List of all items

Structs

• alignment::Alignment
• alignment::AlignmentIter
• alignment::AlignmentStates
• alignment::CigletOpIter
• alignment::LocalProfiles
• alignment::ScalarProfile
• alignment::ScoreAndRanges
• alignment::ScoreEnds
• alignment::ScoreStarts
• alignment::SharedProfiles
• alignment::StripedProfile
• composition::ByteIndexCounts
• composition::FrequencyTable
• composition::NucleotideCounts
• data::ByteIndexMap
• data::ByteMap
• data::ByteValidator
• data::DnaDisambiguation
• data::StdGeneticCode
• data::arbitrary::AlignmentAndQuery
• data::arbitrary::AlignmentAndQuerySpecs
• data::arbitrary::AlignmentAndSeqs
• data::arbitrary::AlignmentAndSeqsSpecs
• data::arbitrary::AlignmentSpecs
• data::arbitrary::AlignmentStatesSpecs
• data::arbitrary::AminoAcidsByteSet
• data::arbitrary::AminoAcidsSpecs
• data::arbitrary::ArraySpecs
• data::arbitrary::ByteSpecs
• data::arbitrary::CigarSpecs
• data::arbitrary::CigletSpecs
• data::arbitrary::FastQSpecs
• data::arbitrary::FloatSpecs
• data::arbitrary::MakeArbitraryIter
• data::arbitrary::NucleotidesByteSet
• data::arbitrary::NucleotidesSpecs
• data::arbitrary::QualityScoresSpecs
• data::arbitrary::SamDataSpecs
• data::arbitrary::StringSpecs
• data::arbitrary::VecSpecs
• data::err::ErrStackDisplay
• data::err::ErrorWithContext
• data::mappings::ByteIndexMap
• data::mappings::ByteMap
• data::mappings::ByteValidator
• data::mappings::DnaDisambiguation
• data::mappings::StdGeneticCode
• data::matrices::WeightMatrix
• data::records::fasta::FastaAA
• data::records::fasta::FastaNT
• data::records::fasta::FastaNTAnnot
• data::records::fasta::FastaReader
• data::records::fasta::FastaSeq
• data::records::fastq::FastQ
• data::records::fastq::FastQReader
• data::records::fastq::FastQView
• data::records::fastq::FastQViewMut
• data::records::sam::SAMReader
• data::records::sam::SamData
• data::records::sam::SamDataView
• data::records::sam::SamDataViewMut
• data::records::sam::SamOptField
• data::records::sam::SamOptRaw
• data::types::amino_acids::AminoAcids
• data::types::amino_acids::AminoAcidsView
• data::types::amino_acids::AminoAcidsViewMut
• data::types::cigar::Cigar
• data::types::cigar::CigarView
• data::types::cigar::CigarViewMut
• data::types::cigar::Ciglet
• data::types::cigar::CigletIterator
• data::types::nucleotides::Nucleotides
• data::types::nucleotides::NucleotidesView
• data::types::nucleotides::NucleotidesViewMut
• data::types::nucleotides::OverlappingCodonsIter
• data::types::nucleotides::TranslatedNucleotidesIter
• data::types::phred::QScoreFloat
• data::types::phred::QScoreInt
• data::types::phred::QualityScores
• data::types::phred::QualityScoresView
• data::types::phred::QualityScoresViewMut
• iter_utils::ProcessResults
• iter_utils::SteppedWindows
• iter_utils::sampling::BernoulliSampler
• iter_utils::sampling::SkipSampler
• kmer::Kmer
• kmer::KmerCounter
• kmer::KmerCounterDecodedIntoIter
• kmer::KmerLen
• kmer::KmerMatchesInSeq
• kmer::KmerMatchesInSeqRev
• kmer::KmerSet
• kmer::KmerSetDecodedIntoIter
• kmer::encoders::three_bit::ThreeBitEncodedKmer
• kmer::encoders::three_bit::ThreeBitKmerEncoder
• kmer::encoders::three_bit::ThreeBitKmerIntoIterator
• kmer::encoders::three_bit::ThreeBitKmerIntoIteratorRev
• kmer::encoders::three_bit::ThreeBitKmerIterator
• kmer::encoders::three_bit::ThreeBitKmerIteratorRev
• kmer::encoders::three_bit::ThreeBitMismatchIter
• kmer::encoders::three_bit::ThreeBitOneMismatchIter
• kmer::encoders::two_bit::TwoBitEncodedKmer
• kmer::encoders::two_bit::TwoBitKmerEncoder
• kmer::encoders::two_bit::TwoBitKmerIntoIterator
• kmer::encoders::two_bit::TwoBitKmerIntoIteratorRev
• kmer::encoders::two_bit::TwoBitKmerIterator
• kmer::encoders::two_bit::TwoBitKmerIteratorRev
• search::RangeSearch

