Versions in this module Expand all Collapse all v1 v1.0.1 Feb 16, 2017 v1.0.0 Jan 5, 2017 Changes in this version + var Debug = false + var ErrBadAlphabet = errors.New("kmerindex: alphabet size != 4") + var ErrBadKmer = errors.New("kmerindex: kmer out of range") + var ErrBadKmerText = errors.New("kmerindex: kmertext contains illegal character") + var ErrBadKmerTextLen = errors.New("kmerindex: kmertext length != k") + var ErrKTooLarge = errors.New("kmerindex: k too large") + var ErrKTooSmall = errors.New("kmerindex: k too small") + var ErrShortSeq = errors.New("kmerindex: sequence to short for k") + var MaxKmerLen = 16 — darwin/amd64, linux/amd64, windows/amd64 + var MinKmerLen = 4 — darwin/amd64, linux/amd64, windows/amd64 + func Distance(a, b map[Kmer]float64) (dist float64) + func Format(kmer Kmer, k int, alpha alphabet.Alphabet) (string, error) + func GCof(k int, kmer Kmer) float64 + type Eval func(index *Index, j, kmer int) + type Index struct + func New(k int, s *linear.Seq) (*Index, error) + func (ki *Index) Build() + func (ki *Index) Check() (ok bool, found int) + func (ki *Index) ComplementOf(kmer Kmer) (c Kmer) + func (ki *Index) Finger() (f []Kmer) + func (ki *Index) FingerAt(p int) int + func (ki *Index) ForEachKmerOf(s *linear.Seq, start, end int, f Eval) (err error) + func (ki *Index) Format(kmer Kmer) string + func (ki *Index) GCof(kmer Kmer) float64 + func (ki *Index) K() int + func (ki *Index) KmerFrequencies() (map[Kmer]int, bool) + func (ki *Index) KmerIndex() (map[Kmer][]int, bool) + func (ki *Index) KmerOf(kmertext string) (kmer Kmer, err error) + func (ki *Index) KmerPositions(kmer Kmer) (positions []int, err error) + func (ki *Index) KmerPositionsString(kmertext string) (positions []int, err error) + func (ki *Index) NormalisedKmerFrequencies() (map[Kmer]float64, bool) + func (ki *Index) Pos() (p []int) + func (ki *Index) PosAt(p int) int + func (ki *Index) Seq() *linear.Seq + func (ki *Index) StringKmerIndex() (map[string][]int, bool) + type Kmer uint32 + func ComplementOf(k int, kmer Kmer) (c Kmer) + func KmerOf(k int, lookUp alphabet.Index, kmertext string) (kmer Kmer, err error)
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