani
• external_command_checker::check_for_minimap2
• external_command_checker::check_for_ngmlr
• external_command_checker::check_for_pggb
• external_command_checker::check_for_prodigal
• external_command_checker::check_for_samtools
• external_command_checker::check_for_svim
• external_command_checker::check_for_svim_asm
• model::fst_calculator::calculate_fst
• parse_percentage
• processing::bams::index_bams::finish_bams
• processing::bams::index_bams::recover_bams
• processing::lorikeet_engine::run_summarize
• processing::lorikeet_engine::start_lorikeet_engine
• reference::reference_reader_utils::read_genome_definition_file
• reference::reference_reader_utils::read_genome_fasta_files
• utils::fragment_utils::adjust_quals_of_overlapping_paired_fragments
• utils::utils::clean_sample_name
• utils::utils::cons
• utils::utils::find_first
• utils::utils::generate_cached_bam_file_name
• utils::utils::get_cleaned_sample_names
• utils::utils::get_streamed_bam_readers
• utils::utils::get_streamed_filtered_bam_readers
• utils::utils::long_generator_setup
• utils::utils::make_permutations
• utils::utils::mean
• utils::utils::parse_mapping_program
• utils::utils::setup_bam_cache_directory
• utils::utils::setup_mapping_index
• utils::utils::std_deviation
• utils::utils::table_roff

Type Aliases

• model::variants::AlleleFreq

Statics

• utils::artificial_read_utils::DEFAULT_PLATFORM_PREFIX
• utils::artificial_read_utils::DEFAULT_PLATFORM_UNIT_PREFIX
• utils::artificial_read_utils::DEFAULT_PROGRAM_NAME
• utils::artificial_read_utils::DEFAULT_READ_GROUP_PREFIX
• utils::artificial_read_utils::DEFAULT_SAMPLE_NAME
• utils::artificial_read_utils::READ_GROUP_ID

Constants

• AUTHOR
• AUTHOR_AND_EMAIL
• bam_parsing::CONCATENATED_FASTA_FILE_SEPARATOR
• utils::fragment_utils::DEFAULT_PCR_SNV_ERROR_RATE
• utils::quality_utils::ONE
• utils::quality_utils::TEN
• utils::utils::CONCATENATED_REFERENCE_CACHE_STEM
• utils::utils::DEFAULT_MAPPING_SOFTWARE_ENUM
• utils::utils::NUMERICAL_EPSILON