umi

Documentation

Index

• type SnapCorrector
  • func NewSnapCorrector(knownUMIs []byte) *SnapCorrector
  • func (c *SnapCorrector) CorrectUMI(umi string) (correctedUMI string, edits int, corrected bool)

Types

type SnapCorrector

type SnapCorrector struct {
	// contains filtered or unexported fields
}

SnapCorrector implements "snap" correction of UMIs. A umi U is snappable if there is a known non-random umi U1 that is closer to U than all other known umis, in terms of Levenshtein edit distance.

func NewSnapCorrector

func NewSnapCorrector(knownUMIs []byte) *SnapCorrector

NewSnapCorrector creates a new snap corrector. The knownUMIs are a \n separated list of UMIs (identical to the file content of a list of UMIs, where each line contains a UMI). Each UMI should consist of characters ACGTN.

func (*SnapCorrector) CorrectUMI

func (c *SnapCorrector) CorrectUMI(umi string) (correctedUMI string, edits int, corrected bool)

CorrectUMI returns a corrected umi, number of edits to the corrected umi, and true if there is exactly one known UMI that is closest to the original umi with respect to Levenshtein edit distance. Otherwise, return the original umi, -1, and false.