List of all items
Structs
- alignment::Alignment
- alignment::pairwise::Aligner
- alignment::pairwise::MatchParams
- alignment::pairwise::Scoring
- alignment::pairwise::TracebackCell
- alignment::pairwise::banded::Aligner
- alignment::poa::Aligner
- alignment::poa::Alignment
- alignment::poa::Poa
- alignment::poa::Traceback
- alignment::poa::TracebackCell
- alignment::sparse::SparseAlignmentResult
- alphabets::Alphabet
- alphabets::QGrams
- alphabets::RankTransform
- data_structures::annot_map::AnnotMap
- data_structures::annot_map::AnnotMapIterator
- data_structures::annot_map::Entry
- data_structures::bit_tree::FenwickTree
- data_structures::bit_tree::MaxOp
- data_structures::bit_tree::SumOp
- data_structures::bitenc::BitEnc
- data_structures::bitenc::BitEncIter
- data_structures::bwt::Occ
- data_structures::fmindex::BiInterval
- data_structures::fmindex::FMDIndex
- data_structures::fmindex::FMIndex
- data_structures::fmindex::Interval
- data_structures::interpolation_table::InterpolationTable
- data_structures::interval_tree::ArrayBackedIntervalTree
- data_structures::interval_tree::Entry
- data_structures::interval_tree::EntryMut
- data_structures::interval_tree::IntervalTree
- data_structures::interval_tree::IntervalTreeIterator
- data_structures::interval_tree::IntervalTreeIteratorMut
- data_structures::qgram_index::ExactMatch
- data_structures::qgram_index::Interval
- data_structures::qgram_index::Match
- data_structures::qgram_index::QGramIndex
- data_structures::rank_select::RankSelect
- data_structures::smallints::Iter
- data_structures::smallints::SmallInts
- data_structures::suffix_array::SampledSuffixArray
- data_structures::wavelet_matrix::WaveletMatrix
- io::bed::Reader
- io::bed::Record
- io::bed::Records
- io::bed::Writer
- io::fasta::Index
- io::fasta::IndexedReader
- io::fasta::IndexedReaderIterator
- io::fasta::Reader
- io::fasta::Record
- io::fasta::Records
- io::fasta::Sequence
- io::fasta::Writer
- io::fastq::Reader
- io::fastq::Record
- io::fastq::Records
- io::fastq::Writer
- io::gff::Reader
- io::gff::Record
- io::gff::Records
- io::gff::Writer
- pattern_matching::bndm::BNDM
- pattern_matching::bndm::Matches
- pattern_matching::bom::BOM
- pattern_matching::bom::Matches
- pattern_matching::horspool::Horspool
- pattern_matching::horspool::Matches
- pattern_matching::kmp::KMP
- pattern_matching::kmp::Matches
- pattern_matching::myers::FullMatches
- pattern_matching::myers::LazyMatches
- pattern_matching::myers::Matches
- pattern_matching::myers::Myers
- pattern_matching::myers::MyersBuilder
- pattern_matching::myers::long::FullMatches
- pattern_matching::myers::long::LazyMatches
- pattern_matching::myers::long::Matches
- pattern_matching::myers::long::Myers
- pattern_matching::pssm::DNAMotif
- pattern_matching::pssm::ProtMotif
- pattern_matching::pssm::ScoredPos
- pattern_matching::shift_and::Matches
- pattern_matching::shift_and::ShiftAnd
- pattern_matching::ukkonen::Matches
- pattern_matching::ukkonen::Ukkonen
- seq_analysis::orf::Finder
- seq_analysis::orf::Matches
- seq_analysis::orf::Orf
- stats::bayesian::bayes_factors::BayesFactor
- stats::bayesian::bayes_factors::evidence::KassRafteryIter
- stats::bayesian::model::Model
- stats::bayesian::model::ModelInstance
- stats::hmm::State
- stats::hmm::StateIter
- stats::hmm::StateTransition
- stats::hmm::StateTransitionIter
- stats::hmm::discrete_emission::Model
- stats::hmm::discrete_emission_opt_end::Model
- stats::hmm::univariate_continuous_emission::Model
- stats::pairhmm::HomopolyPairHMM
- stats::pairhmm::PairHMM
- stats::probs::LogProb
- stats::probs::PHREDProb
- stats::probs::Prob
- stats::probs::cdf::CDF
- stats::probs::cdf::Entry
- utils::Interval
Enums