Enums

• alignment::MaybeAligned
• alignment::ProfileError
• alignment::ScoringError
• alignment::SeqSrc
• data::arbitrary::ByteSet
• data::arbitrary::Case
• data::records::sam::OptArray
• data::records::sam::SamOptValue
• data::records::sam::SamRow
• data::types::cigar::CigarError
• data::types::nucleotides::IsValidDNA
• data::types::nucleotides::RecodeDNAStrat
• data::types::nucleotides::RefineDNAStrat
• distance::DistanceError
• kmer::KmerError

Traits

• alignment::AsSeqSrc
• alignment::IntoSeqSrc
• alignment::NextCiglet
• alignment::NextCigletMut
• alignment::PairwiseSequence
• alignment::PeekCiglet
• alignment::PeekCigletMut
• alignment::PeekOp
• alignment::ProfileSets
• alignment::TakeOp
• composition::AlignmentComposition
• composition::CreateConsensus
• composition::GcContent
• composition::ToBaseCounts
• data::CheckSequence
• data::Recode
• data::RetainSequence
• data::SanitizeBase
• data::StdForSequences
• data::arbitrary::ArbitrarySpecs
• data::err::DisplayErrStack
• data::err::Fail
• data::err::GetCode
• data::err::OrFail
• data::err::ResultWithErrorContext
• data::err::ResultWithSubitem
• data::err::WithErrorContext
• data::err::WithSubitem
• data::records::HeaderReadable
• data::records::SequenceReadable
• data::records::sam::SamDataSort
• data::types::amino_acids::AminoAcidsMutable
• data::types::amino_acids::AminoAcidsReadable
• data::types::cigar::InspectCigar
• data::types::cigar::LenInAlignment
• data::types::cigar::ToCigletIterator
• data::types::nucleotides::CheckNucleotides
• data::types::nucleotides::CodonExtension
• data::types::nucleotides::GetCodons
• data::types::nucleotides::GetCodonsMut
• data::types::nucleotides::NucleotidesMutable
• data::types::nucleotides::NucleotidesReadable
• data::types::nucleotides::RecodeNucleotides
• data::types::nucleotides::RetainNucleotides
• data::types::nucleotides::ToDNA
• data::types::nucleotides::Translate
• data::types::phred::QualityStats
• data::views::AsView
• data::views::AsViewMut
• data::views::AssocOwnedType
• data::views::AssocViewMutType
• data::views::AssocViewType
• data::views::DataView
• data::views::DataViewMut
• data::views::Len
• data::views::Restrict
• data::views::Slice
• data::views::SliceCopy
• data::views::SliceMut
• data::views::SliceRange
• data::views::ToOwnedData
• data::views::ToView
• distance::aa::AminoAcidsDistance
• distance::dna::DistanceFromMatrix
• distance::dna::NucleotidesDistance
• iter_utils::ProcessResultsExt
• iter_utils::sampling::DownsampleBernoulli
• iter_utils::sampling::DownsampleKnownSize
• kmer::EncodedKmerCollection
• kmer::FindKmers
• kmer::FindKmersInSeq
• kmer::GetVariants
• kmer::KmerEncode
• kmer::SupportedKmerLen
• kmer::encoders::KmerEncoder
• math::AlignableIntWidth
• math::AnyInt
• math::FromSameSignedness
• math::Int
• math::SimdAnyInt
• math::Uint
• search::ByteSubstring
• search::ByteSubstringMut
• search::ToRangeSearch

Macros

• assert_fp_eq
• define_whichever
• impl_traits
• is_fp_eq
• math::assert_fp_eq
• math::is_fp_eq
• unwrap_or_return_some_err