- alignment::AlignmentMode
- alignment::AlignmentOperation
- alignment::poa::AlignmentOperation
- data_structures::fmindex::BackwardSearchResult
- data_structures::rank_select::SuperblockRank
- io::fastq::Error
- io::gff::GffType
- pattern_matching::pssm::errors::Error
- stats::bayesian::bayes_factors::evidence::KassRaftery
- stats::hmm::errors::Error
- stats::pairhmm::XYEmission
- stats::probs::errors::Error
Traits
- alignment::pairwise::MatchFunc
- data_structures::bit_tree::PrefixOp
- data_structures::fmindex::FMIndexable
- data_structures::suffix_array::SuffixArray
- io::fasta::FastaRead
- io::fastq::FastqRead
- pattern_matching::myers::BitVec
- pattern_matching::myers::DistType
- pattern_matching::pssm::Motif
- stats::bayesian::model::Likelihood
- stats::bayesian::model::Marginal
- stats::bayesian::model::Posterior
- stats::bayesian::model::Prior
- stats::hmm::Model
- stats::hmm::Trainable
- stats::pairhmm::Emission
- stats::pairhmm::EmissionParameters
- stats::pairhmm::GapParameters
- stats::pairhmm::HopParameters
- stats::pairhmm::StartEndGapParameters
- utils::FastExp
Functions
- alignment::distance::hamming
- alignment::distance::levenshtein
- alignment::distance::simd::bounded_levenshtein
- alignment::distance::simd::hamming
- alignment::distance::simd::levenshtein
- alignment::sparse::expand_kmer_matches
- alignment::sparse::find_kmer_matches
- alignment::sparse::find_kmer_matches_seq1_hashed
- alignment::sparse::find_kmer_matches_seq2_hashed
- alignment::sparse::hash_kmers
- alignment::sparse::lcskpp
- alignment::sparse::sdpkpp
- alignment::sparse::sdpkpp_union_lcskpp_path
- alphabets::dna::alphabet
- alphabets::dna::complement
- alphabets::dna::iupac_alphabet
- alphabets::dna::n_alphabet
- alphabets::dna::revcomp
- alphabets::english_ascii_lower_alphabet
- alphabets::english_ascii_upper_alphabet
- alphabets::protein::alphabet
- alphabets::protein::iupac_alphabet
- alphabets::rna::alphabet
- alphabets::rna::complement
- alphabets::rna::iupac_alphabet
- alphabets::rna::n_alphabet
- alphabets::rna::revcomp
- data_structures::bwt::bwt
- data_structures::bwt::bwtfind
- data_structures::bwt::invert_bwt
- data_structures::bwt::less
- data_structures::interpolation_table::interpolate
- data_structures::suffix_array::lcp
- data_structures::suffix_array::shortest_unique_substrings
- data_structures::suffix_array::suffix_array
- pattern_matching::shift_and::masks
- pattern_matching::ukkonen::unit_cost
- scores::blosum62::blosum62
- scores::pam120::pam120
- scores::pam200::pam200
- scores::pam250::pam250
- scores::pam40::pam40
- seq_analysis::gc::gc3_content
- seq_analysis::gc::gc_content
- stats::bayesian::expected_fdr
- stats::combinatorics::combinations
- stats::combinatorics::combinations_with_repl
- stats::combinatorics::scaled_combinations
- stats::hmm::backward
- stats::hmm::baum_welch
- stats::hmm::forward
- stats::hmm::viterbi
- utils::prescan
- utils::scan
- utils::trim_newline
Typedefs
- alignment::TextSlice
- alignment::poa::POAGraph
- alignment::sparse::HashMapFx
- alphabets::SymbolRanks
- data_structures::bit_tree::MaxBitTree
- data_structures::bit_tree::SumBitTree
- data_structures::bwt::BWT
- data_structures::bwt::BWTFind
- data_structures::bwt::BWTSlice
- data_structures::bwt::Less
- data_structures::suffix_array::LCPArray
- data_structures::suffix_array::RawSuffixArray
- data_structures::suffix_array::RawSuffixArraySlice
- io::fastq::Result
- pattern_matching::pssm::errors::Result
- stats::bayesian::model::JointProbUniverse
- stats::hmm::errors::Result
- stats::hmm::univariate_continuous_emission::GaussianModel
- stats::probs::ScanIter
- stats::probs::cdf::CDFPMFIter
- stats::probs::errors::Result
- utils::Text
- utils::TextSlice