Functions

• alignment::nw::nw_scalar_align
• alignment::nw::nw_scalar_score
• alignment::nw::nw_score_from_path
• alignment::pairwise_align_with
• alignment::sneaky_snake
• alignment::sw::sw_align_3pass
• alignment::sw::sw_banded_align
• alignment::sw::sw_scalar_align
• alignment::sw::sw_scalar_align_override
• alignment::sw::sw_scalar_score
• alignment::sw::sw_score_from_path
• alignment::sw::sw_simd_align
• alignment::sw::sw_simd_score
• alignment::sw::sw_simd_score_ends
• alignment::sw::sw_simd_score_ranges
• composition::gc_content
• composition::gc_content_simd
• data::matrices::aa_mat_from_name
• data::matrices::blosum
• data::matrices::pam
• data::matrices::parse_matrix
• data::types::nucleotides::make_reverse_complement
• data::types::nucleotides::make_reverse_complement_simd
• data::types::nucleotides::reverse_complement
• data::types::nucleotides::reverse_complement_simd
• data::types::nucleotides::translate_sequence
• distance::aa::physiochemical
• distance::dna::dna_substitution_matrix
• distance::dna::felsenstein_81
• distance::dna::jukes_cantor_69
• distance::dna::kimura_80
• distance::dna::kimura_81
• distance::dna::p_distance_acgt
• distance::dna::tamura_nei_93
• distance::hamming
• distance::hamming_simd
• iter_utils::sampling::downsample_reservoir
• prelude::rand_sequence
• search::find_k_repeating
• search::find_k_repeating_mapped
• search::find_mapped_match_simd
• search::fuzzy_substring_match
• search::fuzzy_substring_match_simd
• search::position_by_byte
• search::position_by_byte2
• search::position_by_byte2_mapped
• search::position_by_byte3
• search::position_by_byte_mapped
• search::position_simd
• search::replace_all_bytes
• search::replace_all_bytes_simd
• search::substring_match
• search::substring_match_simd

Type Aliases

• kmer::encoders::three_bit::ThreeBitKmerCounter
• kmer::encoders::three_bit::ThreeBitKmerSet
• kmer::encoders::two_bit::TwoBitKmerCounter
• kmer::encoders::two_bit::TwoBitKmerSet

Statics

• data::matrices::BLOSUM_100
• data::matrices::BLOSUM_30
• data::matrices::BLOSUM_35
• data::matrices::BLOSUM_40
• data::matrices::BLOSUM_45
• data::matrices::BLOSUM_50
• data::matrices::BLOSUM_55
• data::matrices::BLOSUM_60
• data::matrices::BLOSUM_62
• data::matrices::BLOSUM_65
• data::matrices::BLOSUM_70
• data::matrices::BLOSUM_75
• data::matrices::BLOSUM_80
• data::matrices::BLOSUM_85
• data::matrices::BLOSUM_90
• data::matrices::BLOSUM_95
• data::matrices::PAM_120
• data::matrices::PAM_200
• data::matrices::PAM_250
• data::matrices::PAM_30
• data::matrices::PAM_40
• data::matrices::PAM_70

Constants

• data::AA_ALL_AMBIG_PROFILE_MAP_WITH_STOP
• data::AA_PROFILE_MAP
• data::AA_UNAMBIG_PROFILE_MAP
• data::DNA_PROFILE_MAP
• data::DNA_UNAMBIG_PROFILE_MAP
• data::mappings::AA_ALL_AMBIG_PROFILE_MAP_WITH_STOP
• data::mappings::AA_PROFILE_MAP
• data::mappings::AA_UNAMBIG_PROFILE_MAP
• data::mappings::DNA_PROFILE_MAP
• data::mappings::DNA_UNAMBIG_PROFILE_MAP
• data::mappings::RECODE_TO_DNA_ACGTN_NO_GAPS
• data::mappings::RECODE_TO_DNA_ACGTN_NO_GAPS_UC
• data::mappings::RECODE_TO_DNA_ACGTN_WITH_GAPS
• data::mappings::RECODE_TO_DNA_ACGTN_WITH_GAPS_UC
• data::mappings::RECODE_TO_DNA_IUPAC_NO_GAPS
• data::mappings::RECODE_TO_DNA_IUPAC_NO_GAPS_UC
• data::mappings::RECODE_TO_DNA_IUPAC_WITH_GAPS
• data::mappings::RECODE_TO_DNA_IUPAC_WITH_GAPS_UC
• data::mappings::RETAIN_DNA_ACGTN_NO_GAPS_UC
• data::mappings::RETAIN_DNA_ACGTN_WITH_GAPS_UC
• data::mappings::RETAIN_DNA_IUPAC_NO_GAPS_UC
• data::mappings::RETAIN_DNA_IUPAC_WITH_GAPS_UC